Bahnmann, B. D. 2009. Identity and Diversity of Agaricomycetes (Fungi: Basidiomycota) in Temperate Agricultural Soils. MSc Thesis, University of Western Ontario, London, Ontario, Canada.

648

2009 1. Zebra mussels (Dreissena polymorpha) are successful colonisers of lake littoral habitats and they interact strongly with littoral benthos. Previous research suggests that localised areas colonised by zebra mussels may be hotspots of nitrogen (N) cycling. 2. The effects of zebra mussels on nitrification and denitrification rates were examined approximately every other month for 1 year in Gull Lake, Michigan, U.S.A. Littoral sediment was collected from an area free of zebra mussels and distributed into shallow trays; rocks colonised with zebra mussels were placed in half of the trays, while uncolonised rocks were placed in the remaining trays. After an incubation period of 6–8 weeks in the lake, sediment and zebra mussels were collected from the trays, replaced with new sediment and zebra mussels, and placed in the lake for the next interval. In the laboratory, sediment nitrification and denitrification rates were measured for each tray. 3. Sediment nitrification rates did not increase in the presence of zebra mussels; instead nitrification rates were sensitive to changes in water temperature and increased with increasing exchangeable sediment ammonium. In contrast, denitrification rates increased in sediment trays with zebra mussels in the winter when nitrate (NO3−) availability was high and when Chara did not grow in the trays. 4. Sediment denitrification was NO3−-limited in all seasons, regardless of zebra mussel treatment. However, sediment in the presence of zebra mussels responded less to NO3− addition, suggesting that NO3− limitation of denitrification can be reduced by zebra mussel activity. Zebra mussels have a seasonally variable impact on sediment denitrification rates, and this may translate into altered seasonal patterns of N cycling in localised areas of lakes where they are particularly abundant. Bruesewitz, D. A., J. L. Tank, and S. K. Hamilton. 2009. Seasonal effects of zebra mussels (Dreissena polymorpha) on littoral nitrogen transformation rates in Gull Lake, Michigan, U.S.A. Freshwater Biology 54: 1427-1443.

641

2009 There are a number of difficulties associated with the study of adaptation. One is a lack of variation in the trait, which is common in adaptations because past selection has removed unfit variants. This lack of variation makes it difficult to determine the relationship between trait variation and fitness. Another difficulty is proving causation in this trait–fitness relationship, because a correlated trait might be the actual adaptation. These difficulties can be ameliorated at least partially by combining studies of natural variation with studies of experimentally manipulated traits and traits whose variance has been augmented by artificial selection. We review here a number of our studies on the adaptive value of two aspects of anther position in wild radish (Raphanus raphanistrum, Brassicaceae): anther exsertion, i.e. the degree to which anthers protrude from the mouth of the corolla tube, and anther height dimorphism, i.e. the difference in lengths of the filaments between the two short and four long stamens. We have used both functional analyses, in which the response variable is pollen removal, and measurements of selection, in which the response variable is lifetime male fitness estimated by molecular genetic paternity analyses. In these studies we use both the natural variation in populations as well as manipulated variation, the latter through both stamen removal and artificial selection, to re-create the ancestral trait conditions. Our work provides convincing evidence that intermediate anther exsertion values are adaptive, and that this is probably an adaptation to a subset of the pollinator fauna, small bees. The picture for anther height dimorphism is much less clear, as the weight of current evidence suggests that current values of this trait might actually be maladaptive; however, if this is true it is difficult to understand how the dimorphism is maintained across the family Brassicaceae. Conner, J. K., H. F. Sahli, and K. Karoly. 2009. Tests of adaptation: Functional studies of pollen removal and estimates of natural selection on another position in wild radish. Anals of Botany 103: 1547-1556.

643

2009 Dazzo, F. B., and S. Gantner. 2009. Rhizosphere. Pages 335-349 in M. Schaechter, ed. Encyclopedia of Microbiology. Elsevier, Oxford, U.K.

644

2009 This study investigated long-term agronomic management systems and precipitation level effects on soybean [Glycine max (L.) Merr.] total oil content and fatty acid composition. Management systems evaluated included conventional (CT), no-till (NT), low chemical input (LI), and zero chemical input (ORG). Total oil content and major fatty acids profiles were analyzed by accelerated solvent extractor (ASE 200) and gas chromatography with flame ionization detector (FID). The results showed these four management systems have limited influence on soybean grain total oil content and oleic acid (O) and linoleic acid (L) compositions. The NT management system significantly improved soybean oil yield on a land-area basis as a result of higher annual grain yields. Soybeans grown under the NT management system had as high or higher palmitic acid (P) composition than the other three management systems; similarly, the CT treatments had as low or lower linolenic acid (LN) composition in soybean when compared with the other three management systems. The levels of stearic acid (S), O, L, and LN had a significant quadratic relationship (R2 = 0.64–0.75) with total (July–September) precipitation. The oil quality ratio of O/(L + LN) had a quadratic relation with precipitation. Gao, J., X. Hao, K. D. Thelen, and G. P. Robertson. 2009. Agronomic management system and precipitation effects on soybean oil and fatty acid profiles. Crop Science 49: 1049-1057.

670

2009 Arthropod predators and parasitoids provide valuable ecosystem services in agricultural crops by suppressing populations of insect herbivores. Many natural enemies are influenced by non-crop habitat surrounding agricultural fields, and understanding if, and at what scales, land use patterns influence natural enemies is essential to redicting how landscape alters biological control services. Here we focus on biological control of soybean aphid, Aphis glycines Matumura, a specialist crop pest recently introduced to the north-central United States. We measured the amount of biological control service supplied to soybean in 26 replicate fields across Michigan, Wisconsin, Iowa, and Minnesota across two years (2005–2006). We measured the impact of natural enemies by experimentally excluding or allowing access to soybean aphid infested plants and comparing aphid population growth over 14 days. We also monitored aphid and natural enemy populations at large in each field. Predators, principally coccinellid beetles, dominated the natural enemy community of soybean in both years. In the absence of aphid predators, A. glycines increased significantly, with 5.3-fold higher aphid populations on plants in exclusion cages vs. the open field after 14 days. We calculated a biological control services index (BSI) based on relative suppression of aphid populations and related it to landscape diversity and composition at multiple spatial scales surrounding each site. We found that BSI values increased with landscape diversity, measured as Simpson’s D. Landscapes dominated by corn and soybean fields provided less biocontrol service to soybean compared with landscapes with an abundance of crop and non-crop habitats. The abundance of Coccinellidae was related to landscape composition, with beetles being more abundant in landscapes with an abundance of forest and grassland compared with landscapes dominated by agricultural crops. Landscape diversity and composition at a scale of 1.5 km surrounding the focal field explained the greatest proportion of the variation in BSI and Coccinellidae abundance. This study indicates that natural enemies provide a regionally important ecosystem service by suppressing a key soybean pest, reducing the need for insecticide applications. Furthermore, it suggests that management to maintain or enhance landscape diversity has the potential to stabilize or increase biocontrol services. Gardiner, M. M., D. A. Landis, C. Gratton, C. D. DiFonzo, M. O. O'Neal, J. Chacon, M. Wayo, N. Schmidt, E. Mueller, and G. E. Heimpel. 2009. Landscape diversity enhances the biological control of an introduced crop pest in the north-central U.S. Ecological Applications 19:143-154.

621

2009 Metagenomics is providing an unprecedented view of the taxonomic diversity, metabolic potential and ecological role of microbial communities in biomes as diverse as the mammalian gastrointestinal tract, the marine water column and soils. However, we have found a systematic error in metagenomes generated by 454-based pyrosequencing that leads to an overestimation of gene and taxon abundance; between 11% and 35% of sequences in a typical metagenome are artificial replicates. Here we document the error in several published and original datasets and offer a <a href="http://microbiomes.msu.edu.proxy1.cl.msu.edu/replicates">web-based solution</a> for identifying and removing these artifacts. Gomez-Alvarez, V., T. K. Teal, and T. M. Schmidt. 2009. Systematic artifacts in metagenomes from complex microbial communities. ISME Journal: doi: 10. 1038/ismej.2009.72.

661

2009 We measured uptake length of 15NO3- in 72 streams in eight regions across the United States and Puerto Rico to develop quantitative predictive models on controls of NO3- uptake length. As part of the Lotic Intersite Nitrogen eXperiment II project, we chose nine streams in each region corresponding to natural (reference), suburban–urban, and agricultural land uses. Study streams spanned a range of human land use to maximize variation in NO3- concentration, geomorphology, and metabolism. We tested a causal model predicting controls on NO3- uptake length using structural equation modeling. The model included concomitant measurements of ecosystem metabolism, hydraulic parameters, and nitrogen concentration. We compared this structural equation model to multiple regression models which included additional biotic, catchment, and riparian variables. The structural equation model explained 79% of the variation in log uptake length (SWtot). Uptake length increased with specific discharge (Q/w) and increasing NO3- concentrations, showing a loss in removal efficiency in streams with high NO3- concentration. Uptake lengths shortened with increasing gross primary production, suggesting autotrophic assimilation dominated NO3- removal. The fraction of catchment area as agriculture and suburban–urban land use weakly predicted NO3- uptake in bivariate regression, and did improve prediction in a set of multiple regression models. Adding land use to the structural equation model showed that land use indirectly affected NO3- uptake lengths via directly increasing both gross primary production and NO3- concentration. Gross primary production shortened SWtot, while increasing NO3- lengthened SWtot resulting in no net effect of land use on NO3- removal. Hall, R. O., Jr., J. L. Tank, D. J. Sobota, P. J. Mullholland, J. M. O'Brien, W. K. Dodds, J. R. Webster, H. M. Valett, G. C. Poole, B. J. Peterson, W. M. Meyer, W. H. McDowell, S. L. Johnson, S. K. Hamilton, N. B. Grimm, S. V. Gregory, C. N. Dahm, L. W. Cooper, L. R. Ashkenas, S. M. Thomas, R. W. Sheibley, J. D. Potter, B. R. Niederlehner, L. T. Johnson, A. M. Helton, C. L. Crenshaw, A. J. Burgin, M. J. Bernot, J. Beaulieu, and C. Arango. 2009. Nitrate removal in stream ecosystems measured by 15N addition experiments: 1. Total uptake. Limnology and Oceanography 54: 653-665.

646

2009 Lakes in carbonate-rich watersheds commonly precipitate calcium carbonate as calcite, and this is accelerated by photosynthetic uptake of carbon dioxide. Co-precipitation of phosphate with calcite is one reason that algal growth in such lakes tends to be strongly phosphorus (P) limited. The extent to which calcite precipitation can be a sink for added P, and thus act as a potential negative feedback to eutrophication, was demonstrated using large enclosures within a Michigan lake. Nitrogen and P were added over 45 days in the summer to produce mesotrophic and eutrophic conditions. Algal biomass and production increased markedly with the nutrient additions, elevating the pH (9–10) and greatly increasing calcite precipitation, reducing concentrations of calcium and alkalinity by up to 60%. Sediment traps indicated that calcite sedimentation was a major sink for added P. By the end of the experiment, only about half of the added P remained in the water column. Major ion concentrations in a larger set of Michigan lakes showed calcite precipitation to be widespread, reflecting the abundant carbonate minerals in this glacial region. Hamilton, S. K., D. A. Bruesewitz, G. P. Horst, and O. Sarnelle. 2009. Biogenic calcite-phosphorus precipitation as a negative feedback to lake eutrophication. Canadian Journal of Fisheries and Aquatic Sciences 66: 343-350.

647

2009 Beneficial arthropods, including native bees, predators, and parasitoids, provide valuable ecosystem services worth $8 billion to US agriculture each year. These arthropod-mediated ecosystem services (AMES) include crop pollination and pest control, which help to maintain agricultural productivity and reduce the need for pesticide inputs. Maximizing survival and reproduction of beneficial arthropods requires provision of pollen and nectar resources that are often scarce in modern agricultural landscapes. Increasingly, native plants are being evaluated for this purpose. Native plants can outperform recommended non-natives and also provide local adaptation, habitat permanency, and support of native biodiversity. We predict that the success of insect conservation programs using flowering plants to increase AMES on farmland will depend on landscape context, with the greatest success in landscapes of moderate complexity. Reintegration of native plants into agricultural landscapes has the potential to support multiple conservation goals, and will require the collaboration of researchers, conservation educators, and native plant experts. Isaacs, R., J. Tuell, A. Fiedler, M. Gardiner, and D. Landis. 2009. Maximizing arthropod-mediated ecosystem services in agricultural landscapes: The role of native plants. Frontiers in Ecology and the Environment 7: 196-203.

635

2009 Isaacs, R., J. Tuell, A. Fiedler, M. Gardiner, and D. Landis. 2009. Maximizing arthropod-mediated ecosystem services in agricultural landscapes: The role of native plants. Frontiers in Ecology and the Environment (in press).

622

2009 Agriculture is a managed ecosystem. The decisions of its managers, the farmers, drive the mix of ecosystem services (ES) that it produces. The thesis is divided into two essays. Essay 1 develops tradeoff analysis between profitability and selected environmental indicators for different types of cropping systems using data from agronomic field trials. The tradeoff frontiers developed in the study are profit vis-à-vis global warming potential (GWP) and nitrate leaching. Both reveal that the conventional corn-soybean-wheat rotation treatment is dominated. The organic treatment is dominated unless certified organic prices are used. The no-till cropping system shows potential as an efficient choice for the farmer, as does alfalfa for its GWP. The tradeoffs between no-till and alfalfa for GWP and no-till with certified organic imply that there are opportunity costs to changing cropping systems in order to provide more nonmarketed ES. Essay 2 uses survey data to examine farmers’ willingness to enroll in a program that compensates them for adopting environmental stewardship. Results show that Michigan farmers’ acreage enrollment decisions depend consistently on farm size and the perception of environmental improvements from the practices. For farms over 500 acres, the payment offered was also a significant inducement to acreage enrollment in all systems examined. The second essay advances the literature on adoption of agroenvironmental practices by developing a supply function for crop acreage managed for environmental stewardship. Like prior studies of environmental technology adoption in agriculture, we find that environmental attitudes and affiliations, age, education and current farming practices are influential. But we also find that the low cost suppliers of environmental services are the largest farms. Agricultural policies based on payment for environmental services that aim for cost-effective environmental impact will likely achieve most of their impact from larger farms. Jolejole, M. C. B. 2009. Trade-offs, Incentives, and the Supply of Ecosystem Services from Cropland. MS Thesis, Michigan State University, East Lansing, Michigan, USA.

631

2009 Joo, W. 2009. Environmental Acoustics as an Ecological Variable to Understand the Dynamics of Ecosystems. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

659

2009 Multifractal methods have the potential to be useful tools for characterizing spatial distributions of soil pores from microtomographic images of undisturbed soil cores and soil aggregates. The objective of this study was to examine the limitations of multifractal analyses in binary (void and solid) soil images and to explore conditions under which multifractal spectra can be obtained. Multifractal characteristics of binary soil images are bounded within certain limiting values corresponding to nonfractal scaling. In this study, we first addressed the theoretical limitations of multifractal analysis of binary images and examined the nonfractal scaling boundaries in multifractal calculations by the method of moments. Then we developed boundary conditions for multifractal calculations by the direct method. Results revealed that fractal scaling is potentially possible only across a relatively narrow range of cell sizes restricted by the nonfractal scaling boundaries. Moreover, the range of cell sizes where fractal scaling is potentially possible varies with pore size. That is, in multifractal calculations it changes continuously with changes in the q value. For the soil aggregates examined in this study, this range varied from two to eight pixels for low q values to 128 pixels for high q values. The varying range makes calculations of true multifractal spectra for binary soil image data impossible. These results are consistent with a general theoretical notion that binary soil images are not multifractal in a strict mathematical sense. We suggest, however, that application of multifractal formalism can generate "pseudo-multifractal spectra" that might still be useful for summarizing pore distribution information and for comparing pore data among different agricultural management regimes and soil types. Kravchenko, A. N., M. A. Martin, A. J. M. Smucker, and M. L. Rivers. 2009. Theoretical and practical limitations in the determination of multiofractal spectra from pore/solid soil aggregate images. Vadose Zone Journal 8: 220-226.

651

2009 Genetically engineered corn (Zea mays L.) containing a gene from the soil bacterium Bt (Bacillus thuringiensis) constitutes a large proportion of all corn planted in the United States. In a number of studies, Bt plant residues have been reported to have higher lignin content and to decompose slower than those of non-Bt plants, possibly due to the presence of the Cry endotoxin. We hypothesize that after multiple years of continuous cultivation of Bt corn, the combined results of alleged differences in Bt corn residues and of Cry endotoxin presence will be reflected in soil characteristics, specifically in an increase in soil total carbon (C) and nitrogen (N) levels. We collected soil samples at 0–7.5 cm depth in 2006 from continuous Bt and non-Bt corn treatments in a randomized complete block design experiment with four replications. The experiment was established in 1999 at the Kellogg Biological Station long-term ecological research (LTER) site in southwest Michigan. We found that, after 7 years of Bt cropping, neither total soil C and N nor soil C mineralized during a 35-day incubation were significantly different between Bt and non-Bt corn treatments (P > 0.05). Total soil C was equal to 7.3 g kg−1 and 7.4 g kg−1, in Bt and non-Bt corn, respectively, with a standard error of the means (SEM) = 0.2, and total N was 0.67 g kg−1 (SEM 0.02) in both treatments. Post-hoc power analysis indicated that, given the number of samples collected in this study and the observed level of variability, the minimal differences between the Bt and non-Bt treatments that could be detected as statistically significant at α = 0.05 with a power of 0.80 were equal to 1.0 g kg−1, 0.14 g kg−1 and 0.125 g kg−1 for total C, total N, and soil C mineralized during a 35-day incubation, respectively. The results indicate that continuous Bt corn production during a 7-year period did not lead to sizeable changes in total soil C and N. Kravchenko, A. N., X. Hao, and G. P. Robertson. 2009. Seven years of continuously planted Bt corn did not affect mineralizable and total soil C and total N in surface soil. Plant Soil 318: 269-274.

630

2009 A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB <a href=>"http://ribosome.mmg.msu.edu/rrndb/index.php"</a>, the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes. Lee, Z. M.-P., C. Bussema, III, and T. M. Schmidt. 2009. rrnDB: Documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Research 37: D489-D493.

662

2009 To better understand the role of resource heterogeneity in decomposition and nitrous oxide (N2O) flux we systematically altered the degree of plant litter aggregation in soil, from uniformly distributed to highly aggregated. In laboratory incubations, we distributed 4.5 g of dried clover shoots (_Trifolium pratense_ L.) in two particle sizes (1 or >5 mm) into 1, 3, or 9 patches versus uniformly distributed. Soil moisture content was also varied to manipulate soil oxygen (O2) concentrations. In moist soil (50% waterfilled pore space, WFPS), litter aggregation delayed the peak litter decomposition rate by 3–5 days compared to uniformly distributed litter regardless of the litter particle size. In contrast, under near-saturated soil conditions (80% WFPS) litter aggregation suppressed decomposition throughout the 26-day incubation period. This significant interaction between litter aggregation and soil moisture treatments suggests that diffusion of soil resources (likely O2) plays an important role in the influence of litter aggregation on decomposition. Specifically, O2 diffusion may more adequately meet O2 consumption rates when litter is distributed than when aggregated. In contrast to the temporary influence of aggregation on litter decomposition, N2O fluxes under 50% WFPS conditions were consistently greater and on average 7.9, 7.2, and 4.7-fold greater than fine aggregated litter (1, 3, and 9 patches, respectively) than when uniformly distributed. Coarse litter aggregation also stimulated N2O emissions, but not as much as fine litter. Under field conditions with growing maize (Zea mays L.), litter aggregation also stimulated N2O emissions. The results suggest that litter aggregation plays a role in N2O flux from agricultural soils and it might be manipulated to provide an additional N2O mitigation strategy. 2008 Elsevier Ltd. All rights reserved. Loecke, T. D., and G. P. Robertson. 2009. Soil resource heterogeneity in terms of litter aggragation promotes nitrous oxide fluxes and slows decomposition. Soil Biology and Biochemistry 41: 228-235.

625

2009 Lupold, S. 2009. Sexual Selection and Sperm Design in Passerine Birds. Ph.D. Dissertation, University of Sheffield, Sheffield, England, United Kingdom.

652

2009 Post-copulatory sexual selection (PCSS) is thought to be one of the evolutionary forces responsible for the rapid and divergent evolution of sperm design. However, whereas in some taxa particular sperm traits are positively associated with PCSS, in other taxa, these relationships are negative, and the causes of these different patterns across taxa are poorly understood. In a comparative study using New World blackbirds (Icteridae), we tested whether sperm design was influenced by the level of PCSS and found significant positive associations with the level of PCSS for all sperm components but head length. Additionally, whereas the absolute length of sperm components increased, their variation declined with the intensity of PCSS, indicating stabilising selection around an optimal sperm design. Given the diversity of, and strong selection on, sperm design, it seems likely that sperm phenotype may influence sperm velocity within species. However, in contrast to other recent studies of passerine birds, but consistent with several other studies, we found no significant link between sperm design and velocity, using four different species that vary both in sperm design and PCSS. Potential reasons for this discrepancy between studies are discussed. Lupold, S., G. M. Linz, and T. R. Birkhead. 2009. Sperm design and variation in the New World blackbirds (Icteridae). Behavioral Ecology Sociobiology 63: 899-909.

654

2009 Sperm velocity is one of the main determinants of the outcome of sperm competition. Since sperm vary considerably in their morphology between and within species, it seems likely that sperm morphology is associated with sperm velocity. Theory predicts that sperm velocity may be increased by enlarged midpiece (energetic component) or flagellum length (kinetic component), or by particular ratios between sperm components, such as between flagellum length and head size. However, such associations have rarely been found in empirical studies. In a comparative framework in passerine birds, we tested these theoretical predictions both across a wide range of species and within a single family, the New World blackbirds (Icteridae). In both study groups, sperm velocity was influenced by sperm morphology in the predicted direction. Consistent with theoretical models, these results show that selection on sperm morphology and velocity are likely to be concomitant evolutionary forces. Lupold, S., S. Calhim, S. Immler, and T. R. Birkhead. 2009. Sperm morphology and sperm velocity in passerine birds. Proceedings of the Royal Society B 276: 1175-1181.

653

2009 Plant species can both directly and indirectly affect soil processes in various ways, including through functional traits related to the quantity and chemistry of biomass produced. Understanding how functional traits affect soil processes may be particularly important in restorations that specifically select a target plant community. In this study, I examined how species differing in litter traits alter decomposition, both directly via chemistry and indirectly via influences on soil microclimate. Decomposition dynamics of two old-field grasses were compared with the native prairie grass, _Andropogon gerardii_, in two Michigan old-fields. Decomposition rates were strongly, negatively related to tissue chemistry, but showed little effect of microclimate differences. Soil bacterial community composition differed between species at one site, while extracellular enzyme activities differed between species at the other site. These findings suggest plant species may be altering microbial community function. Overall, litter chemistry was the dominant factor determining decomposition rates, suggesting that restoring native prairie grasses with ecalcitrant litter into grass-dominated old-fields could slow litter decomposition and ultimately lead to changes in soil carbon and nitrogen cycling. Eventually, this could lead to soils that more closely resemble the more organic-rich soils of native prairies and ultimately increase prairie plant community restoration success. Mahaney, W. M. 2009. Plant controls on decomposition rates: The benefits of restoring abandoned agricultural lands with native prairie grasses. Plant and Soil DOI 10.1007/s11104-009-0178-8.

671

2009 Density dependent feedback, based on cumulative population size, has been advocated to explain and mathematically characterize “boom and bust” population dynamics. Such feedback results in a bell-shaped population trajectory of the population density. Here, we note that this trajectory is mathematically described by the logistic probability density function. Consequently, the cumulative population follows a time trajectory that has the same shape as the cumulative logistic function. Thus, the Pearl–Verhulst logistic equation, widely used as a phenomenological model for density dependent population growth, can be interpreted as a model for cumulative rather than instantaneous population. We extend the cumulative density dependent differential equation model to allow skew in the bell-shaped population trajectory and present a simple statistical test for skewness. Model properties are exemplified by fitting population trajectories of the soybean aphid, _Aphis glycines_. The linkage between the mechanistic underpinnings of the logistic probability density function and cumulative distribution function models could open up new avenues for analyzing population data. Matis, J. H., T. R. Kiffe, W. van der Werf, A. C. Costamagna, T. J. Matis, and W. E. Grant. 2009. Population dynamics models based on cumulative density dependent feedback: A link to the logistic growth curve and a test for symmetry using aphid data. Ecological Modelling 220: 1745-1751.

632

2009 Phylogenetic and “fingerprinting” analyses of the 16S rRNA genes of prokaryotes have been a mainstay ofmicrobial ecology during the last two decades. However, many methods and results from studies that rely onthe 16S rRNA gene for detection and quantification of specific microbial taxa have seemingly received onlycursory or even no validation. To directly examine the efficacy and specificity of 16S rRNA gene-based primersfor phylum-, class-, and operational taxonomic unit-specific target amplification in quantitative PCR, wecreated a collection of primers based solely on an extensive soil bacterial 16S rRNA gene clone librarycontaining _5,000 sequences from a single soil sample (i.e., a closed site-specific library was used to createPCR primers for use at this site). These primers were initially tested in silico prior to empirical testing by PCRamplification of known target sequences and of controls based on disparate phylogenetic groups. Although allprimers were highly specific according to the in silico analysis, the empirical analyses clearly exhibited a highdegree of nonspecificity for many of the phyla or classes, while other primers proved to be highly specific. These findings suggest that significant care must be taken when interpreting studies whose results were obtained with target specific primers that were not adequately validated, especially where population densities or dynamics have been inferred from the data. Further, we suggest that the reliability of quantification of specific target abundance using 16S rRNA-based quantitative PCR is case specific and must be determined through rigorous empirical testing rather than solely in silico. Morales, S. E., and W. E. Holben. 2009. Empirical testing of 16S rRNA gene PCR primer pairs reveals ariance in target specificity and efficacy not suggested by in silico analysis. Applied and Environmental Microbiology 75: 2677-2683.

633

2009 To thoroughly investigate the bacterial community diversity present in a single composite sample from an agricultural soil and to examine potential biases resulting from data acquisition and analytical approaches, we examined the effects of percent G_C DNA fractionation, sequence length, and degree of coverage of bacterial diversity on several commonly used ecological parameters (species estimation, diversity indices, and evenness). We also examined variation in phylogenetic placement based on multiple commonly used approaches (ARB alignments and multiple RDP tools). The results demonstrate that this soil bacterial community is highly diverse, with 1,714 operational taxonomic units demonstrated and 3,555 estimated (based on the Chao1 richness estimation) at 97% sequence similarity using the 16S rRNA gene. The results also demonstrate a fundamental lack of dominance (i.e., a high degree of evenness), with 82% of phylotypes being encountered three times or less. The data also indicate that generally accepted cutoff values for phylum-level taxonomic classification might not be as applicable or as general as previously assumed and that such values likely vary between prokaryotic phyla or groups. Morales, S. E., T. F. Cosart, J. V. Johnson, and H. W.E. 2009. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters. Applied and Environmental Microbiology 75: 668-675.

634

2009 We measured denitrification rates using a field 15NO3- tracer-addition approach in a large, cross-site study of nitrate uptake in reference, agricultural, and suburban–urban streams. We measured denitrification rates in 49 of 72 streams studied. Uptake length due to denitrification (SWdenn) ranged from 89 m to 184 km (median of 9050 m) and there were no significant differences among regions or land-use categories, likely because of the wide range of conditions within each region and land use. N2 production rates far exceeded N2O production rates in all streams. The fraction of total NO3- removal from water due to denitrification ranged from 0.5% to 100% among streams (median of 16%), and was related to NH4+ concentration and ecosystem respiration rate (ER). Multivariate approaches showed that the most important factors controlling SWden were specific discharge (discharge / width) and NO3- concentration (positive effects), and ER and transient storage zones (negative effects). The relationship between areal denitrification rate (Uden) and NO3- concentration indicated a partial saturation effect. A power function with an exponent of 0.5 described this relationship better than a Michaelis–Menten equation. Although Uden increased with increasing NO3- concentration, the efficiency of NO3- removal from water via denitrification declined, resulting in a smaller proportion of streamwater NO3- load removed over a given length of stream. Regional differences in stream denitrification rates were small relative to the proximate factors of NO3- concentration and ecosystem respiration rate, and land use was an important but indirect control on denitrification in streams, primarily via its effect on NO3- concentration. Mullholland, P. J., R. O. Hall, Jr., D. J. Sobota, W. K. Dodds, D. L. Findlay, N. B. Grimm, S. K. Hamilton, W. H. McDowell, J. M. O'Brien, J. L. Tank, L. R. Ashkenas, L. W. Cooper, C. N. Dahm, S. V. Gregory, S. L. Johnson, W. M. Meyer, B. J. Peterson, G. C. Poole, H. M. Valett, J. R. Webster, C. Arango, J. Beaulieu, M. J. Bernot, A. J. Burgin, C. L. Crenshaw, A. M. Helton, L. T. Johnson, B. R. Niederlehner, J. D. Potter, R. W. Sheibley, and S. M. Thomas. 2009. Nitrate removal in stream ecosystems measured by 15N addition experiments: 2. Denitrification. Limnology and Oceanography 54: 666-680.

656

2009 Ohl, C., and S. M. Swinton. 2009. LInking environmental and societal dynamics in long-term research. Pages (in press) in F. Muller, C. Baessler, H. Schubert, and S. Klotz, eds. Long-term Ecological Research: Between Theory and Application. Springer.

664

2009 Payne, E. K., A. J. Burgin, and S. K. Hamilton. 2009. Nitrate stimulation of sulfur oxidation in freshwaters: Evidence from sediment nitrate manipulation using porewater equlibrators. Aquatic Microbial Ecology (in press).

583

2009 Quintanilla, M. 2009. Acoustical and Nematode Community Assessment for Ecosystem Characterization. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

627

2009 Agricultural management practices in the Long Term Ecological Research (LTER) experiment at the W.K. Kellogg Biological Station (KBS) range from high intensity (Conventional Row Crop Management) to low intensity (Old Growth Forest). Many of these practices are visible in this mid-summer photo. Alfalfa, which will be harvested for animal feed, is growing in the foreground. Corn harvested for grain is growing on the right side of the photo while an old field successional plot is on the left side. Poplar trees, which are harvested for biomass, and hardwood forests are visible in the background. Photo taken from the W.K. Kellogg Biological Station Long Term Ecological Research website Wilke, B. J., and J. Kunkle. 2009. <a href="http://tiee.ecoed.net/vol/v6/figure_sets/climate_change/abstract.html">What does agriculture have to do with climate change? Teaching Issues and Experiments in Ecology 6.</a>

626

2009 Agricultural and urban land use increase nitrogen (N) concentrations in streams, which can saturate biotic demand by plants, algae, and bacteria via assimilative uptake, and by nitrification and denitrification. We studied six streams per year in each of three land-use categories (agricultural, urban, and forested) for 3 yr (n = 18 streams), and we compared whole-stream N uptake and microbial N transformation rates during spring, summer, and autumn. We measured whole-stream removal of added ammonium (NH4+) and nitrate (NO3-) in the field and quantified sediment nitrification and denitrification rates in laboratory assays. Relative demand for NNH4+ (as uptake velocity, Vf) was highest in spring and in streams with open canopies, implying a link with aquatic autotrophy. In agricultural and urban streams, whole-stream removal (as areal uptake, U) of NH4+ and NO3-, nitrification, and denitrification rates approached saturation at higher inorganic N concentrations. Nitrification and denitrification rates measured in redox-optimized laboratory assays were roughly equivalent, suggesting that in situ redox conditions will determine whether stream sediments are a net source or sink of NO3-. Though nitrification and denitrification rates were measured under ideal redox conditions, they were always more than an order of magnitude lower than whole-stream NO{3 uptake, demonstrating their limited influence on wholestream NO3- dynamics. Assimilatory processes, which temporarily store N removed from the water column, dominated whole-stream N demand and controlled downstream N flux. The ultimate fate of assimilated N remains unknown; in-channel storage cannot account for it, and thus a key question is what fraction may eventually be stored in downstream depositional zones or denitrified upon remineralization. Arango, C. P., J. L. Tank, L. T. Johnson, and S. K. Hamilton. 2008. Assimilatory uptake rather than dissimilatory transformation determines seasonal patterns in nitrogen removel in streams of varying land use. Limnology and Oceanography 53: 2558-2572.

562

2008 The emission of nitrous oxide (N2O) from streams draining agricultural landscapes is estimated by the Intergovernmental Panel on Climate Change (IPCC) to constitute a globally significant source of this gas to the atmosphere, although there is considerable uncertainty in the magnitude of this source. We measured N2O emission rates and potential controlling variables in 12 headwater streams draining a predominantly agricultural basin on glacial terrain in southwestern Michigan. The study sites were nearly always supersaturated with N2O and emission rates ranged from −8.9 to 266.8 μg N2O-N m−2 h−1 with an overall mean of 35.2 μg N2O-N m−2 h−1. Stream water NO3− concentrations best-predicted N2O emission rates. Although streams and agricultural soils in the basin had similar areal emission rates, emissions from streams were equivalent to 6% of the anthropogenic emissions from soils because of the vastly greater surface area of soils. We found that the default value of the N2O emission factor for streams and groundwater as defined by the IPCC (EF5-g) was similar to the value observed in this study lending support to the recent downward revision to EF5-g. However, the EF5-g spanned four orders of magnitude across our study sites suggesting that the IPCC's methodology of applying one emission factor to all streams may be inappropriate. Beaulieu, J. J., C. P. Arango, S. K. Hamilton, and J. L. Tank. 2008. The production and emission of nitrous oxide from headwater streams in the upper Midwest. Global Change Biology 14: 878-894.

569

2008 Bruesewitz, D. A. 2008. The Effects of Invasive Zebra Mussels (Dreissena Polymorpha) on Nitrogen Cycling in Freshwater Ecosystems of the Midwestern United States. Ph.D. Dissertation, University of Notre Dame, South Bend, Indiana, USA.

642

2008 Massive anthropogenic acceleration of the global nitrogen (N) cycle has stimulated interest in understanding the fate of excess N loading to aquatic ecosystems. Nitrate (NO3 −) is traditionally thought to be removed mainly by microbial respiratory denitrification coupled to carbon (C) oxidation, or through biomass assimilation. Alternatively, chemolithoautotrophic bacterial metabolism may remove NO3 − by coupling its reduction with the oxidation of sulfide to sulfate (SO4 2−). The NO3 − may be reduced to N2 or to NH4 +, a form of dissimilatory nitrate reduction to ammonium (DNRA). The objectives of this study were to investigate the importance of S oxidation as a NO3 − removal process across diverse freshwater streams, lakes, and wetlands in southwestern Michigan (USA). Simultaneous NO3 − removal and SO4 2− production were observed in situ using modified “push-pull” methods in nine streams, nine wetlands, and three lakes. The measured SO4 2− production can account for a significant fraction (25–40%) of the overall NO3 − removal. Addition of 15NO3 − and measurement of 15NH4 + production using the push–pull method revealed that DNRA was a potentially important process of NO3 − removal, particularly in wetland sediments. Enrichment cultures suggest that Thiomicrospira denitrificans may be one of the organisms responsible for this metabolism. These results indicate that NO3 −-driven SO4 2− production could be widespread and biogeochemically important in freshwater sediments. Removal of NO3 − by DNRA may not ameliorate problems such as eutrophication because the N remains bio-available. Additionally, if sulfur (S) pollution enhances NO3 − removal in freshwaters, then controls on N processing in landscapes subject to S and N pollution are more complex than previously appreciated. Burgin, A. J., and S. K. Hamilton. 2008. NO3- driven SO42- production in freswhwater ecosystems: Implications for N and S cycling. Ecosystems 11: 908-922.

571

2008 Campbell, B. M. 2008. Characterization of Tetracycline Efflux Genes in Soil Bacteria and an Analysis of Environmental Factors Controlling Their Expression. MS Thesis, Michigan State University, East Lansing, Michigan, USA.

605

2008 This synthetic data set contains plant species relative abundance measures from 35 nitrogen (N) fertilization experiments conducted at 10 sites across North America. The data set encompasses the fertilization responses of 575 taxa from 1159 experimental plots. The methodology varied among experiments, in particular with regard to the type and amount of N added, plot size, species composition measure (biomass harvest, pin count, or percent cover), additional experimental manipulations, and experimental duration. At each site, each species has been classified according to a number of easily identified categorical functional traits, including life history, life form, the number of cotyledons, height relative to the canopy, potential for clonal growth, and nativity to the United States. Additional data are available for many sites, indicated by references to publications and web sites. Analyses of these data have shown that N enrichment significantly alters community composition in ways that are predictable on the basis of plant functional traits as well as environmental context. This data set could be used to answer a variety of questions about how plant community composition and structure respond to environmental changes. Cleland, E. E., C. Clark, S. Collins, J. Fargione, L. Gough, K. L. Gross, D. G. Milchunas, S. Pennings, W. D. Bowman, I. C. Burke, W. K. Lauenroth, G. P. Robertson, J. Simpson, D. Tilman, and K. N. Suding. 2008. Species responses to nitrogen fertilization in herbaceous plant communities and associated species traits (Data Paper). Ecology 89: p. 1175.

596

2008 Summarizing complex temporal dynamics in communities is difficult to achieve in a way that yields an intuitive picture of change. Rank clocks and rank abundance statistics provide a graphical and analytical framework for displaying and quantifying community dynamics. We used rank clocks, in which the rank order abundance for each species is plotted over time in temporal clockwise direction, to display temporal changes in species abundances and richness. We used mean rank shift and proportional species persistence to quantify changes in community structure in long-term data sets from fertilized and control plots in a late successional old field, frequently and infrequently burned tallgrass prairie, and Chihuahuan desert grassland and shrubland communities. Rank clocks showed that relatively constant species richness masks considerable temporal dynamics in relative species abundances. In the old field, fertilized plots initially experienced high mean rank shifts that stabilized rapidly below that of unfertilized plots. Rank shifts were higher in infrequently burned vs. annually burned tallgrass prairie and in desert grassland compared to shrubland vegetation. Proportional persistence showed that arid grasslands were more dynamic than mesic grasslands. We conclude that rank clocks and rank abundance statistics provide important insights into community dynamics that are often hidden by traditional univariate approaches. Collins, S., K. N. Suding, E. E. Cleland, M. Batty, S. Pennings, K. L. Gross, J. B. Grace, L. Gough, J. Fargionne, and C. M. Clark. 2008. Rank clocks and plant community dynamics. Ecology 89: 3534-3541.

619

2008 Corbin, A. T. 2008. Transitional Dynamics in Converting Conventional Field Cropping Systems to Certified Organic. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

590

2008 Costamagna, A. C., D. A. Landis, and M. J. Brewer. 2008. The role of natural enemy guilds in Aphis glycines suppression. Biological Control 45: 368-379.

572

2008 Advances in spectroscopic and other chemical methods have greatly enhanced our ability to characterize soil organic matter chemistry. As a result, the molecular characteristics of soil C are now known for a range of ecosystems, soil types, and management intensities. Placing this knowledge into a broader ecological and management context is difficult, however, and remains one of the fundamental challenges of soil organic matter research. Here we present a conceptual model of molecular soil C dynamics to stimulate inter-disciplinary research into the ecological implications of molecular C turnover and its management- and process-level controls. Our model describes three properties of soil C dynamics: 1) soil size fractions have unique molecular patterns that reflect varying degrees of biological and physical control over decomposition; 2) there is a common decomposition sequence independent of plant inputs or other ecosystem properties; and 3) molecular decomposition sequences, although consistent, are not uniform and can be altered by processes that accelerate or slow the microbial transformation of specific molecules. The consequences of this model include several key points. First, lignin presents a constraint to decomposition of plant litter and particulate C (> 53 μm) but exerts little influence on more stable mineral-associated soil fractions < 53 μm. Second, carbon stabilized onto mineral fractions has a distinct composition related more to microbially processed organic matter than to plant-related compounds. Third, disturbances, such as N fertilization and tillage, which alter decomposition rates, can have “downstream effects”; that is, a disturbance that directly alters the molecular dynamics of particulate C may have a series of indirect effects on C stabilization in silt and clay fractions. Grandy, A. S., and J. C. Neff. 2008. Molecular soil C dynamics downstream: The biochemical decomposition sequence and its effects on soil organic matter structure and function. Science of the Total Environment 404: 297-307.

660

2008 Gunckel, K. 2008. Preservice elementary teachers learning to use curriculum materials to plan and teach science. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

600

2008 Soil organic matter (SOM) in agricultural soils comprises a significant part of the global terrestrial C pool. It has often been characterized by utilizing a combination of chemical dispersion of the soil followed by physical separation. We fractionated soil samples under continuous corn (Zea mays L.) rotations at four long-term sites in the Corn Belt to determine the concentration of C and N associated with soil fractions (light fraction [LF], particulate organic matter [POM], silt size, clay size, and Bradford reactive soil protein [BRSP]) and to identify the change in C concentration and {delta}13C signal of each fraction using laboratory incubations. Light fractions comprised 3 to 5% of the soil organic carbon (SOC), with no significant difference between conventional tillage (CT) and no-till (NT) treatments. The POM fraction accounted for 5 to 11% of the SOC in the soils with >30% clay and 17 to 23% for the soils with <20% clay. The clay-size fraction contained the highest proportion of SOC. Measurement of 13C during long-term incubation showed that the average mean residence time (MRT) of corn-derived C in the LF was 3.5 yr, whereas the POM fractions ranged from 6 to 12 yr. The 13C changes during incubation show that both fractions consist of a mixture of active and resistant materials, with movement between fractions. The BRSP has long MRTs except in the NT Hoytville soil. Measurement of the dyna mics of these fractions provides a basis for C models to test the impacts of land use and management on C sequestration. Haile-Mariam, S., H. P. Collins, and E. A. Paul. 2008. Dynamics of soil organic matter constituents determined by 13C changes during long-term incubation. Soil Science Society America Journal 72: 370-378.

645

2008 Hamilton, S. K. 2008. Flood plains. Pages (in press). Encyclopedia of Inland Waters. Elsevier.

592

2008 Hamilton, S. K. 2008. Floodplain wetlands of large river systems. Pages (in press). Encyclopedia of Inland Waters. Elsevier.

593

2008 Crop yields are highly variable spatially and temporally as a result of complex interactions among topography, weather conditions, and management practices. The objective of this study was to analyze the effects of management practices on the relationship between crop yields and precipitation and crop yields and topography using 10 yr of yield data from a long-term corn (_Zea mays_ L.)-soybean [_Glycine max_ (L.) Merr.]-wheat (_Triticum aestivum_ L.) rotation experiment in southwest Michigan. The four agronomic treatments studied were chisel plowed with conventional chemical inputs (CT), no-till with conventional chemical inputs (NT), chisel plowed with low chemical input and a winter leguminous cover crop (CTL), and organic-based chisel plowed with a winter leguminous cover crop (CTO). A nonparametric (spline) regression was used to characterize the relationship between the maximal yields, as characteristics of yield potential, and a wetness index (WI), as an integrative characteristic of topographical features related to water flow, and to compare the yield differences between the treatments across a range of the WI values. Variability of yields in NT and CTO systems was better explained by precipitation in early spring and during pollination and grain fill than that in CT and CTL. No-till and CTL tended to produce higher maximal yields than CT at the summit/steep-sloped areas (lower WI), while at intermediate and high WI levels the differences between them were inconsistent. The CTL often produced higher maximal yields than CTO at low and intermediate WI values, while the difference between them was mostly not significant at high WI levels (depression areas). The nonparametric spline regression algorithm used in the study was robust and efficient in comparing the yield differences between treatments across a range of WI values. Huang, X., L. Wang, L. Yang, and A. N. Kravchenko. 2008. Management practice effects on relationships of grain yields with topography and precipitation. Agronomy Journal 100: 1463-1471.

573

2008 The upper Midwest USA features glacial-derived till materials enriched in carbonate minerals, but with the uppermost soil layer progressively leached of carbonates in the interval since glaciation. Groundwaters and groundwater-fed surface waters are profoundly influenced by carbonate mineral dissolution. Stable carbon isotope compositions of soil waters and groundwaters in two southern Michigan watersheds (Huron and Kalamazoo) were studied as a function of pH, δ13CCO2, types of weathering reactions (silicate vs. carbonate), and degree of isotope equilibration. This comprehensive study of carbon isotope biogeochemistry in the vadose zone, including soil gas, soil water/groundwater, and soils (organic matter/carbonate phases), elucidates relations between the chemical weathering rates and CO2 fluxes in the soil zone. Such information is important to evaluate responses of terrestrial ecosystems to global climate change. In shallow soil zones where only silicate weathering was occurring, respiratory CO2 was the major source of soil water DIC with little addition from the atmospheric CO2. Isotopic equilibration between δ13CDIC and δ13CCO2 occurred in an open system with respect to soil CO2. In the deeper soil horizons carbonate dissolution dominated soil water chemistry and saturation with respect to calcite and dolomite was attained rapidly. Mass balance calculation showed that large amounts of soil CO2 were consumed by carbonate dissolution, such that the deeper soil zone may not have been an open system with respect to CO2. Constant δ13CDIC values (not, vert, similar − 11‰) were observed in these deep soil waters and also in shallow groundwaters of the Huron watershed. Thus, isotopic equilibrium might not be reached between DIC and CO2, possibly due to a rapid kinetics of carbonate dissolution and limited gas–water exchange in the soils. If so, DIC was equally contributed by carbonate minerals (δ13CCaCO3 = 0‰) in reaction with soil CO2 (δ13CCO2 = − 22‰). Soils beneath an agricultural site with a wheat/corn/soybean rotation (the Kalamazoo watershed) displayed a wide range in δ13CCO2 values (− 22 to − 12‰), and the δ13CDIC of deeper soil waters in contact with carbonate minerals was controlled by seasonal variations of δ13CCO2 as well as by strong acids produced by nitrification and to a lesser degree by pyrite oxidation, both of which could react to dissolve carbonate minerals, in addition to carbonic acid dissolution. Jin, L., N. Ogrinc, S. K. Hamilton, K. Szramek, T. Kanduc, and L. M. Walter. 2008. Inorganic carbon isotope systematics in soil profiles undergoing silicate and carbonate weathering (Southern Michigan, USA). Chemical Geology 264: 139-153.

650

2008 We investigated long-term and seasonal patterns of N imports and exports, as well as patterns following climate perturbations, across biomes using data from 15 watersheds from nine Long-Term Ecological Research (LTER) sites in North America. Mean dissolved inorganic nitrogen (DIN) import-export budgets (N import via precipitation-N export via stream flow) for common years across all watersheds was highly variable, ranging from a net loss of - 0·17 ± 0·09 kg N ha-1mo-1 to net retention of 0·68 ± 0·08 kg N ha-1mo-1. The net retention of DIN decreased (smaller import-export budget) with increasing precipitation, as well as with increasing variation in precipitation during the winter, spring, and fall. Averaged across all seasons, net DIN retention decreased as the coefficient of variation (CV) in precipitation increased across all sites (r2 = 0·48, p = 0·005). This trend was made stronger when the disturbed watersheds were withheld from the analysis (r2 = 0·80, p < 0·001, n = 11). Thus, DIN exports were either similar to or exceeded imports in the tropical, boreal, and wet coniferous watersheds, whereas imports exceeded exports in temperate deciduous watersheds. In general, forest harvesting, hurricanes, or floods corresponded with periods of increased DIN exports relative to imports. Periods when water throughput within a watershed was likely to be lower (i.e. low snow pack or El Niño years) corresponded with decreased DIN exports relative to imports. These data provide a basis for ranking diverse sites in terms of their ability to retain DIN in the context of changing precipitation regimes likely to occur in the future. Copyright © 2008 John Wiley & Sons, Ltd. Kane, E. S., E. F. Betts, A. J. Burgin, H. M. Clilverd, C. L. Crenshaw, J. B. Fellan, I. H. Myers-Smith, J. A. O'Donnell, D. J. Sobota, W. J. Van Verseveld, and J. B. Jones. 2008. Precipitation control over nitrogen retention across watersheds: A synthesis of long-term ecological research. Ecohydrology 1: 105-117.

575

2008 Kravchenko, A. N., and X. Hao. 2008. Management effects on spatial variability characteristics of surface mineralizable C. Geoderma 144: 387-394.

577

2008 Increased demand for corn grain as an ethanol feedstock is altering U.S. agricultural landscapes and the ecosystem services they provide. From 2006 to 2007, corn acreage increased 19% nationally, resulting in reduced crop diversity in many areas. Biological control of insects is an ecosystem service that is strongly influenced by local landscape structure. Here, we estimate the value of natural biological control of the soybean aphid, a major pest in agricultural landscapes, and the economic impacts of reduced biocontrol caused by increased corn production in 4 U.S. states (Iowa, Michigan, Minnesota, and Wisconsin). For producers who use an integrated pest management strategy including insecticides as needed, natural suppression of soybean aphid in soybean is worth an average of $33 ha−1. At 2007–2008 prices these services are worth at least $239 million y−1 in these 4 states. Recent biofuel-driven growth in corn planting results in lower landscape diversity, altering the supply of aphid natural enemies to soybean fields and reducing biocontrol services by 24%. This loss of biocontrol services cost soybean producers in these states an estimated $58 million y−1 in reduced yield and increased pesticide use. For producers who rely solely on biological control, the value of lost services is much greater. These findings from a single pest in 1 crop suggest that the value of biocontrol services to the U.S. economy may be underestimated. Furthermore, we suggest that development of cellulosic ethanol production processes that use a variety of feedstocks could foster increased diversity in agricultural landscapes and enhance arthropod-mediated ecosystem services. Landis, D. A., M. M. Gardiner, W. van der Werf, and S. M. Swinton. 2008. Increasing corn for biuofuel production reduces biocontrol services in agricultural landscapes. PNAS 105: 20552-20557.

629

2008 While recent research has focused on the effects of exotic plant species on ecosystem properties, less is known about how restoring individual native plant species, differing in biomass and tissue chemistry, may impact ecosystems. We examined how three native C4 prairie grasses affected soil C and N cycling 11 years after reintroduction into successional old-field communities dominated by non-native C3 grasses. The species examined in this study differ in traits that are expected to influence soil C and N cycling (biomass and tissue chemistry). Thus, we hypothesized that cycling rates would decrease, thereby increasing pool sizes in soils under C4 species compared under C3 species. As predicted, the C4 species had greater biomass and more recalcitrant tissue [higher C:N, acid detergent fiber (ADF):N] compared to the dominant C3 species. The three C4 species did not differ in tissue C:N, ADF:N, or root biomass, but Andropogon had more than twice the shoot biomass of Schizachyrium and Sorghastrum. Soils under the C4 species did not differ in inorganic N levels, but levels were lower than in soils under the C3 species, and soils under Andropogon had slightly lower in situ net N mineralization rates compared to those under C3 species. We found little evidence of larger surface soil C pools under C4 species versus C3 species after 11 years and no differences in subsurface soil C or N among species. The C4 species contributed a significant amount of C to both soil depths after 11 years. Our results demonstrate that C4 species reintroduction into old-fields can alter C and N cycling on relatively short timescales, and that individual C4 species differ in the magnitude of these effects. Improving our understanding of how species influence ecosystem properties is essential to predicting the ecosystem-level consequences of plant community alterations due to land use changes, global change, and species introductions. Mahaney, W. M., K. A. Smemo, and K. L. Gross. 2008. Impacts of C4 grass introductions on soil carbon and nitrogen cycling in C3-dominated successional systems. Oecologia 157: 295-305.

637

2008 While recent research has focused on the effects of exotic plant species on ecosystem properties, less is known about how restoring individual native plant species, differing in biomass and tissue chemistry, may impact ecosystems. We examined how three native C4 prairie grasses affected soil C and N cycling 11 years after reintroduction into successional old-field communities dominated by non-native C3 grasses. The species examined in this study differ in traits that are expected to influence soil C and N cycling (biomass and tissue chemistry). Thus, we hypothesized that cycling rates would decrease, thereby increasing pool sizes in soils under C4 species compared under C3 species. As predicted, the C4 species had greater biomass and more recalcitrant tissue [higher C:N, acid detergent fiber (ADF):N] compared to the dominant C3 species. The three C4 species did not differ in tissue C:N, ADF:N, or root biomass, but Andropogon had more than twice the shoot biomass of Schizachyrium and Sorghastrum. Soils under the C4 species did not differ in inorganic N levels, but levels were lower than in soils under the C3 species, and soils under Andropogon had slightly lower in situ net N mineralization rates compared to those under C3 species. We found little evidence of larger surface soil C pools under C4 species versus C3 species after 11 years and no differences in subsurface soil C or N among species. The C4 species contributed a significant amount of C to both soil depths after 11 years. Our results demonstrate that C4 species reintroduction into old-fields can alter C and N cycling on relatively short timescales, and that individual C4 species differ in the magnitude of these effects. Improving our understanding of how species influence ecosystem properties is essential to predicting the ecosystem-level consequences of plant community alterations due to land use changes, global change, and species introductions. Mahaney, W. M., K. A. Smemo, and K. L. Gross. 2008. Impacts of C4 grass introductions on soil carbon and nitrogen cycling in C3-dominated successional systems. Oecologia 157: 295-305.

578

2008 Degree of oxidation of organic carbon (Cox) is a fundamental property of the carbon cycle, reflecting the synthesis and decomposition of natural organic matter. Cox is also related to ecosystem oxidative ratio (OR), the molar ratio of O2 to CO2 fluxes associated with net ecosystem exchange (NEE). Here we compare two methods for measuring Cox and OR: (1) %C, %H, %N, and %O elemental analysis, and (2) heat of combustion (ΔHc) measured by means of bomb calorimetry coupled with %C elemental analysis (hereafter referred to as calorimetry). Compared with %C, %N, %H, and %O elemental analysis, calorimetry generates Cox and OR data more rapidly and cheaply. However, calorimetric measurements yield less accurate Cox and OR data. We additionally report Cox and OR data for a pair of biomass standards and a suite of biomass samples. The OR values we measured in these samples were less variable than OR data reported in the literature (generated by simultaneous measurement of ecosystem O2 and CO2 gas mixing ratios). Our biomass OR values had a mean of 1.03 and range of 0.99–1.06. These estimates are lower than the OR value of 1.10 that is often used to partition uptake of fossil fuel CO2 between the ocean and the terrestrial biosphere. Masiello, C. A., M. E. Gallagher, J. T. Randerson, R. M. Deco, and O. A. Chadwick. 2008. Evaluating two experimental approaches for measuring ecosystem carbon oxidation state and oxidative ratio. Journal of Geophysical Research 113: G03010, doi:10.1029/2007JG000534.

579

2008 Mason, R., P. Roe, M. Towsey, J. Zhang, J. Gibson, and S. Gage. 2008. Towards an acoustic environmental observatory. Pages 135-142. Fourth IEEE International Conference on eScience.

666

2008 Mishra, R., R. Singh, K. Hemant, K. Jaiswal, M. Singh, Y. G. Yanni, and F. B. Dazzo. 2008. Rice-rhizobia association: Evolution of an alternate niche of beneficial plant-bacteria association. Pages 165-194 in I. Ahmad, J. Pichtel, and S. Hayat, eds. Plant-Bacteria Interactions: Strategies and Techniques to Promote Plant Growth. Wiley-VCH Verlag GmbH, Weinheim, Germany.

655

2008 In order to retrieve phylogenetic information from distance matrices generated from large-scale clone libraries, and to explore OTU distribution among them, we have developed downstream applications for use with the already available DOTUR program. These programs enhance and ease data extraction, providing phylogeny to the already generated distance data. Morales, S. E., T. F. Cosart, J. V. Johnson, and W. E. Holben. 2008. Supplemental programs for enhanced recovery of data from the DOTUR application. Journal of Microbiological Methods 75: 572-575.

639

2008 Mulholland, P. J., A. M. Helton, G. C. Poole, R. O. Hall, S. K. Hamilton, B. J. Peterson, J. L. Tank, L. R. Ashkenas, L. W. Cooper, C. N. Dahm, W. K. Dodds, S. Findlay, S. V. Gregory, and N. B. Grimm. 2008. Stream denitrification across biomes and its response to anthropogenic nitrate loading. Nature 452: 202-206.

580

2008 Mutch, D. R., S. A. Thalman, T. E. Martin, and D. G. Bass, eds. 2008. Flaming as a Method of Weed Control in Organic Farming Systems; Extension Bulletin E-3038. Michigan State University, East Lansing, Michigan.

594

2008 Noma, T., and M. J. Brewer. 2008. Seasonal abundance of resident parasitoids and predatory flies and corresponding soybean aphid mortality, with comments on classical biological control of soybean aphid in the U.S. Midwest. Journal of Economic Entomology 101: 278-287.

582

2008 Paul, E. A., K. Magrini-Baer, R. Conant, R. F. Follet, and S. J. Morris. 2008. Biological and molecular structure analysis of the controls on soil organic matter dynamics. Pages 167-170 in I. V. Permanova and N. A. Kulikova, eds. International Humic Substance Society Proceedings, Moscow, Russia.

657

2008 Pore network geometries of intra-aggregate pore spaces are of great importance for water and ion flux rates controlling C sequestration and bioremediation. Advances in non-invasive three-dimensional imaging techniques such as synchrotron-radiation-based x-ray microtomography (SR-µCT), offer excellent opportunities to study the interrelationships between pore network geometry and physical processes at spatial resolutions of a few micrometers. In this paper we present quantitative three-dimensional pore-space geometry analyses of small scale (~5 mm across) soil aggregates from different soil management systems (conventionally tilled vs. grassland). Reconstructed three-dimensional microtomography images at approximate isotropic voxel resolutions between 3.2 and 5.4 µm were analyzed for pore-space morphologies using a suite of image processing algorithms associated with the software published by Lindquist et al. Among the features quantified were pore-size distributions (PSDs), throat-area distributions, effective throat/pore radii ratios as well as frequency distributions of pore channel lengths, widths, and flow path tortuosities. We observed differences in storage and transport relevant pore-space morphological features between the two aggregates. Nodal pore volumes and throat surface areas were significantly smaller for the conventionally tilled (Conv.T.) aggregate (mode {approx} 7.9 x 10–7 mm3/{approx} 63 µm2) than for the grassland aggregate (mode {approx} 5.0 x 10–6 mm3/{approx} 400 µm2), respectively. Path lengths were shorter for the Conv.T. aggregate (maximum lengths < 200 µm) compared with the grassland aggregate (maximum lengths > 600 µm). In summary, the soil aggregate from the Conv.T site showed more gas and water transport limiting micromorphological features compared with the aggregate from the grassland management system. Peth, S., R. Horn, F. Beckmann, and T. Donath. 2008. Three-dimensional quantification of intra-aggregate pore-space features using synchrotron-radiation-based microtomography. Soil Science Society of America Journal 72: 897-907.

658

2008 Qi, J., S. H. Gage, W. Joo, B. Napoletano, and S. Biswas. 2008. Soundscape characteristics of an environment: A new ecological indicator of ecosystem health. Pages 201-211 in W. Ji, ed. Wetland and Water Resource Modeling and Assessment. CRC Press, New York, New York.

591

2008 Robertson, G. P. 2008. Long-term ecological research: Re-inventing network science. Frontiers in Ecology and the Environment 6: 281.

609

2008 Robertson, G. P., V. G. Allen, G. Boody, E. R. Boose, N. G. Creamer, L. E. Drinkwater, J. R. Gosz, L. Lynch, J. L. Havlin, L. E. Jackson, S. T. A. Pickett, L. Pitelka, A. Randall, A. S. Reed, T. R. Seastedt, R. B. Waide, and D. H. Wall. 2008. Long-term agricultural research: A research education, and extension imperative. BioScience 58: 640-643.

584

2008 Robertson, G. P., V. H. Dale, O. C. Doering, S. P. Hamburg, J. M. Melillo, M. M. Wander, W. J. parton, P. R. Adler, J. N. Barney, R. M. Cruse, C. S. duke, P. M. Fearnside, R. F. Follett, H. K. Gibbs, J. Goldemberg, D. J. Miadenoff, D. Ojima, M. W. Palmer, A. Sharpley, L. Wallace, K. C. Weathers, J. A. Wiens, and W. W. Wilhelm. 2008. Sustainable biofuels redux. Science 322: 49.

604

2008 Rudy, A. P., C. K. Harris, B. J. Thomas, M. R. Worosz, S. C. Kaplan, and E. C. O'Donnell. 2008. The political ecology of Southwest Michigan Agriculture, 1837-2000. Pages 152-205 in C. L. Redman and D. R. Foster, eds. Agrarian Landscapes in Transition. Oxford University Press, New York, New York.

595

2008 Safir, G. R., S. H. Gage, M. Colunga-Garcia, P. R. Grace, and S. Rowshan. 2008. Simulation of corn yields in the upper great lakes region of the U.S. using a modeling framework. Computers and Electronics in Agriculture 60: 301-305.

585

2008 The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML). The LTER is one of the top National Science Foundation (NSF) programs in biology since 1980, representing diverse ecosystems and creating long-term, interdisciplinary research, synthesis of information, and theory. The adoption of EML as the LTER network standard has been key to building network synthesis architectures based on high-quality standardized metadata. EML is the NSF-recognized metadata standard for LTER, and EML is a criteria used to review the LTER program progress. At the workshop, a potential crosswalk between the GCDML and EML was explored. Also, collaboration between the LTER and GSC developers was proposed to join efforts toward a common metadata cataloging designer's tool. The community adoption success of a metadata standard depends, among other factors, on the tools and trainings developed to use the standard. LTER's experience in embracing EML may help GSC to achieve similar success. A possible collaboration between LTER and GSC to provide training opportunities for GCDML and the associated tools is being explored. Finally, LTER is investigating EML enhancements to better accommodate genomics data, possibly integrating the GCDML schema into EML. All these action items have been accepted by the LTER contingent, and further collaboration between the GSC and LTER is expected. San, I. G., W. Sheldon, T. M. Schmidt, M. Servilla, R. Aguilar, C. Gries, T. Gray, D. Field, J. J. Cole, J. Yun Pan, G. Palanisamy, D. L. Henshaw, M. O'Brien, L. L. Kinkel, K. McMahon, R. Kottmann, L. Armaral-Zettler, J. E. Hobbie, P. Goldstein, R. P. Guralnick, J. W. Brunt, and W. K. Michener. 2008. Defining linkages between the GSC and NSF's LTER program: How the ecologivcal metadata language (EML) relates to GCDML and other outcomes. OMICS 12: 151-156.

663

2008 Understanding how communities of important soil invertebrates vary with land use may lead to the development of more sustainable land-use strategies. We assessed the abundance and species composition of earthworm communities across six replicated long-term experimental ecosystems that span a gradient in agricultural land-use intensity. The experimental systems include a conventional row-crop agricultural system, two lower-intensity row-crop systems (no-till and tilled organic input), an early successional old-field system, a 40–60 years old coniferous forest plantation, and an old-growth deciduous forest system. Earthworm populations varied among systems; they were lowest in the most intensively managed row-crop system (107 m−2) and coniferous forest (160 m−2); intermediate in the old-field (273 m−2), no-till (328 m−2) and tilled organic (344 m−2) cropping systems; and highest in the old-growth deciduous forest system (701 m−2). Juvenile Aporrectodea species were the most common earthworms encountered in intensively managed systems; other species made up a larger proportion of the community in less intensively managed systems. Earthworm community biomass and species richness also varied and were lowest in the conventional row-crop system and greatest in the old-growth forest system. These results suggest that both land-use intensity and land-use type are strong drivers of the abundance and composition of earthworm communities in agricultural ecosystems. Smith, R. G., C. P. McSwiney, A. S. Grandy, P. Suwanwaree, R. M. Snider, and G. P. Robertson. 2008. Diversity and abundance of earthworms across an agricultural land-use intensity gradient. Soil & Tillage Research 100: 83-88.

601

2008 Smith, R. G., K. L. Gross, and G. P. Robertson. 2008. Effects of crop diversity on agrecosystem function: Crop yield response Ecosystems 11: 355-366.

586

2008 Swinton, S. M. 2008. Reimagining farms as managed ecosystems. Choices 23: 28-31.

588

2008 I investigated how agricultural systems can be managed to minimize the environmental impact of agriculture without sacrificing productivity—or, conversely, to maximize the ecosystem services provided by agriculture, including productivity. Agricultural systems have a large impact on nutrient cycling, climate regulation, and fresh water and food provisioning, and I have used nitrate leaching, drainage, carbon sequestration, soil inorganic nitrogen, greenhouse gas fluxes, annual net primary productivity, and agronomic yield across a management intensity gradient as a measure of the provision of these services. Research was conducted at Kellogg Biological Station’s Long-Term Ecological Research site in southwest Michigan. Treatments included four annual maize-soybean-wheat rotations with conventional, no-till, reduced-input, and organic management; three perennial systems in alfalfa, poplar, and conifer crops; and four native successional systems ranging from early successional (~20 years since abandonment from agriculture) systems to old growth forest. All systems were replicated in the landscape on the same soil series. Nitrate leaching over an 11 year period ranged from less than 1 kg NO3--N ha-1y-1 in poplars to 62 kg NO3--N ha-1y-1 in the conventional row-crop system. The no-till, reduced input, and organic systems leached 34%, 61%, and 68% less nitrogen, respectively, than did the conventional system. The alfalfa and conifer stands leached nitrogen at rates similar to the organic system. The successional and poplar systems leached the least amount of nitrogen. Drainage levels were highest in the no-till annual system and deciduous forest. Our findings show that long-term water quality is substantially affected by crops and management practices. Soil carbon levels 11 years post-establishment differed substantially among systems in the surface soil, where carbon contents were significantly greater than the conventional system in the no-till, organic, alfalfa, poplar, conifer, early successional, never tilled mid-successional, and deciduous forest systems. However, soil carbon levels in the deeper portions of the soil profile were more variable, and showed very few significant differences among treatments. Subsequently soil carbon levels in the total profile to 1 meter differed little among treatments, with only the early successional and never-tilled mid-successional systems containing more soil carbon than the conventional system. Deeper soil carbon was much more variable than carbon in upper soil layers, which suggests that finding differences among treatments when including deeper soils will be more difficult. Results demonstrate the importance of measuring carbon to depth but also the need for more intensive sampling than has been undertaken to date. The additional measured ecosystem services also differed by management system. Yield was highest in the no-till system, and the lowest in the organic system. The reduced input and conventional treatments had similar yields, despite differences in management. Nitrous oxide production was highest in the alfalfa and annual cropping systems, and lowest in the poplar system. Nitrous oxide fluxes were tightly linked to soil nitrate levels. Soil methane oxidation was highest in deciduous forest system, and lowest in the conventional system. Net primary productivity was highest in the reduced input system, and lowest in the poplar system. Soil inorganic nitrogen levels were highest in the alfalfa and early successional system, and lowest in the reduced-input, conventional, and poplar systems. As systems were managed more intensely, soil carbon levels decreased, nitrate leaching increased, methane oxidation decreased, and nitrous oxide production increased. Trade-off curves and flower diagrams provide a means to display these alternative services and their effects. Analyses of multiple ecosystem services are a first step towards better understanding the large scale trade-offs that occur with land management decisions. Trade-offs in multiple ecosystem services can be used to help develop models incorporating the complexity of the different components of the ecosystem. Future research might focus on using such models to predict the outcome of individual management decisions on the services delivered by managed systems. Syswerda, S. P. 2008. Ecosystem Services from Agriculture Across a Management Intensity Gradient in Southwest Michigan. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

624

2008 Biogeochemical transformations in wetlands impact water quality, nutrient transport across landscapes, and greenhouse gas exchanges with the atmosphere. This study examined anaerobic microbial respiration and methanogenesis in surficial sediments of six wetlands lying on glacial terrain in southwest Michigan, USA. Three of the wetlands were mainly groundwater-fed and three were mainly precipitation-fed. Ambient rates of denitrification, sulfate reduction, iron reduction, methanogenesis, and acetate turnover were measured at each wetland. Ambient denitrification rates were not detectable in any wetland, but denitrifying enzyme activity, measured in two wetlands, indicated that the potential to remove nitrate was higher in a groundwater-fed wetland. Iron reduction was measurable mainly in precipitation-fed wetlands while sulfate reduction was only measurable in the groundwater-fed wetlands. Methanogenesis was measurable in all wetlands, with no differences between wetlands with contrasting water sources, indicating that methanogenesis is important regardless of water source. Acetate turnover rates, which reflect total anaerobic respiration and methanogenesis, were higher in the groundwater-fed wetlands and proportional to the sum of the individual carbon mineralization rates across all wetlands. Even though there was substantial variation in the process rates among these wetlands, the general patterns indicate that water source influences the biogeochemical function of wetlands. Whitmire, S. L., and S. K. Hamilton. 2008. Rates of anaerobic microbial metabolism in wetlands of divergent hydrology on a glacial landscape. Wetlands 28: 703-714.

614

2008 Beaulieu, J. J. 2007. Controls on Greenhouse Gas Emissions from Headwater Streams. Ph.D. Dissertation, University of Notre Dame, South Bend, Indiana, USA.

608

2007 Brewer, M., A. Fiedler, E. Grafius, R. Isaacs, M. E. Kaiser, D. Landis, S. Langley, T. E. Martin, D. Mutch, and J. Tuell. 2007. IPM benefits of managing field borders, covercrops and other noncrop vegetation in S. Deming, L. Johnson, D. Lehnert, and D. Mutch, eds. Building a Sustainable Future: Ecologically Based farming Systems. Extension Bulletin E-2983. Michigan State University, East Lansing, Michigan.

527

2007 The removal of nitrogen (N) in aquatic ecosystems is of particular interest because excessive nitrate in ground and surface waters is a growing problem. Research on nitrate removal processes has emphasized biotic uptake (assimilation) or respiratory denitrification by bacteria. The increasing application of tracer techniques (e.g., stable isotopes) has yielded a growing body of evidence for alternative microbially mediated processes of nitrate transformation, including dissimilatory reduction of nitrate to ammonium (DNRA), chemoautotrophic denitrification via sulfur or iron oxidation, and anaerobic ammonium oxidation (Anammox). In Chapter 1, I review evidence for the importance of alternative nitrate removal pathways in aquatic ecosystems and discuss how the possible prevalence of these pathways may alter views of N cycling and its controls. Anaerobic microbial processes are responsible for much of the nutrient cycling in freshwater systems. Nitrate disappearance in sediments is usually assumed to be due to respiratory denitrification. Push-pull tracer experiments entail adding nitrate and a conservative solute to sediment porewater, followed by in-situ incubation with periodic subsampling. While performing such tracer experiments to quantify rates of nitrate removal in aquatic sediments of Michigan streams and wetlands, I found that nitrate removal coincided with sulfate production. Push-pull experiments in a diverse set of streams, lakes and wetlands revealed a persistent pattern of sulfate production during nitrate removal (Chapter 2). Push-pull experiments done with 15NO¬3- also indicate the importance of DNRA to overall nitrate removal in these sediments. To compare the relative importance of alternative pathways of NO¬3- reduction (e.g., to NH4+ or N2), I used of stable isotopes with a flow-through cores (Chapter 3). Using a flow-through set up, treatment water (15NO3-, 15NH4+/14NO3-, or control) was pumped over cores from six different sites. Results indicate that conversion to N2 was the predominant nitrate loss across all six sites. I also found that conversion into the 15NH4+ pool, indicative of DNRA, can account for a variable fraction of the dissimilatory nitrate removal, but that anammox accounted for very little of the overall nitrate removal. I tested the relative importance of carbon vs. sulfide in regulating DNRA using a laboratory assay (Chapter 4), by adding nitrate along with a gradient of organic carbon (as acetate) and free sulfide to anoxic sediments. I found that both carbon and sulfide were important in controlling nitrate removal rates and end-products in both sites. While denitrification tended to be the more important removal pathway in the low ambient sulfide site, DNRA was of equal importance in the high ambient sulfide site. Burgin, A. J. 2007. Alternative microbial pathways of nitrate removal from freshwater ecosystems. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA

555

2007 The removal of nitrogen (N) in aquatic ecosystems is of great interest because excessive nitrate in groundwater and surface water is a growing problem. High nitrate loading degrades water quality and is linked to eutrophication and harmful algal blooms, especially in coastal marine waters. Past research on nitrate removal processes has emphasized plant or microbial uptake (assimilation) or respiratory denitrification by bacteria. The increasing application of stable isotopes and other tracer techniques to the study of nitrate removal has yielded a growing body of evidence for alternative, microbially mediated processes of nitrate transformation. These include dissimilatory (the reduction of nitrogen into other inorganic compounds, coupled to energy producing processes) reduction of nitrate to ammonium (DNRA), chemoautotrophic denitrification via sulfur or iron oxidation, and anaerobic ammonium oxidation (anammox), as well as abiotic nitrate removal processes. Here, we review evidence for the importance of alternative nitrate removal pathways in aquatic ecosystems and discuss how the possible prevalence of these pathways may alter views of N cycling and its controls. These alternative pathways are of particular importance for the management of excess N in the environment, especially in cases where nitrate is transformed to ammonium, a biologically available and less mobile N form, rather than to dinitrogen gas Burgin, A. J., and S. K. Hamilton. 2007. Have we overemphasized the role of dentirification in aquatic ecosystems? A review of nitrate removal pathways. Frontiers in Ecology and the Environment 5: 89-96

521

2007 Butler, R., M. Servilla, S. Gage, J. Basney, V. Welch, B. Baker, T. Fleury, P. Duda, D. Gehrig, M. Bletzinger, J. Tao, and D. M. Freemon. 2007. Cyberinfrastructure for the analysis of ecological acoustic sensor data: A use case study in grid deployment. Cluster Computing 10: 301-310.

669

2007 Global energy use and food production have increased nitrogen inputs to ecosystems worldwide, impacting plant community diversity, composition, and function. Previous studies show considerable variation across terrestrial herbaceous ecosystems in the magnitude of species loss following nitrogen (N) enrichment. What controls this variation remains unknown. We present results from 23 N-addition experiments across North America, representing a range of climatic, soil and plant community properties, to determine conditions that lead to greater diversity decline. Species loss in these communities ranged from 0 to 65% of control richness. Using hierarchical structural equation modelling, we found greater species loss in communities with a lower soil cation exchange capacity, colder regional temperature, and larger production increase following N addition, independent of initial species richness, plant productivity, and the relative abundance of most plant functional groups. Our results indicate sensitivity to N addition is co-determined by environmental conditions and production responsiveness, which overwhelm the effects of initial community structure and composition. Clark, C. M., E. E. Cleland, and S. L. Collins. 2007. Environmental and plant community determinants of species loss flooowing nitrogen enrichment. Ecology Letters 10: 596-607.

618

2007 Top-down regulation of herbivores in terrestrial ecosystems is pervasive and can lead to trophic cascades that release plants from herbivory. Due to their relatively simplified food webs, agroecosystems may be particularly prone to trophic cascades, a rationale that underlies biological control. However, theoretical and empirical studies show that, within multiple enemy assemblages, intraguild predation (IGP) may lead to a disruption of top-down control by predators. We conducted a factorial field study to test the separate and combined effects of predators and parasitoids in a system with asymmetric IGP. Specifically we combined ambient levels of generalist predators (mainly Coccinellidae) of the soybean aphid, Aphis glycines Matsumura, with controlled releases of the native parasitoid Lysiphlebus testaceipes (Cresson) and measured their impact on aphid population growth and soybean biomass and yield. We found that generalist predators provided strong, season-long aphid suppression, which resulted in a trophic cascade that doubled soybean biomass and yield. However, contrary to our expectations, L. testaceipes provided minor aphid suppression and only when predators were excluded, which resulted in nonadditive effects when both groups were combined. We found direct and indirect evidence of IGP, but because percentage parasitism did not differ between predator exclusion and ambient predator treatments, we concluded that IGP did not disrupt parasitism during this study. Our results support theoretical predictions that intraguild predators which also provide strong herbivore suppression do not disrupt top-down control of herbivores. Costamagna, A. C., D. A. Landis, and C. D. DiFonzo. 2007. Suppression of soybean aphid by generalist predators results in a trophic cascade in soybeans. Ecological Applications 17: 441-451

559

2007 1 There is ample evidence that the life history and population dynamics of aphids are closely linked to plant phenology. Based on life table studies, it has been proposed that the growth of aphid populations could be modeled with an exponential growth model, with r decreasing linearly with time. This model has never been tested under field conditions. 2 The soybean aphid Aphis glycines is a new invasive pest to soybean production in the U.S.A. In the present study, we present five datasets on the growth of colonies of _A. glycines_, monitored during population growth and decline under predator-free conditions in three soybean fields, from 2003 to 2006. 3 We demonstrate that an exponential growth model, with r decreasing linearly with time, gives a much better description of _A. glycines_ dynamics for all datasets (R2 = 0.94–0.99) than the exponential (R2 = 0.42–0.98) or logistic growth models (R2 = 0.77–0.99). Furthermore, it is shown by cross-validation that the exponential model with decreasing r can be used to make population predictions, as shown by the coefficient of prediction, ranging from 0.55 to 0.97. An improved fit of the model was obtained using both aphid ( ) and soybean ( ) degree-days scales, indicating temperature effects on the phenological time scale for the decrease in r. 4 Our model suggests important bottom-up control of _A. glycines_ population growth, which may interact with other mortality factors. The generality and potential applications of these results are discussed. Costamagna, A. C., W. van der Werf, F. J. J. A. Bianchi, and D. A. Landis. 2007. An exponential growth model with decreasing r captures bottom-up effects on the population growth Aphis glycines Matsumura (Hemiptera: Aphiddae). Agricultural and Forest Entomology 9: 297-305.

551

2007 Protein synthesis is the predominant activity of growing bacteria; the protein synthesis system accounts for more than one-half the cell's dry mass and consumes most of the cell's energy during rapid growth. Translation has been studied extensively using model organisms, and the translational apparatus is qualitatively similar in terms of structure and function across all known forms of life. However, little is known about variation between organisms in translational performance. Using measurements of macromolecular content in a phylogenetically diverse collection of bacteria with contrasting ecological strategies, we found that the translational power (the rate of protein synthesis normalized to the mass of the protein synthesis system) is three- to fourfold higher among bacteria that respond rapidly to nutrient availability than among bacteria that respond slowly. An analysis of codon use in completely sequenced bacterial genomes confirmed that the selective forces acting on translation vary with the ecological strategy. We propose that differences in translational power result from ecologically based variation among microbes in the relative importance of two competing benefits: reducing the biomass invested in the protein synthesis system and reducing the energetic expense of protein synthesis. Dethlefsen, L., and T. M. Schmidt. 2007. Performance of the translational apparatus varies with the ecological strategies of bacteria. Journal of Bacteriology 189: 3237-3245

558

2007 Agricultural intensification has greatly increased the productive capacity of agroecosystems, but has had unintended environmental consequences including degradation of soil and water resources, and alteration of biogeochemical cycles. Current nutrient management strategies aim to deliver soluble inorganic nutrients directly to crops and have uncoupled carbon, nitrogen, and phosphorus cycles in space and time. As a result, agricultural ecosystems are maintained in a state of nutrient saturation and are inherently leaky because chronic surplus additions of nitrogen and phosphorus are required to meet yield goals. Significant reductions of nutrient surpluses can only be achieved by managing a variety of intrinsic ecosystem processes at multiple scales to recouple elemental cycles. Rather than focusing solely on soluble, inorganic plant-available pools, an ecosystem-based approach would seek to optimize organic and mineral reservoirs with longer mean residence times that can be accessed through microbially and plant-mediated processes. Strategic use of varied nutrient sources, including inorganic fertilizers, combined with increases in plant diversity aimed at expanding the functional roles of plants in agroecosystems will help restore desired agroecosystem functions. To develop crops that can thrive in this environment, selection of cultivars and their associated microorganisms that are able to access a range of nutrient pools will be critical. Integrated management of biogeochemical processes that regulate the cycling of nutrients and carbon combined with increased reservoirs more readily retained in the soil will greatly reduce the need for surplus nutrient additions in agriculture. (c) 2007, Elsevier Inc. Drinkwater, L. E., and S. S. Snapp. 2007. Nutrients in agroecosystems: Rethinking the management paradigm. Advances in Agronomy 92: 163-186.

615

2007 The soil environment is an abundant source of microbial life; recent studies have estimated that in one gram of soil, there are over one million species. These microbes are essential to the environment as major contributors to biogeochemical cyles (e.g. carbon and nitrogen). Unfortunately only 0.1 to 1% of the total microbial community has been cultivated, leaving a wealth of unexplored diversity; one such phylum is the Acidobacteria. The phylum Acidobacteria is an ubiquitous group of microorganisms found in various soil and sediment environments. Historically, it contains eight monophyletic subdivisions and only three cultivated representatives. This dissertation explored members of this unknown phylum by using molecular and growth-based approaches to increase our understanding of acidobacteria ecology in the soil environment. A phylogenetic survey of soil taken from the KBS LTER revealed the presence of subdivisions 1, 3, 4, 5, and 6, with members of subdivision 4 being more dominant in the conventional agriculture treatment and subdivisions 1 and 6 being more dominant in the successional community treatment. Additionally, the acidobacteria community composition changed in relation to edaphic properties such as soil moisture (subdivision 3), carbon concentration (subdivision 4), soil pH (subdivision 1), methane fluxes (subdivision 1), and nitrous oxide fluxes (subdivision 4). These trends were used to isolate strains of acidobacteria and helped to provide insight into their physiology. Successful attempts were made to cultivate members of this phylum with soil collected from the KBS LTER using cultivation strategies designed to mimic the native soil environment. After ca. 30 days of growth, total recoveries ranged from ca. 3 to 6% of the total microbial community; soils containing high moisture content had significantly increased total recovery. In order to screen for the presence of acidobacteria on cultivation plates, a facile high-throughput method called Plate Wash PCR (PWPCR) was developed to rapidly screen enrichment plates using phylum-specific 16S rRNA gene primers. Additionally, PWPCR revealed that acidobacteria were more frequently detected with elevated levels of carbon dioxide (significantly), the presence of the catalase enzyme, low nutrients, and low oxygen concentrations. The use of these cultivation strategies along with PWPCR was instrumental in isolating more than a dozen members of the phylum Acidobacteria from subdivisions 1 and 3. Colonies of these strains were approximately 1 mm in diameter and either white, pale yellow or pink in color, the latter due to a carotenoid that was synthesized preferentially under 20% as compared to 2% oxygen. Strains were Gram negative, aerobic, chemoorganotrophic, nonmotile rods that produced an extracellular matrix causing cells to clump in liquid culture. All strains contained either 1 or 2 copies of the 16S ribosomal RNA encoding gene, which along with a relatively slow doubling time suggests an oligotrophic lifestyle. Genotypic, physiological, and morphological data revealed the presence of a novel genus in subdivision 1, Terriglobus, which contained pigmented strains of acidobacteria. The physiological and nutritional characteristics of these acidobacteria are consistent with their potential widespread distribution in soil. Eichorst, S. A. 2007. Isolation and characterization of members of the phylum acidobacteria from soils. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA

520

2007 Bacteria in the phylum Acidobacteria are widely distributed and abundant in soils, but their ecological roles are poorly understood, owing in part to a paucity of cultured representatives. In a molecular survey of acidobacterial diversity at the Michigan State University Kellogg Biological Station Long-Term Ecological Research site, 27% of acidobacterial 16S rRNA gene clones in a never-tilled, successional plant community belonged to subdivision 1, whose relative abundance varied inversely with soil pH. Strains of subdivision 1 were isolated from these never-tilled soils using low-nutrient medium incubated for 3 to 4 weeks under elevated levels of carbon dioxide, which resulted in a slightly acidified medium that matched the pH optima of the strains (between 5 and 6). Colonies were approximately 1 mm in diameter and either white or pink, the latter due to a carotenoid(s) that was synthesized preferentially under 20% instead of 2% oxygen. Strains were gram-negative, aerobic, chemo-organotrophic, nonmotile rods that produced an extracellular matrix. All strains contained either one or two copies of the 16S rRNA encoding gene, which along with a relatively slow doubling time (10 to 15 h at ca. 23°C) is suggestive of an oligotrophic lifestyle. Six of the strains are sufficiently similar to one another, but distinct from previously named Acidobacteria, to warrant creation of a new genus, Terriglobus, with Terriglobus roseus defined as the type species. The physiological and nutritional characteristics of Terriglobus are consistent with its potential widespread distribution in soil. Eichorst, S. A., J. A. Breznak, and T. M. Schmidt. 2007. Isolation and characterization of bacteria from soil that define Terriglobus gen. nov., in the phylum Acidobacteria. Applied and Environmental Microbiology 73: 2708-2717.

519

2007 Understanding mechanisms that promote efficient nutrient cycling is key to creating more sustainable agricultural landscapes. Many legumes have a unique ability to mobilize soil P. Phosphorus cycling was quantified at the Long Term Ecological Research (LTER) experiment at Kellogg Biological Station, in four systems initiated in 1989: 1) conventional corn-soybean-wheat, 2) organic corn-soybean-wheat with two years of red clover cover crops, 3) continuous alfalfa, and 4) a successional system, taken out of farmland in 1989. These treatments allow for comparisons between cropping systems with annual and perennial legumes and different intensities of legumes. In 2006, soybeans were planted as an assay of P bioavailability in the conventional, organic and alfalfa systems. Soil samples from the four systems, from 1992, 2001 and 2006, were analyzed for particulate organic matter phosphorus (POM-P), total organic P, total soil P, and soil extractable P (Bray P) to examine changes in soil P pools over time. Phosphorus bioavailability was greatest in the alfalfa system. Changes in soil pools occurred over time, with more P being stored in the organic and plant available soil pools in systems with a greater presence of legumes. Overall, these findings argue for an integrated approach to phosphorus nutrient management in low-input or organic agricultural systems, which utilize a variety of legumes to improve the bioavailability of P and build up P in soil pools with rapid turnover, such as POM-P. Gallaher, C. M. 2007. Phosphorus availability in annual and perennial cropping systems. M.S. Thesis, Michigan State University, East Lansing, Michigan, USA.

522

2007 Restoring soil C pools by reducing land use intensity is a potentially high impact, rapidly deployable strategy for partially offsetting atmospheric CO2 increases. However, rates of C accumulation and underlying mechanisms have rarely been determined for a range of managed and successional ecosystems on the same soil type. We determined soil organic matter (SOM) fractions with the highest potential for sequestering C in ten ecosystems on the same soil series using both density- and incubation-based fractionation methods. Ecosystems included four annual row-crop systems (conventional, low input, organic and no-till), two perennial cropping systems (alfalfa and poplar), and four native ecosystems (early successional, midsuccessional historically tilled, midsuccessional never-tilled, and late successional forest). Enhanced C storage to 5 cm relative to conventional agriculture ranged from 8.9 g C m-2 y-1 in low input row crops to 31.6 g C m-2 y-1 in the early successional ecosystem. Carbon sequestration across all ecosystems occurred in aggregate-associated pools larger than 53 �m. The density-based fractionation scheme identified heavy-fraction C pools (SOM > 1.6 g cm-3 plus SOM < 53 �m), particularly those in macroaggregates (>250 �m), as having the highest potential C accumulation rates, ranging from 8.79 g C m-2 y-1 in low input row crops to 29.22 g C m-2 y-1 in the alfalfa ecosystem. Intra-aggregate light fraction pools accumulated C at slower rates, but generally faster than in inter-aggregate LF pools. Incubation-based methods that fractionated soil into active, slow and passive pools showed that C accumulated primarily in slow and resistant pools. However, crushing aggregates in a manner that simulates tillage resulted in a substantial transfer of C from slow pools with field mean residence times of decades to active pools with mean residence times of only weeks. Our results demonstrate that soil C accumulates almost entirely in soil aggregates, mostly in macroaggregates, following reductions in land use intensity. The potentially rapid destruction of macroaggregates following tillage, however, raises concerns about the long-term persistence of these C pools. Grandy, A.S. and G.P. Robertson. 2007. Land-use intensity effects on soil organic carbon accumulation rates and mechanisms. Ecosystems 10:59-74.

511

2007 Gross, K., and S. A. Emery. 2007. Succession and restoration in Michigan old-field communities. Pages (in press) in V. Kramer and R. J. Hobbs, eds. Old-Fields: Dynamics and Restoration of Abandoned Farmland. Island Press.

350

2007 Agricultural lime can be a source or a sink for CO2, depending on whether reaction occurs with strong acids or carbonic acid. Here we examine the impact of liming on global warming potential by comparing the sum of Ca2+ and Mg2+ to carbonate alkalinity in soil solutions beneath unmanaged vegetation versus limed row crops, and of streams and rivers in agricultural versus forested watersheds, mainly in southern Michigan. Soil solutions sampled by tension indicated that lime can act as either a source or a sink for CO2. However, infiltrating waters tended to indicate net CO2 uptake, as did tile drainage waters and streams draining agricultural watersheds. As nitrate concentrations increased in infiltrating waters, lime switched from a net CO2 sink to a source, implying nitrification as a major acidifying process. Dissolution of lime may sequester CO2 equal to roughly 50% of its C content, in contrast to the prevailing assumption that all of the carbon in lime becomes CO2. The 30 Tg/yr of agricultural lime applied in the United States could thus sequester up to1.9 Tg C/yr, about 15% of the annual change in the U.S. CO2 emissions (12 Tg C/yr for 2002–2003). The implications of liming for atmospheric CO2 stabilization should be considered in strategies to mitigate global climate change. Hamilton, S. K., A. L. Kurzman, C. Arango, L. Jin, and G. P. Robertson. 2007. Evidence for carbon sequestration by agricultural liming. Global Biogeochem. Cycles 21: GB2021, doi:10.1029/2006GB002738.

354

2007 Stable isotope addition experiments seeking to trace the denitrification of combined forms of nitrogen (N) to gaseous N2 in aquatic environments typically need to measure the stable isotope ratio of dissolved nitrogen gas. This measurement presents challenges because of the potential for contamination of samples by N in air, and because field experiments conducted in situ often do not produce a marked enrichment in the isotope ratio of the N2 pool. Field experiments also require numerous samples, sometimes processed under arduous conditions, and thus methods have to be convenient and low in cost. This paper describes the methods for sampling and measurement of the N isotope ratio of dissolved nitrogen that were developed for the isotope addition experiments in the Lotic Intersite Nitrogen Experiment (LINX), a cross-site study examining N biogeochemistry in headwater streams. Headspace equilibration was performed in the field and gas samples were stored in re-evacuated glass vials (Exetainers). Samples were processed and stored underwater to minimize the potential for contamination of samples by air. Isotope ratios were measured using a gas chromatograph interfaced to the isotope ratio mass spectrometer and equipped with custom sample entry system. Hamilton, S. K., and N. E. Ostrom. 2007. Measurement of the stable isotope ratio of dissolved N2 in 15N tracer experiments. Limnology and Oceanography Methods 5: 233-240.

355

2007 Management practice and soil texture are known to affect soil C. Relatively little information exists, however, on interactions between textural and management effects. The objective of this study was to evaluate management effects on soil total C along a textural gradient in well-drained Typic Hapludalfs in southwest Michigan. Three management practices considered in this study were conventional tillage (CT) and no-till (NT) both with conventional chemical inputs, and conventional tillage with leguminous cover crops and no chemical inputs (CT-cover). Four replicate plots were sampled for each practice, with approximately 100 soil samples taken at the 0- to 5-cm depth in each plot. In all management practices, the relationships of total C and N with clay + silt varied depending on the range of clay + silt values, with regression slopes at clay + silt < 570 g kg(-1) being 1.5 to 6 times lower than those at clay + silt > 570 g kg(-1). Total C in the CT-cover and NT treatments was higher than that in the CT treatment across the whole range of studied textures; however, a greater difference in total C between NT and CT occurred at greater clay + silt contents. Total C in the CT-cover and NT treatments were not different when clay + silt was < 600 g kg(-1), while the NT treatment had higher total C than the CT-cover treatment when clay + silt was > 600 g kg(-1). The results indicate that the potential for C accumulation in surface soils via NT treatment depends on soil texture. Hao, X., and A. N. Kravchenko. 2007. Management practive effects on surface total carbon: Differences along a textural gradient. Agronomy Journal 99: 18-26.

534

2007 Huang, X. 2007. Analysis of effects of soil properties, topographicaql variables and management practices on spatial-temporal variability of crop yields. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

369

2007 We examined spatial patterns of trends in ice phenology and duration for 65 waterbodies across the Great Lakes region (Minnesota, Wisconsin, Michigan, Ontario, and New York) during a recent period of rapid climate warming (1975–2004). Average rates of change in freeze (3.3 d decade-1) and breakup (22.1 d decade-1) dates were 5.8 and 3.3 times more rapid, respectively, than historical rates (1846–1995) for Northern Hemisphere waterbodies. Average ice duration decreased by 5.3 d decade-1. Over the same time period, average fall through spring temperatures in this region increased by 0.7°C decade-1, while the average number of days with snow decreased by 5.0 d decade-1, and the average snow depth on those days decreased by 1.7 cm decade-1. Breakup date and ice duration trends varied over the study area, with faster changes occurring in the southwest. Trends for each site were compared to static waterbody characteristics and meteorological variables and their trends. The trend toward later freeze date was stronger in large, low-elevation waterbodies; however, freeze date trends had no geographic patterns or relationships to meteorological variables. Variability in the strength of trends toward earlier breakup was partially explained by spatial differences in the rate of change in the number of days with snow cover, mean snow depth, air temperature (warmer locations showed stronger trends), and rate of change in air temperature. Differences in ice duration trends were explained best by a combination of elevation and the local rate of change in either temperature or the number of days with snow cover. Jensen, O. P., B. J. Benson, J. J. Magnuson, V. M. Card, M. N. Futter, P. A. Soranno, and K. M. Stewart. 2007. Spatial analysis of ice phenology trends across the Laurentian Great Lakes region during a recent warming period. Limnol. and Oceanogr. 52: 2013-2026.

628

2007 Jinhai, C., D. Ee, A. Lau, R. Mason, B. Pham, P. Roe, J. Zhang, and S. Gage. 2007. Acoustic sensor networks for environmental monitoring. Pages 391-392. Proceedings of the 5th International Conference on Embedded Networked Sensor Systems, Sydney, Australia.

668

2007 Chemical weathering of carbonate and silicate minerals in continental rocks is an important process in regulating global climate and ocean chemistry because of the interplay between organic/inorganic carbon reservoirs. Chemical weathering studies have dominantly focused on riverine chemistry and ion fluxes, with much less information available on soil zone processes. This dissertation investigates organic matter-mineral-water interactions in soil profiles developed on the recently deglaciated landscapes of Michigan. Importantly, these soils span a range of parent drift mineralogy and climate. As well, the regional geochemistry of surface and groundwaters are well characterized, so the contributions of early reactions in the soil zone can be determined. Study sites include natural soil profiles in forests as well as experimental soil monoliths which permit quantification of solute/water budget. At each site, soil solids, pore waters and gases were sampled with depth over the annual seasonal cycle and were characterized by geochemical analyses including elemental concentrations and isotope ratios (Sr and C). Silicate mineral weathering is largely restricted to the shallowest soil horizons where pH is low and dissolved organic carbon concentrations are high. The transition from silicate weathering to carbonate weathering in soil profiles is abrupt, reflected by large shifts in soil water Sr isotopes, C isotopes and elemental chemistry. Soil waters become saturated with calcite and dolomite within the carbonate layer suggesting that dissolved inorganic carbon transport is only limited by soil CO2-dependent carbonate solubility. Comparisons of soil water chemistries with regional surface waters/shallow groundwaters identify the soil zone as a key site of solute acquisition. Solute chemistry data, as well as endmember compositions identified by isotope analyses of soil minerals and pore waters, were utilized to calculate silicate versus carbonate weathering mass balance. These yield consistent results and show that silicate mineral sources of Ca2+ and Mg2+ contribute <10% of the divalent cations, with carbonate minerals dominating the weathering-derived cation fluxes from soil profiles. In particular, the soil solution data clearly suggest dolomite dissolution, rather than silicate dissolution, dominates as a riverine Mg2+ source. This places new constraints on variations of the global carbon cycle on short and long time scales Jin, L. 2007. Mg- and Ca-carbonate versus silicate dissolution rates in mid-latitude, glaciated soil profiles: Implicatons for riverine weathering fluxes and global biogeochemical budgets. Ph.D. Dissertation, University of Michigan, Ann Arbor, Michigan.

550

2007 Parasitoids and predatory flies that can attack soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), in soybean, Glycine max (L.) Merr., fields were identified 3 to 4 yr after the aphid was first sighted in the north central United States. We detected 15 species by exposing soybean aphid to ovipositing parasitoids and predatory flies at two locations in southern Michigan. The species detected were (in order of the number of specimens recovered from high to low) Aphidoletes aphidimyza Rondani (Diptera: Cecidomyiidae), Lysiphlebus testaceipes Cresson (Hymenoptera: Braconidae), Allograpta obliqua Say (Diptera: Syrpbidae), Aphidius colemani Viereck (Hymenoptera: Braconidae), Eupeodes americanus Wiedemann (Diptera: Syrpbjdae), Leucopis glyphinivora Tanasijtshuk (Diptera: Chamaemyiidae), Aphelinus asychis Walker (Hymenoptera: Aphelinidae), Sphaerophoria contigua Macquart (Diptera: Syrphidae), Binodoxys kelloggensis Pike, Star & Brewer (Hymenoptera: Braconidae), Eupeodes volucris Osten Sacken (Diptera: Syrphidae), Paragus hemorrhous Meigen (Diptera: Syrphidae), Toxomerus marginatus Say (Diptera: Syrphidae), Aphelinus albipodus Hayat & Fatima (Hymenoptera: Aphelinidae), Syrphus rectus Osten Sacken (Diptera: Syrphidae), and Praon sp. (Hymenoptera: Braconidae). These species were capable of finding, attacking, and completing development on soybean aphid in soybean fields. Based on a literature review, host aphid ranges of the species detected varied widely, with a tendency toward broader host ranges. These data add to the existing information on the predatory complex currently known to attack soybean aphid in the north central United States. Implications for biological control of soybean aphid are discussed. Kaiser, M. E., T. Noma, M. J. Brewer, K. S. Pike, J. R. Vockeroth, and S. D. Gaimari. 2007. Hymenopteran parasitoids and dipteran predators found utilizing soybean aphid after its midwestern United States invasion. Annals of the Entomological Society of America 100: 196-205.

516

2007 Agricultural land provides a wide variety ecosystem services to individuals. These agroecosystem services include wildlife and biodiversity, which in turn support recreational opportunities such as hunting and wildlife viewing. Using the random utility travel cost model, we provide an estimate to illustrate the potential value of the white-tailed deer (Odocoileus virginianus) provisioning and recreational services provided by these ecosystems to deer hunters, as well as the value of providing deer hunters public access to a percentage of agricultural land. Knoche, S., and F. Lupi. 2007. Valuing deer hunting ecosystem services from farm landscapes. Ecological Economics 64: 313-320.

636

2007 Accurate mapping of total soil C on the field scale is essential for evaluating efforts to sequester soil C and for providing individual producers with information on C sequestration potentials of their fields. Data on easily measured secondary variables that are strongly related to soil C are believed to be helpful in improving mapping accuracy. The objective of this study was to assess improvement in mapping accuracy due to dense topographical and long-term yield monitoring information. Approximately 1200 total C measurements at the 0- to 5-cm depth along with topographical and 7-yr crop grain yield data were collected at twelve 60- by 60-m plots at the Long-Term Ecological Research Site in Michigan. Total C was found to be significantly related to topography and 7-yr average standardized yield in all studied plots, with regression R-2 > 0.5 in approximately half of the plots. Accounting for either topographical or yield information in regression kriging, however, produced only modest (< 10%) improvement in mapping accuracy compared with ordinary kriging. Plots with promisingly strong relationships of total C with topography or yield were also found to be the ones where spatial distributions of total C were highly continuous, thus leading to no advantages in using regression kriging. The results indicated that under soil and topographical conditions similar to those of this study, dense topographical data or dense long-term yield data might not lead to substantial improvement in C mapping accuracy. Kravchenko, A. N., and G. P. Robertson. 2007. Can topographical and yield data substantially improve total soil carbon mapping by regression kriging? Agronomy Journal 99: 12-17.

533

2007 Resource spatial distribution alone can alter ecosystem process rates. Soil resource aggregation within the scale of individual plants can potentially affect primary productivity, plant C allocation, plant N acquisition, decomposition, net N mineralization, N2O emissions, and ecosystem N retention. To understand how plant litter aggregation affects these processes I distributed Trifolium pratensis litter in soil across an aggregation gradient from uniformly distributed to highly aggregated. I examined the effects of this aggregation gradient on decomposition rates and N2O emissions with two laboratory studies and plant growth and N cycling with two field experiments. Results show that litter aggregation in soil delayed decomposition for 5 to 7 days and that this delay was likely caused by insufficient O2 supply to the interior of the litter aggregates. In contrast, aggregated litter stimulated emissions of the greenhouse gas N2O 7-fold compared to uniformly distributed litter. Elevated N2O emissions in response to litter aggregation were found regardless if the litter was finely ground or chopped into 5 mm pieces. Plant root systems can respond to litter aggregation by foraging into resource-rich microsites; however, the degree to which plants benefit from root foraging into microsites of varying quality is largely unknown. I examined whether root foraging into microsites of varying quality depended on plant growth. I found that Avena sativa L. root foraging was positively correlated with growth in response to pairwise choices of contrasting microsite qualities. In contrast, root foraging by Bromus inermis L. was not related to plant growth response. In addition, I found that plant N status plays an important role in regulating Zea mays L. root foraging under field conditions. These two results suggest that root foraging is only an important mechanism for plant N acquisition under heterogeneous conditions where N is limiting plant productivity. To better understand the effects of litter aggregation on plant growth and N cycling I distributed 15N-labeled litter across an aggregation gradient and followed the fate of the litter-N into plant and soil N pools. Under N-limited conditions maize was 14% more productive in response to aggregated than uniformly distributed T. pratensis litter. In contrast, Secale cereale litter aggregation did not affect maize growth. Litter distribution did not affect root to shoot ratio; however, total belowground C allocation appeared to be greater in response to uniformly distributed than to aggregated T. pratensis litter. Plant N acquisition was greater in response to aggregated than uniformly distributed litter. Litter aggregation also increased litter-derived N mineralization by 20%, shoot N by 18%, and root N by 33% relative to uniformly distributed litter. I suggest that the spatial coupling of roots and litter aggregates is an important factor regulating C and N cycling in agricultural system with heterogeneous resource distributions and where N is limiting plant productivity. Loecke, T. D. 2007. Soil resource heterogeneity and ecosystem processes: Effects of litter aggregation on soil micorbial processes and plant root foraging. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA

557

2007 Human activities have altered biodiversity on a global scale, but the ecological implications of shifts in plant species distributions and abundances are poorly understood. While a number of studies have shown that exotic species can dramatically and rapidly alter ecosystem properties (Vitousek and Walker 1989, Evans et al. 2001, Mack and D'Antonio 2003a), little is known about how reintroductions of extirpated species may impact ecosystem properties in restored systems. My dissertation research focuses on how the reintroduction of native prairie C4 grasses into abandoned agricultural fields (old-fields) influences soil carbon (C) and nitrogen (N) cycling compared to non-native C3 grasses typical of successional communities in southwestern Michigan, USA. In this dissertation, I explore three main aspects of plant species controls on soil processes: 1) What are the decadal scale impacts of a shift from a C3-dominated to a C4-dominated system on soil properties and processes (Chapter Two), 2) How quickly do the differences in species traits and soil conditions arise (Chapter Three), and 3) Which plant traits are responsible for these differences (Chapter Four)? I addressed these questions in several old-fields at Michigan State University’s W. K. Kellogg Biological Station, using previously established experimental plots of prairie grasses in Chapters Two and Four, and setting up new experimental studies in Chapter Three. In Chapters Two and Three, I found that C4 species had significantly greater shoot biomass and more recalcitrant tissue compared to the dominant C3 species, and these differences became apparent within two years after the species were established. However, differences between the two groups of species in surface litter and root biomass took longer than two years to develop but were apparent after 11 years. While there was some evidence to suggest that the C4 species had reduced soil inorganic N levels relative to the C3 species after just two years, many of the changes in soil properties took longer than two growing seasons to develop. After 11 years, soils under C4 species had significantly lower inorganic N levels, and slightly lower in situ net N mineralization and nitrification rates when compared to soils under C3 species. I also found limited evidence for increasing soil C pools under C4 species 11 years after reintroduction. Nevertheless, the 13C signal of the C4 species became measurable in the soil within two years. I examined how litter quality and microclimate affected litter decomposition rates, and found that while Andropogon gerardii (C4 prairie grass) differed from the C3 species in their effect on soil moisture and temperature, these differences did not correspond to differences in decomposition. Instead, species litter quality was more important than microclimate in determining decomposition rates of both C3 and C4 species. Overall, my results demonstrated that reintroduction of C4 species into old-fields can alter soil processes related to C and N cycling on relatively short timescales. Process rates changed first, with changes in pool sizes of C and N taking longer to become measurable. Improving our understanding of how plant species impact ecosystem properties and what species traits are driving these changes is imperative if we hope to predict the ecosystem-level consequences of changes in species distribution or composition that could occur, and are occurring, as a consequence of changes in agricultural and land use practices, global change, and species introductions. Mahaney, W. 2007. Soil processes and plant species: Does the reintroduction of native grasses alter soil carbon and nitrogen cycling? Ph.D. Dissertation, Michigan State University, East Lansing, Michigan.

553

2007 This study evaluated the relationship between diversity and activity-density of carabid beetles and invertebrate weed seed predation in conventional, no-till, and organic management systems in the Midwest USA. Carabid beetles were sampled with pitfall traps and invertebrate seed predation rates of fall panicum and common lambsquarters were assayed with exclosure cages. Total carabid activity-density was over two times higher in the conventional systems compared to the no-till and organic management systems. In contrast, activity-densities of seed-predating carabid species were over three times higher in the no-till compared to the conventional and organic systems. Carabid diversity was higher in the no-till and organic systems compared to the conventional system, and a multivariate analysis showed that carabid community structure was distinct among the three systems. Predation of fall panicum and common lambsquarters seeds was often over two times higher in the no-till compared to the conventional and organic systems, and there was a strong correlation (r > 0.94) between seed removal rates and the total number of carabid seed predators captured in each system. Menalled, F. D., R. G. Smith, J. T. Dauer, and T. B. Fox. 2007. Impact of agricultural management systems on carabid communities and weed seed predation. Agriculture, Ecosystems, and Environment 118: 49-54.

398

2007 Afforestation of agricultural lands can provide economically and environmentally realistic C storage to mitigate for elevated CO2 until other actions such as reduced fossil fuel use can be taken. Soil carbon sequestration following afforestation of agricultural land ranges from losses to substantial annual gains. The present understanding of the controlling factors is inadequate for understanding ecosystem dynamics, modeling global change and for policy decision-makers. Our study found that planting agricultural soils to deciduous forests resulted in ecosystem C accumulations of 2.4 Mg C ha−1 yr−1 and soil accumulations of 0.35 Mg C ha−1 yr−1. Planting to conifers showed an average ecosystem sequestration of 2.5 and 0.26 Mg C ha−1 yr−1 in the soils but showed greater field to field variability than when planted to deciduous forest. Path analysis showed that Ca was positively related to soil C accumulations for both conifers and deciduous afforested sites and played a significant role in soil C accumulations in these sites. Soil N increases were closely related to C accumulation and were two times greater than could be explained by system N inputs from atmospheric deposition and natural sources. Our results suggest that the addition of Ca to afforested sites, especially conifers, may be an economical means to enhance soil C sequestration even if it does not result in increasing C in aboveground pools. The mechanism of N accumulation in these aggrading stands needs further investigation. Morris, S. J., S. Bohm, S. Haile-Mariam, and E. A. Paul. 2007. Evaluation of carbon accrual in afforested agricultural soils. Global Climate Change 13: 1145-1156.

617

2007 Noma, T., and M. J. Brewer. 2007. Fungal pathogens infecting soybean aphid and aphids on other crops grown in soybean production areas of Michigan. Great Lakes Entomologist 40: 41-49.

581

2007 Site preference (SP), the difference in delta N-15 between the central and outer nitrogen atoms in N2O, is a powerful approach for apportioning fluxes of N2O from soils to nitrification and denitrification (Sutka et al., 2006). A critical aspect of the use of SP data to apportion sources of N2O to nitrification and denitrification is the need to evaluate data for isotope shifts that may have occurred during N2O reduction in soils prior to its escape to the atmosphere. We present data on the isotopologue effects during reduction of N2O during anaerobic incubation of soils and pure cultures of denitrifying bacteria. Isotopic enrichment factors for N2O reduction in soil mesocosms experiments varied between -9.2 and -1.8% for nitrogen and between -25.1 and -5.1% for oxygen. In pure cultures of Psuedomonas stutzeri and Psuedomonas denitrificans we observed isotopic enrichment factors for SP of -5.0 and -6.8%, respectively. We further find that N2O consumption produces consistent relationships between delta O-18 and delta N-15 and delta O-18 and the delta N-15 of the central N atom in N2O of 2.5 and 1.6, respectively, which are clearly diagnostic of this process. Our results indicate that SP may be altered during reduction of N2O and thus bias evaluations of its origins. To understand the impacts of N2O reduction in soil flux studies on source isotope signals we modeled the isotope effects of N2O production occurring simultaneous with reduction and find increasingly curvilinear relationships between delta O-18 and delta N-15 and delta O-18 and delta N-15 a with increased reduction. Consequently, a deviation from the linear mixing relationship between soil-derived and atmospheric N2O is an indication of extensive reduction. On the basis of our characterization of isotopic fractionation during N2O reduction, we show that the rate of reduction would have to be substantially greater than 10% of that of production to impact SP estimates of N2O from denitrification by more than a few percent. Nonetheless, reduction results in a small, but potentially important, increase in SP away from values proposed for bacterial denitrification (0%) toward those associated with production from nitrification (33%) (Sutka et al., 2006). On this basis, estimates of the proportion of N2O derived from denitrification obtained from SP values are underestimates and therefore conservative. Ostrom, N. E., A. J. Pitt, R. L. Sutka, P. H. Ostrom, A. S. Grandy, K. H. Huizinga, and G. P. Robertson. 2007. Isotopologue effects during N2O reduction in soils and in pure cultures of denitrifiers. Journal of Geophysical Research 112:

408

2007 Cycles of wetting and drying (WD) occur naturally in soils and affect the pore structure through altered hydraulic stresses. Two organic-rich soils, a Eutric Histosol and a Histic Gleysol, and two inorganic soils, a Calcic Gleysol and a Dystric Gleysol, ranging in texture and microstructure, were investigated. Undisturbed soil samples were predried to either –100 kPa water potential by using a ceramic plate or to 30°C by using an oven and then resaturated for one or three WD cycles. In addition, different combinations defined by the intensity, frequency, and sequence of WD cycles were analyzed. Soil structure was altered significantly if the intensity of drying was severe at 30°C, while drying to –100 kPa had only a small effect. The frequency and sequence of WD cycles did not alter the structure and shrinkage behavior significantly. Compared with the initial pore volume, intense WD cycles decreased it by 23.6 to 60.1% in the two organic-rich soils, whereas it increased by 1.5 to 4.8% in the silty Calcic Gleysol and by 3.6 to 15.1% in the clayey Dystric Gleysol. Both organic-rich soils showed more shrinkage but less swelling than did the two inorganic soils. Intense WD cycles altered the water potential vs. void ratio curves of the two organic-rich soils more gradually, while steeper patterns were observed for the two inorganic soils. This study shows that the changes in soil structure and pore shrinkage depend mostly on the maximum intensity of previous WD cycles. Peng, X., R. Horn, and A. J. M. Smucker. 2007. Pore shrinkage dependency of inorganic and organic soils on wetting and drying cycles. Soil Science Society of America Journal 71: 1095-1104.

613

2007 Binodoxys kelloggensis Pike, Star, and Brewer, n. sp. (Hymenoptera: Braconidae: Aphidiinae), is described and illustrated. This aphidiine parasitoid, found in southcentral Michigan, is considered a native species, reared from the exotic soybean aphid, Aphis glycines Matsumura, from naturally infested field soybeans and from aphid-infested potted soybeans placed outdoors among assorted plants. It is one of eight parasitoid species now known to attack A. glycines in North America. Pike, K. S., P. Stary, M. J. Brewer, T. Noma, S. Langley, and M. E. Kaiser. 2007. A new species of Binodoxys (Hymenoptera: Braconidae, Aphidlinae), parasitoid of the soybean aphid, Aphis glycines Matsumura, with comments on biocontrol. Proceedings of the Entomological Society Washington 109: 359-365.

526

2007 Reid, N. J., and S. K. Hamilton. 2007. Controls on algal abundance in a eutrophic river with varying degrees of impoundment (Kalamazoo River, Michigan, USA). Lake and Reservoir Management 23: 219.230.

433

2007 Robertson, G. P., and P. Groffman. 2007. Nitrogen transformations. Pages 341-364 in E. A. Paul, ed. Soil Microbiology, Ecology, and Biochemistry. Elsevier Academic Press, Oxford, UK.

447

2007 Robertson, G. P., L. W. Burger, C. L. Kling, R. Lowrance, and D. J. Mulla. 2007. New approaches to environmental management research at landscape and watershed scales. Pages 27-50 in M. Schnepf and C. Cox, eds. Managing Agricultural Landscapes for Environmental Quality. Soil and Water Conservation Society, Ankeny, Iowa, USA.

445

2007 Plant–pollinator interactions are one of the most important and variable mutualisms in nature. Multiple pollinators often visit plants and can vary in visitation rates, pollen removal and deposition, and spatial and temporal distribution, altering plant reproduction and patterns of pollinator-mediated selection. Although some visitors may not be effective pollinators, pollinator effectiveness is rarely estimated directly as seed set resulting from a single visit by each taxon visiting generalist plants. For two years, effectiveness of visitors to wild radish, Raphanus raphanistrum, was quantified by counting seeds set and pollen grains removed as a result of a single visit. We calculated a pollinator's importance to plant reproduction as the product of visitation rate and single-visit seed set, and regressed pollinator body size on pollen-removal and on seed set effectiveness. Although pollinators differed in effectiveness and visitation rates, pollinator importance was primarily determined by visitation rates. In contrast to similar 2-yr studies, pollinator assemblage composition varied little, suggesting pollinator-mediated selection can be consistent across years for this generalist. Larger pollinators were more effective than smaller at effecting seed set, but body size was a poor predictor of pollen removal ability. Instead, pollen-removal effectiveness may be more influenced by foraging behavior than size. Sahli, H. F., and J. K. Conner. 2007. Visitation, effectiveness, and efficiency of 15 genera of visitors to wild radish, Raphanus raphanistrum (Brassicaceae). American Journal of Botany 94: 203-209.

532

2007 Do specialists exhibit a greater efficiency and/ or rate of using their food resources for faster growth than generalists? For various reasons, this “feeding-specialization/ physiological-efficiency hypothesis” has had mixed support. Failure to reject the hypothesis may often be due to its complex definition (whether physiological, genetic, or ecological “trade-offs” are intended). Empirical tests of this concept with phytophagous insects have produced inconclusive evidence due to inconsistent nutritional quality in plants, genetic variation and phenotypic plasticity in the herbivores assayed, as well as the various types of “specialist/generalist” definitions employed. Complications for meaningfully comparing larval performances of monophagous and polyphagous species on different host (and non-host) species include constitutive (interspecific, inter- and intra-plant) differences as well as seasonal or induced variation in the allelochemical phytochemistry and leaf energy/nutritional value. Such experimental complications were largely circumvented by using concurrent bioassays with congeneric species groups of specialized and generalized Papilio that are both Lauraceae-feeders. Another complication was avoided by evaluating population and individual differences as well as insect species-level differences. Neonate larval survival of all populations of P. glaucus on spicebush across its geographic range was very poor (14% for 39 different populations) compared to P. troilus across all of its range (68% for 20 populations). P. troilus on spicebush outperformed 23 species of Lepidoptera on many of their favorite host plant species, in controlled environments, including other family-specialized insects on Annonaceae, Aristolochiaceae, Simaroboucaceae, Pinaceae, Rutaceae, Magnoliaceae, as well as the multi-family feeders. General problems in measuring physiological costs as well as the broader significance of other nutrients and minerals in organism fitness, evolutionary divergence, and ecosystem stoichiometry are discussed. Scriber, J. M. 2007. A mini-review of the "feeding specialization/physiological efficiency" hypothesis: 50 years of difficulties, and strong support from the North American Lauraceae-specialist, Papilio troilus (Papilionidae: Lepidoptera). Trends in Entomology 4: 1-42.

459

2007 Scriber, J. M., G. Ording, and R. Mercader. 2007. Hybrid introgression and parapatric speciation in a hybrid zone. Pages (in press) in K. Tilman, ed. Populations, Species, and Phylogenies: Evolution in Insect - Plant Systems. University of California Press.

463

2007 1. Increasing cropping system diversity is one strategy for reducing reliance on external chemical inputs in agriculture and may have important implications for agro-ecosystem functions related to the regulation of weed populations and community assembly. However, the impacts of cropping system diversity on weed communities have not been evaluated formally in a study comparable with those performed in experimental grasslands, where much of the evidence regarding diversity–ecosystem function has been reported. We performed a field experiment in Michigan, USA, in which we manipulated the number of crop species grown in rotation and as winter cover crops over a 3-year period and in the absence of fertilizer and pesticides, to determine the impact of crop diversity on the abundance, composition and structure of the weed community. 2. Crop diversity treatments consisted of three row-crops, corn Zea mays L., soybean Glycine max (L.) Merr. and winter wheat Triticum aestivum L., grown in continuous monoculture and in 2- and 3-year annual rotations with and without cover crops (zero, one or two legume/small grain species). Weed communities were measured each year at peak biomass, with soil resources and light availability being measured over the course of the growing season in the final year of the study. 3. The effects on weed communities of the crop diversity treatments were dependent on rotation phase. In winter wheat, weed abundance and diversity (species richness, H and D) were lowest in the two highest crop diversity treatments. Across all phases of the rotation, weed community structure was affected more by crop identity than crop diversity per se. 4. In general, the effects of crop diversity on weed ommunities were mainly the result of the presence of cover crops, which had strong effects on soil resource and light levels, particularly in winter wheat. 5. Synthesis and applications. Increasing crop diversity in the absence of external chemical inputs can result in changes in soil resource availability without a concomitant increase in the abundance of weeds or a shift to weed ommunities that are more difficult to manage. Smith, R. G., and K. L. Gross. 2007. Assembly of weed communities along a crop diversity gradient. Journal of Applied Ecology 44: 1046-1056.

544

2007 Year to year variation in yield is an inherent risk associated with crop production and many growers rely on intensive mechanical or chemical inputs to preserve crop yield in the face of fluctuating environmental conditions. However, as interest grows in alternative crop management systems which depend less on external inputs, determining the degree to which management systems can impact the temporal yield variability will help the development of sustainable agroecosystems. This study assessed average crop yields and temporal yield variability over a 12-yr period in four agricultural management systems that are part of a long-term cropping systems experiment at the W.K. Kellogg Biological Station (KBS) Long Term Ecological Research (LTER) site in southwestern Michigan. The four systems follow a corn (Zea mays L.), soybean [Glycine max (L.) Merr.], and winter wheat (Triticum aestivum L.) 3-yr rotation under conventional (CT), no-till (NT), low-input (LI), or organic (ORG) management, and each crop phase was present in the rotation four times from 1993 to 2004. Yields were measured each year and crop yield variability was estimated using the coefficient of variation calculated separately for each crop phase. Averaged over the study period, yields in the CT and NT systems were similar across all crop phases of the rotation and of higher magnitude than the LI system only in the winter wheat phase of the rotation. Compared to the other three management systems, yields in the ORG system were lower in the corn and winter wheat phases of the rotation. Yields in the soybean phase were similar across the four management systems. Temporal yield variability differed among management systems and rotation phases and was highest in the ORG system during the soybean (CV = 48%) and winter wheat (CV = 33%) phases of the rotation. Compared to the CT system, yield variability was 40% lower in the LI (corn phase), 33% lower in the NT (soybean phase) and similar in the NT (corn and winter wheat phases) systems. Results of this study suggest that yield and temporal yield variability under alternative management systems such as no-till and low-input can be comparable to that in conventional systems. However, temporal yield variability can be as high or higher in organic cropping systems without external inputs of manure or compost. Smith, R. G., F. D. Menalled, and G. P. Robertson. 2007. Temporal yield variability under conventional and alternative management systems. Agronomy Journal 99: 1629-1634.

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2007 Soil biophysical transport mechanisms promoting biogeochemical sorption of soluble organic carbon (SOC) compounds within macroaggregates control the retention and release of most soil nutrients, C- and N-based polysaccharides, and contaminants. Ecosystems containing continuous supplies of soluble root exudates and particulate organic matter (POM) provide a constant supply of mobile SOC compounds to surfaces and internal pore networks of soil aggregates. Intra-aggregate pores, especially the ultrafine pores, appear to be developed, interconnected, and blocked or disconnected by repeated drying and wetting (DW) cycling with direct but unknown contributions to movement and retention of SOC compounds. There is evidence that the severity (e.g., range of soil water potential) and frequency of severe DW cycles control intra-aggregate micro- and nanopore formation and function. Heterogeneously distributed microsites within aggregates contain microbial communities that readily mineralize available C and N compounds, producing mobile SOC that can be tightly sorbed to additional mineral surfaces made available within micro- and nanosized fissures during repeated DW cycling. Mechanical removal of concentric soil layers of aggregates, synchrotron imaging and computer microtomographic (CMT) image processing software of three-dimensional pore networks and connectivities, coupled with synchrotron X-ray small angle scattering to measure pore sizes. Natural isotopes of 13C and 15N to quantify C and N sorption and CO2 respiration provide new and integrated approaches for quantifying spatially heterogeneous changes of pore diameters, connectivities, and organo-ion-mineral sorption within intra-aggregate pore networks. Net C and N alterations at surfaces and within aggregates appear to modify both the microbial activities and bacterial community structures, producing integrated feedback and feed-forward processes between the soil biological and physical components of soil aggregates. Smucker, A. J. M., E. J. Park, J. Dormer, and R. Horn. 2007. Soil micropore contributions to soluble carbon flux rates and microbial community responses within macro-aggregates. Vadose Zone Journal 6: 282-290.

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2007 Crop and rangelands are over 25% of the Earth's land area, and they are expanding. Agricultural ecosystems rely on a suite of supporting ecosystem services to provide food, fiber and fuel as well as a range of accompanying but non-marketed ecosystem services (ES). Ecosystem services from agriculture include regulation of water and climate systems, aesthetic and cultural services, as well as enhanced supporting services (such as soil fertility). Many of these ES are appreciated by people, but they lack markets, so they lack the incentives for provision that come with prices. For public policy decisions to take them into account, non-market valuation techniques are needed, such as travel cost, contingent valuation, hedonic valuation, and cost-based or factor-income approaches. This article offers an overview of ES from agriculture and non-market valuation methods as it introduces the articles in this special section on “Ecosystem Services and Agriculture.” Understanding how ecological functions generate ES is fundamental to management, but so too is understanding how humans perceive and value those services. Research is required both to design cost-effective incentives to provide ES and to measure which kinds of ES could provide the greatest overall welfare benefits to society. Agricultural ecosystems offer newly recognized potential to deliver more diverse ecosystem services and mitigate the level of past ecosystem disservices. This special section of Ecological Economics conveys both how these are becoming possible and the challenges to science and public policy design of turning that potential into reality. Swinton, S. M., F. Lupi, G. P. Robertson, and S. K. Hamilton. 2007. Ecosystem services and agriculture: cultivating agriculture ecosystems for diverse benefits. Ecological Economics: 245-252.

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2007 Thorn, R. G., and M. D. Lynch. 2007. Soil fungi. Pages 145-162 in E. A. Paul, ed. Soil Microbiology, Biochemistry, and Ecology. Elsevier Academic Press, Oxford, UK.

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2007 Velbel, M. A. 2007. Surface textures and dissolution processes of heavy minerals in the sedimentary cycle: Examples from pyroxenes and amphiboles. Pages 113-150 in M. Mange and D. Wright, eds. Heavy Minerals in Use: Developments in Sedimentology. Elsevier Press.

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2007 Velbel, M. A., J. T. McGuire, and A. S. Madden. 2007. Scanning electron microscopy of garnet from souther Michigan soils: Etching rates and inheritance of pre-glacial and pre-pedogenic grain-surface textures. Pages 413-432 in M. Mange and D. Wright, eds. Heavy Minerals in Use: Developments in Sedimentology. Elsevier Press.

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2007 This paper highlights how farmers' willingness to supply non-marketed ecosystem services (ES) is influenced by whether or not the non-marketed ES are produced jointly with agricultural products. When marketed products and non-marketed ES share some production inputs the production relationships between the two may be complementary, competitive or substitutive. Using a cost minimization framework, it is shown how complementary relationships lead to costless voluntary provision of non-marketed ES (typically the case for ES that are supportive of provisioning ES for marketed farm products). It is also shown how competitive production relationships lead to provision of non-marketed ES at lower cost than when non-marketed ES are direct substitutes for farm products or are produced outside of agriculture. The paper closes by showing how the minimum willingness to accept (WTA) payment for ES that are complementary/competitive is less than or equal to the minimum WTA for the same ES produced in substitute or independent production relationships. Wossink, A., and S. Swinton. 2007. Jointness in production and farmers' willingness to supply non-marketed ecosystem services. Ecological Economics 64: 297-304.

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2007 By integrating natural pest control services into managerial decision-making, there are new opportunities for improving agricultural pest management in an economically appealing and socially desirable manner. This research develops dynamic and spatial bioeconomic models to investigate optimal economic management of an insect pest in the presence of natural enemies. Of central economic importance are the opportunity cost of natural enemy mortality due to broad-spectrum insecticides and the opportunity cost of setting aside land as non-crop habitats for the enhancement of natural enemy populations. The models are applied to a recent invasive pest of U.S. soybean, the soybean aphid, whose management is of both economic and environmental importance to the North Central region of the United States. The thesis is divided into three essays. Essay 1 develops a dynamic bioeconomic The thesis is divided into three essays. Essay 1 develops a dynamic bioeconomic model for the insecticide-based management of soybean aphid that explicitly takes into account both the predation effect of natural enemies on pest density and the nontarget mortality effect of aphid insecticides on the level of natural predation supplied. The study develops a natural enemy-adjusted economic threshold that represents the pest population density at which pesticide control becomes optimal in spite of the opportunity cost of injury to natural enemies of the target pest. Essay 2 applies the bioeconomic model developed in Essay 1 for a simulation experiment on the optimal control of soybean aphid. The study examines the difference in optimal control choices and associated economic gains with and without consideration of natural enemies. For instance, the presence of one ladybeetle would justify a change of optimal control choice from spray to no-spray when the pest density is 20 per plant. The results highlight the importance of assessing both pest and natural enemy populations in making insecticide application decisions and accounting for the opportunity cost of insecticide collateral damage to natural enemies. The study also estimates the private economic value to farmers of the natural control services of ladybeetles in suppressing soybean aphid damage. The estimate constitutes a lower bound for the total economic value of this ecosystem service, because it omits such benefits as the avoidance of health and environmental risks from insecticide spraying. Farmers desiring to rely on natural pest control in lieu of insecticide-based control can try to manage the habitat for natural enemies. Essay 3 develops a spatial optimization model to explore economically optimal habitat configurations for the natural enemies of crop pests. The model is applied to soybean aphid management in representative conventional and organic farming systems. Results indicate that non-crop habitat management can potentially be a promising pest management option for organic cropping systems. However, it tends to reduce farm net returns for conventional farms. Both area and shape of non-crop habitats affect economic performance, with the greatest value coming from small, scattered areas of habitat. new entry Zhang, W. 2007. Optimal Pest Management in the Presence of Natural Pest Control Ecosystem Services. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

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2007 Agricultural ecosystems are actively managed by humans to optimize the provision of food, fiber, and fuel. These ecosystem services from agriculture, classified as provisioning services by the recent Millennium Ecosystem Assessment, depend in turn upon a web of supporting and regulating services as inputs to production (e.g., soil fertility and pollination). Agriculture also receives ecosystem dis-services that reduce productivity or increase production costs (e.g., herbivory and competition for water and nutrients by undesired species). The flows of these services and dis-services directly depend on how agricultural ecosystems are managed and upon the diversity, composition, and functioning of remaining natural ecosystems in the landscape. Managing agricultural landscapes to provide sufficient supporting and regulating ecosystem services and fewer dis-services will require research that is policy-relevant, multidisciplinary and collaborative. This paper focuses on how ecosystem services contribute to agricultural productivity and how ecosystem dis-services detract from it. We first describe the major services and dis-services as well as their key mediators. We then explore the importance of scale and economic externalities for the management of ecosystem service provision to agriculture. Finally, we discuss outstanding issues in regard to improving the management of ecosystem services and dis-services to agriculture. Zhang, W., T. H. Ricketts, C. Kremen, K. Carney, and S. M. Swinton. 2007. Ecosystem services and disservices to agriculture. Ecological Economics 64: 253-260.

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2007 Atmospheric nitrogen deposition is anticipated to increase over the next decades with possible implications for future forest-atmosphere interactions. Increased soil N2O emissions, depressed CH4 uptake and depressed soil respiration CO2 loss is considered a likely response to increased N deposition. This study examined fluxes of N2O, CH4 and CO2 over two growing seasons from soils in unmanaged forest and grassland communities on abandoned agricultural areas in Michigan. All sites were subject to simulated increased N-deposition in the range of 1–3 g N m−2 annually. Nitrous oxide fluxes and soil N concentrations in coniferous and grassland sites were on the whole unaffected by the increased N-inputs. It is noteworthy though that N2O emissions increased three-fold in the coniferous sites in the first growing season in response to the low N treatment, although the response was barely significant (p<0.06). In deciduous forests, we observed increased levels of soil mineral N during the second year of N fertilization, however N2O fluxes did not increase. Rates of methane oxidation were similar in all sites with no affect of field N application. Likewise, we did not observe any changes in soil CO2 efflux in response to N additions. The combination of tillage history and vegetation type was important for the trace gas fluxes, i.e. soil CO2 efflux was greater in successional grassland sites compared with the forested sites and CH4 uptake was reduced in post-tillage coniferous- and successional sites compared with the old-growth deciduous site. Our results indicate that short-term increased N availability influenced individual processes linked to trace gas turnover in the soil independently from the ecosystem N status. However, changes in whole system fluxes were not evident and were very likely mediated by competitive N uptake processes. Ambus, P., and G. P. Robertson. 2006. The effect of increased N deposition on nitrous oxide, methane, and carbon dioxide fluxes from unmanaged forest and grassland communities in Michigan. Biogeochemistry 79:315-337

2006 Bird, G. W., and M. J. Brewer. 2006. Innovative integrated pest management for sustainable systems. Pages 25-49 in C. Francis, R. Poincelot, and G. W. Bird, eds. Developing and Extending Sustainable Agriculture: A New Social Contract. The Haworth Press, Binghampton, New York, USA.

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2006 The effects of enriched CO2 atmosphere on partitioning of recently assimilated carbon were investigated in a plant-soil-microorganism system in which Lolium perenne seedlings were planted into cores inserted into the resident soil within a sward that had been treated with elevated CO2 for 9 consecutive years, under two N fertilisation levels (Swiss FACE experiment). The planted cores were excavated from the ambient (35 Pa pCO2) and enriched (60 Pa pCO2) rings at two dates, in spring and autumn, during the growing season. The cores were brought back to the laboratory for 14C labelling of shoots in order to trace the transfer of recently assimilated C both within the plant and to the soil and microbial biomass. At the spring sampling, high N supply stimulated shoot and total dry matter production. Consistently, high N enhanced the allocation of recently fixed C to shoots, and reduced it to belowground compartments. Elevated CO2 had no consequences for DM or the pattern of C allocation. At the autumn sampling, at high N plot, yield of L. perenne was stimulated by elevated CO2. Consistently, 14C was preferentially allocated aboveground and, consequently belowground recent C allocation was depressed and rhizodeposition reduced. At both experimental periods, total soil C content was similar in all treatments, providing no evidence for soil carbon sequestration in the Swiss Free Air CO2 Enrichment experiment (FACE) after 9 years of enrichment. Recently assimilated C and soil C were mineralised faster in soils from enriched rings, suggesting a CO2-induced shift in the microbial biomass characteristics (structure, diversity, activity) and/or in the quality of the root-released organic compounds. Blackwood, C. B., C. J. Dell, A. J. M. Smucker, and E. A. Paul. 2006. Eubacterial communities in different soil macroaggregate environments and cropping systems. Soil Biology and Biochemistry 38: 720-728.

2006 The LTER grid pilot study was conducted by the National Center for Supercomputing Applications, the University of New Mexico, and Michigan State University, to design and build a prototype grid for the ecological community. The featured grid application, the Biophony Grid Portal, manages acoustic data from field sensors and allows researchers to conduct real-time digital signal processing analysis on high-performance systems via a Web-based portal. Important characteristics addressed during the study include the management, access, and analysis of a large set of field collected acoustic observations from microphone sensors, single signon, and data provenance. During the development phase of this project new features were added to standard grid middleware software and have already been successfully leveraged by other, unrelated grid projects. This paper provides an overview of the Biophony Grid Portal application and requirements, discusses considerations regarding grid architecture and design, details the technical implementation, and summarizes key experiences and lessons learned that are generally applicable to all developers and administrators in a grid environment. Butler, R., M. Servilla, S. Gage, J. Basney, V. Welch, B. Baker, T. Fleury, P. duda, D. Gehrig, M. Bletzinger, J. Tao, and D. M. Freemon. 2006. Cyberinfrastructure for the analysis of ecological acoustic sensor data: A use case study in grid deployment. Proceedings Challenges of Large Applications in Distributed Environments: 25-33.

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2006 The soybean aphid Aphis glycines Matsumura (Hemiptera: Aphididae), was detected for the first time in North America in Wisconsin during 2000, and it is currently present in 22 states. Since its detection, it has developed outbreak populations that resulted in up to 50% yield reduction during alternating years. I conducted field studies that demonstrated the crucial role of existing generalist natural enemies in suppressing soybean aphid population growth below economic threshold levels. By using predator exclusion cages, I demonstrated that ambient levels of predators exert strong suppression on soybean aphid (3 to 20-fold reduction) in comparison with open controls and sham cages. Through work at the NSF-Long Term Ecological Research site at the Kellogg Biological Station of Michigan State University, I found that this control occurs over a broad range of agricultural production systems, ranging from conventional practices with or without tillage, to organic soybeans. This suppression occurs regardless of initial aphid infestation, with aphid populations being reduced below threshold levels at high, medium and low initial aphid densities. The strength of this suppression results in a trophic cascade, with similar soybean biomass and yield in treatments where aphids were exposed to predation as in treatments completely protected from aphids by aphid exclusion cages. Direct field observations revealed that the coccinellids Harmonia axyridis and Coccinella septempunctata combined provided most of the mortality on soybean aphid, were very effective on a per capita basis, and responded to aphid density by increasing their abundance, time within the aphid patch, and consumption rate. Exposure to predation significantly shifted the aphid's within-plant distribution towards lower nodes on the plants, suggesting indirect effects of predation. I also conducted studies using cages that differentially excluded large versus small predators and parasitoids, which showed that ambient levels of naturally occurring parasitoids provide only minor or no reduction of soybean aphid populations, even in treatments in which parasitoids were provided with a refuge from intraguild predation by coccinellids. Similar results were obtained in a separate study using artificial infestations with the parasitoid Lysiphlebus testaceipes. I observed direct evidence of intraguild predation on parasitoid mummies by generalist predators, in which up to 80% of mummies were killed by predators, but percentage parasitism did not differ from controls, suggesting that intraguild predation did not disrupt parasitism. Finally, I developed a mathematical model for soybean aphid population growth by fitting the data of field studies under predator exclusion conditions, using a novel approach that assumes a linear decrease in the intrinsic rate of increase of the aphids. Overall, these findings provide one of the first empirical tests of recent theoretical models in which the role of generalist predators is predicted to be an important source of insect population regulation. In addition, these results support theoretical predictions that intraguild predators with strong impacts on herbivores may not disrupt, or may even enhance biological control. From the pest management perspective, it suggests the incorporation of natural enemies as an important factor to take into account when determining soybean aphid thresholds. Costamagna, A. C. 2006. Do varying natural enemy assemblages impact aphis glyucines population dynamics? Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

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2006 The discovery of soybean aphid, Aphis glycines Matusumura, in North America in 2000 provided the opportunity to investigate the relative strength of top-down and bottom-up forces in regulating populations of this new invasive herbivore. At the Kellogg Biological Station Long Term Ecological Research site in agroecology, we contrasted A. glycines establishment and population growth under three agricultural production systems that differed markedly in disturbance and fertility regimes. Agricultural treatments consisted of a conventional-tillage high-input system, a no-tillage high-input system, and a zero-chemical-input system under conventional tillage. By selectively restricting or allowing predator access we simultaneously determined aphid response to top-down and bottom-up influences. Irrespective of predator exclusion, our agricultural manipulations did not result in bottom-up control of A. glycines intrinsic rate of increase or realized population growth. In contrast, we observed strong evidence for top-down control of A. glycines establishment and overall population growth in all production systems. Abundant predators, including Harmonia axyridis, Coccinella septempunctata, Orius insidiosus, and various predaceous fly larvae, significantly reduced A. glycines establishment and population increase in all trials. In contrast to other systems in which bottom-up forces control herbivore populations, we conclude that A. glycines is primarily controlled via top-down influences of generalist predators under a wide range of agricultural management systems. Understanding the role of top-down and bottom-up forces in this context allows agricultural managers to focus on effective strategies for control of this invasive pest. Costamagna, A. C., and D. A. Landis. 2006. Predators exert top-down control of soybean aphid across a gradient of agricultural management systems. Ecological Applications 16: 1619-1628.

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2006 It has been proposed that cropping systems can be managed to promote the development of soil microbial communities that accelerate weed seed mortality. We examined soil fungal and bacterial communities, soil C:N ratio, soil particle size fractions, and weed seed mortality in soil from fields with over 10 yr of five contrasting management histories with the objective of determining if seed mortality could be explained by differences in soil properties. Seed mortality of giant foxtail and velvetleaf were greatest in soil from the conventionally managed systems and lowest in soil from a reduced input system. Principal-components analysis of soil microbial communities, as determined through denaturing gradient gel electrophoresis of polymerase chain reaction–amplified ribosomal RNA genes (PCR-DGGE), showed distinct differences in the composition of fungal and bacterial communities among the study soils. The first principal component of the 18S rDNA PCR-DGGE analysis of fungal community composition showed a strong negative correlation with both giant foxtail (−0.52, P < 0.05) and velvetleaf (−0.57, P < 0.01) seed mortality, as did ordination with nonmetric multidimensional scaling (NMS) [giant foxtail (−0.54, P < 0.01) and velvetleaf (−0.60, P < 0.01)], suggesting that seeds of the two species were affected similarly by changes in the soil fungal community. For giant foxtail, weed seed mortality was also positively correlated (r = 0.48, P < 0.05) with the first NMS axis of the bacterial 16S rDNA analysis. None of the other measured soil properties were significantly correlated with weed seed mortality. Thus, for the soils tested here, management history, microbial community composition, and weed seed mortality were linked. To extend these results to the field, more work is needed to identify components of the fungal and bacterial communities that are active in seed degradation, and to develop conservation biocontrol recommendations for these species. Davis, A. S., S. G. Hallett, and K. A. Renner. 2006. Weed seed mortality in soils with contrasting agricultural management histories. Weed Science 54: 291-297.

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2006 Dazzo, F. B., and Y. G. Yanni. 2006. The natural rhizobium-cereal crop association as and example of plant-bacteria interaction. Pages 109-127 in N. Uphoff, A. S. Ball, E. Fernandes, H. Herren, O. Husson, M. Laing, C. Palm, J. Pretty, P. Sanchez, N. Snanginga, and J. Thies, eds. Biological Approaches to Sustainable Soil Systems. CRC Press, Taylor and Francis Group, Boca Raton, Florida, USA.

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2006 This article outlines an approach, based on ecosystem services, for assessing the trade-offs inherent in managing humans embedded in ecological systems. Evaluating these trade-offs requires an understanding of the biophysical magnitudes of the changes in ecosystem services that result from human actions, and of the impact of these changes on human welfare. We summarize the state of the art of ecosystem services-based management and the information needs for applying it. Three case studies of Long Term Ecological Research (LTER) sites-coastal, urban, and agricultural-illustrate the usefulness, information needs, quantification possibilities, and methods for this approach. One example of the application of this approach, with rigorously established service changes and valuations taken front the literature, is used to illustrate the potential for full economic valuation of several agricultural landscape management options, including managing for water quality biodiversity, and crop productivity. Farber, S., R. Costanza, D. L. Childers, J. Erickson, K. L. Gross, M. Grove, C. S. Hopkinson, J. Kahn, S. Pincetl, A. Troy, P. Warren, and M. A. Wilson. 2006. Linking ecology and economics for ecosystem management. BioScience 56: 121-133.

2006 new entry Fiedler, A. 2006. Evaluation of Michigan Native Plants to Provide Resources for Natural Enemy Arthropods. MS Thesis. Michigan State University, East Lansing, MI.

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2006 Francis, C. R., C. R. Poincelot, and G. W. Bird, eds. 2006. Developing and Extending Sustainable Agriculture: A New Social Contract. Haworth Press, Binghamton, New York.

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2006 We used computer-assisted microscopy at single cell resolution to quantify the in situ spatial scale of N-acylhomoserine lactone (AHL)-mediated cell-to-cell communication of Pseudomonas putida colonized on tomato and wheat root surfaces. The results of this in situ quantification study on close-to-natural surfaces challenge the conventional view of a quorum group requirement of high cell densities for this type of bacterial communication. In situ image analysis indicated that the effective 'calling distance' on root surfaces was most frequent at 4-5 mu m, extended to 37 mu m in the root tip/elongation zone and further out to 78 mu m in the root hair zone. The spatial scale of these calling distances is very long-range in proportion to the size of individual bacteria. Geostatistical modeling analysis implicated the importance of AHL-gradients mediating effective communication between remote cells. We conclude that AHL-mediated cell-to-cell communication occurs not only within dense populations, but also in very small groups and over long ranges between individual bacteria, and therefore this cellular activity is more commonplace and effective than hitherto predicted. We propose that this cell-to-cell communication is governed more by the in situ spatial proximity of cells within AHL-gradients than the requirement for a quorum group of high population density. Gantner, S., M. Schmid, C. Durr, R. Schuhegger, A. Steidle, P. Hutzler, C. Langebartels, L. Eberl, A. Hartmann, and F. B. Dazzo. 2006. In situ quantitation of the spatial scale of calling distances and population density-independent N-acylhomoserine lactone-mediated communication by rhizobacteria colonized on plant roots. FEMS Microbial Ecology 56: 188-194.

2006 Gardiner, M., C. DiFonzo, M. Brewer, and T. Noma. 2006. Identifying Natural Enemies in Field Crops, Extension Bulletin E-2949. Michigan State University, East Lansing, Michigan.

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2006 The CERES (Crop Estimation through Resource and Environment Synthesis) family of crop models predicts cereal growth, development, and yield. CERES simulates nitrogen (N) as a yield-limiting macronutrient. Because N leaching is an economic and environmental concern, this study evaluated if CERES can be used to predict N leaching under different N management scenarios: background leaching in unfertilized corn (Zea mays L.), alfalfa (Medicago sativa L.) residue mineralization, and till versus no-till management. Data were collected during a 7-yr field experiment on tillage practices in a maize-alfalfa-maize succession. Sensitivity analyses were performed for decomposition rates of the different residue pools and the relative proportions of carbohydrate, cellulose, and lignin in the residues. During the last 5 yr, under corn, CERES accurately simulated nitrate leaching from the no-till lysimeters. Nitrate leaching was underestimated in the tillage treatments, possibly because CERES does not simulate tillage. The model is not very sensitive to the decomposition rates and to the composition of the residues. Gerakis, A., D. Rasse, Y. Kavdir, A. Smucker, and J. T. Ritchie. 2006. Simulation of leaching losses in the nitrogen cycle. Communications in Soil Science and Plant Analysis 13: 1-25.

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2006 The maintenance of soil organic carbon (SOC) in terrestrial ecosystems is critical for long-term productivity. Simulation models of SOC dynamics are valuable tools in predicting the impacts of climate on carbon storage and developing management strategies for the mitigation of Greenhouse gas emissions, however, their utility is Generally reduced due to need for specific data. The SOCRATES model is a simple process based representation of soil SOC dynamics in terrestrial ecosystems, which requires minimal data inputs and specifically designed to examine the impact of land use and land use change on soil carbon storage. SOCRATES was successful in predicting SOC change at eighteen long-term crop, pasture and forestry trials from North America, Europe and Australasia. These trials ranged from 8 to 86 years in duration, over a wide range of climates and soil types with annual changes in SOC ranging from -3.0 to 4.2%. (c) 2005 Elsevier Ltd. All rights reserved. Grace, P. R., J. N. Ladd, G. P. Robertson, and S. H. Gage. 2006. SOCRATES - A simple model for predicting long-term changes in soil organic carbon in terrestrial ecosystems. Soil Biology and Biochemistry 38: 1172-1176.

2006 Soil organic carbon (SOC) represents a significant pool of carbon within the biosphere. Climatic shifts in temperature and precipitation have a major influence on the decomposition and amount of SOC stored within an ecosystem. We have linked net primary production algorithms, which include the impact of enhanced atmospheric CO2 on plant growth, to the Soil Organic Carbon Resources And Transformations in EcoSystems (SOCRATES) model to develop a SOC map for the North Central Region of the United States between the years 1850 and 2100 in response to agricultural activity and climate conditions generated by the CSIRO Mk2 Global Circulation Model (GCM) and based on the Intergovernmental Panel for Climate Change (IPCC) IS92a emission scenario. We estimate that the current day (1990) stocks of SOC in the top 10 cm of the North Central Region to be 4692 Mt, and 8090 Mt in the top 20 cm of soil. This is 19% lower than the pre-settlement steady state value predicted by the SOCRATES model. By the year 2100, with temperature and precipitation increasing across the North Central Region by an average of 3.9°C and 8.1 cm, respectively, SOCRATES predicts SOC stores of the North Central Region to decline by 11.5 and 2% (in relation to 1990 values) for conventional and conservation tillage scenarios, respectively. Grace, P. R., M. Colunga-Garcia, S. H. Gage, G. P. Robertson, and G. R. Safir. 2006. The potential impact of agricultural management and climate change on soil organic carbon resources in terrestrial ecosystems of the North Central Region of the United States. Ecosystems 9: 816-827.

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2006 Understanding the effects of tillage on soils following years or decades of no-till is critical for developing C conservation strategies. To date, short-term responses to tillage in previously uncultivated or other long-term no-till soils have primarily focused on total C changes, which are difficult to detect. Tillage effects on soil conservation and C permanence may be better predicted by changes in more readily detected factors known to affect C storage such as aggregation and physically protected C. We annually plowed replicated plots in a previously uncultivated midsuccessional field between 2002 and 2004 and investigated changes in the distribution of aggregates, physically protected C, and light fraction (LF) organic matter. Within 60 d of initial cultivation, soil aggregates in the 2000- to 8000-mu m size class declined from 0.47 to 0.15 g g(-1) at 0- to 7-cm soil depth and from 0.32 to 0.23 g g(-1) at 7 to 20 cm. Lower levels of aggregation persisted through the winter and spring of the following year. Inter-aggregate, unprotected light fraction (LF) increased following cultivation, as did particulate C in soil fractions with densities < 1.9 g cm(-3). Changes in the mass of total soil C were not detectable after 3 yr but the vertical distribution of all soil C pools was altered by plowing. Our study demonstrates that plowing once immediately and substantially alters aggregation and LF and particulate C dynamics and that these conditions persist. Results suggest that no-till soils need to be continuously maintained to protect aggregation and physically stabilized C pools. Grandy, A. S., and G. P. Robertson. 2006. Aggregation and organic matter protection following tillage of an undisturbed soil profile. Soil Science Society of America Journal 70: 1398-1406.

2006 <notextile>The immediate effects of tillage on protected soil C and N pools and on trace gas emissions from soils at precultivation levels of native C remain largely unknown. We measured the response to cultivation of CO2 and N2O emissions and associated environmental factors in a previously uncultivated U.S. Midwest Alfisol with C concentrations that were indistinguishable from those in adjacent late successional forests on the same soil type (3.2%). Within 2 days of initial cultivation in 2002, tillage significantly (P=0.001, n=4) increased CO2 fluxes from 91 to 196 mg CO2-C m(-2) h(-1) and within the first 30 days higher fluxes because of cultivation were responsible for losses of 85 g CO2-C m(-2). Additional daily C losses were sustained during a second and third year of cultivation of the same plots at rates of 1.9 and 1.0 g C m(-2) day(-1), respectively. Associated with the CO2 responses were increased soil temperature, substantially reduced soil aggregate size (mean weight diameter decreased 35% within 60 days), and a reduction in the proportion of intraaggregate, physically protected light fraction organic matter. Nitrous oxide fluxes in cultivated plots increased 7.7-fold in 2002, 3.1-fold in 2003, and 6.7-fold in 2004 and were associated with increased soil NO3- concentrations, which approached 15 mu g N g(-1). Decreased plant N uptake immediately after tillage, plus increased mineralization rates and fivefold greater nitrifier enzyme activity, likely contributed to increased NO3- concentrations. Our results demonstrate that initial cultivation of a soil at precultivation levels of native soil C immediately destabilizes physical and microbial processes related to C and N retention in soils and accelerates trace gas fluxes. Policies designed to promote long-term C sequestration may thus need to protect soils from even occasional cultivation in order to preserve sequestered C. </notextile> Grandy, A. S., and G. P. Robertson. 2006. Initial cultivation of a temperate-region soil immediately accelerates aggregate turnover and CO2 and N2O fluxes . Global Change Biology 12: 1507-1520.

2006 No-till management has been shown to increase soil aggregation, reduce erosion rates, and increase soil organic matter across a range of soil types, cropping systems, and climates. Few agricultural practices provide similar opportunities to deliver positive benefits for farmers, society, and the environment. The potential benefits of no-till are not being fully realized, however, in large part because no-till is rarely practiced continuously and many fields suitable for no-till are still conventionally tilled. We present here three arguments, based on recent research, in support of the agronomic and environmental benefits of continuous no-till: (i) although there exist agronomic challenges with no-till, long-term yields in these systems can equal or exceed those in tilled soils; (ii) cultivating no-till systems can decrease soil aggregation and accelerate C and N losses so rapidly that years of soil restoration can be undone within weeks to months; and (iii) over time, changes in soil structure and organic matter, coupled with producer adaptation to the need for spatially and temporally explicit chemical applications, increase plant N availability and reduce environmental N losses. At least in theory, then, continuous no-till can be widely practiced to improve the environment and maintain yields with little or no economic sacrifice by producers. In practice, however, many diverse challenges still limit no-till adoption in different regions. These challenges are surmountable, but potential solutions need to be interdisciplinary and address the ecological and especially the social and economic constraints to deploying continuous no-till. Grandy, A. S., G. P. Robertson, and K. D. Thelen. 2006. Do productivity and environmental tradeoffs justify periodically cultivating no-till cropping systems? Agronomy Journal 98: 1377-1383.

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2006 No-till cropping can increase soil C stocks and aggregation but patterns of long-term changes in N2O emissions, soil N availability, and crop yields still need to be resolved. We measured soil C accumulation, aggregation, soil water, N2O emissions, soil inorganic N, and crop yields in till and no-till corn-soybean-wheat rotations between 1989and 2002 in southwestern Michigan and investigated whether tillage effects varied over time or by crop. Mean annual NO3- concentrations in no-till were significantly less than in conventional till in three of six corn years and during one year of wheat production. Yields were similar in each system for all 14 years but three, during which yields were higher in no-till, indicating that lower soil NO3- concentrations did not result in lower yields. Carbon accumulated in no-till soils at a rate of 26 g C m22 yr21 over 12 years at the 0- to 5-cm soil depth. Average nitrous oxide emissions were similar in till (3.27 + 0.52 g N ha d-1) and no-till (3.63 + 0.53 g N ha d-1) systems and were sufficient to offset 56 to 61% of the reduction in CO2 equivalents associated with no-till C sequestration. After controlling for rotation and environmental effects by normalizing treatment differences between till and no-till systems we found no significant trends in soil N, N2O emissions, or yields through time. In our sandy loam soils, no-till cropping enhances C storage, aggregation, and associated environmental processes with no significant ecological or yield tradeoffs. Grandy, A. S., T. D. Loecke, S. Parr, and G. P. Robertson. 2006. Long-term trends in nitrous oxide emissions, soil nitrogen, and crop yields of till and no-till cropping systems. Journal of Environmental Quality 35: 1487-1495.

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2006 Huizinga, K. M. 2006. The Diversity of Dissimilatory Nitrate Reducers in an Agroecosystem. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

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2006 Geochemistry of soil, soil water, and soil gas was characterized in representative soil profiles of three Michigan watersheds. Because of differences in source regions, parent materials in the Upper Peninsula of Michigan (the Tahquamenon watershed) contain only silicates, while those in the Lower Peninsula (the Cheboygan and the Huron watersheds) have significant mixtures of silicate and carbonate minerals. These differences in soil mineralogy and climate conditions permit us to examine controls on carbonate and silicate mineral weathering rates and to better define the importance of silicate versus carbonate dissolution in the early stage of soil–water cation acquisition. Soil waters of the Tahquamenon watershed are the most dilute; solutes reflect amphibole and plagioclase dissolution along with significant contributions from atmospheric precipitation sources. Soil waters in the Cheboygan and the Huron watersheds begin their evolution as relatively dilute solutions dominated by silicate weathering in shallow carbonate-free soil horizons. Here, silicate dissolution is rapid and reaction rates dominantly are controlled by mineral abundances. In the deeper soil horizons, silicate dissolution slows down and soil–water chemistry is dominated by calcite and dolomite weathering, where solutions reach equilibrium with carbonate minerals within the soil profile. Thus, carbonate weathering intensities are dominantly controlled by annual precipitation, temperature and soil pCO2. Results of a conceptual model support these field observations, implying that dolomite and calcite are dissolving at a similar rate, and further dissolution of more soluble dolomite after calcite equilibrium produces higher dissolved inorganic carbon concentrations and a Mg2+/Ca2+ ratio of 0.4. Mass balance calculations show that overall, silicate minerals and atmospheric inputs generally contribute <10% of Ca2+ and Mg2+ in natural waters. Dolomite dissolution appears to be a major process, rivaling calcite dissolution as a control on divalent cation and inorganic carbon contents of soil waters. Furthermore, the fraction of Mg2+ derived from silicate mineral weathering is much smaller than most of the values previously estimated from riverine chemistry. Jin, L., E. Williams, K. Szramek, L. M. Walter, and S. K. Hamilton. 2006. Silicate and carbonate mineral weathering in soil profiles developed on pleistocene glacial drift (Michigan, USA): Mass balances based on soil water geochemistry. Geochemica Acta 72: 1027-1042.

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2006 We examined the effects of fertilization and gypsy moth defoliation on condensed tannin concentration (%CT) of hybrid poplar (Populus canadensis cv 'Eugeneii') fine roots in the summers of 1997 and 1998. This factorial experiment included two defoliation treatments (defoliated and a foliated control) and fertilization treatments (100 kg nitrogen (N) ha-1 and an unfertilized control). Gypsy moth (Lymantria dispar L.) populations were experimentally increased to obtain defoliation in the summers of 1996, 1997 and 1998; fertilization subplots were supplemented with NH4NO3 (100 kg N ha-1) in the spring of each year. Despite the severity of defoliation, the effects were small, and significant on only two sampling dates: in May 1997, when fine root %CT was 23% lower in the defoliated trees, and in November 1997, when trees in the defoliated unfertilized plots had 35% higher root %CT than trees in all other plots. Defoliation effects on root %CT did not follow the same seasonal pattern as defoliation effects on root starch content, N uptake capacity or leaf %CT. Regulation of root condensed tannin concentration appeared to be partially uncoupled from these traits. The small transient effects on root defense reflect the resilience of this early successional tree to severe early season defoliation. Kosola, K. R., D. Parry, and B. A. Workmaster. 2006. Response of condensed tannins in poplar roots to fertilization and gypsy moth defoliation. Tree Physiology 26: 1607-1611.

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2006 Changes in soil C as a result of changes in management are relatively slow, and several years of experimentation are needed before differences in management practices can be detected using traditional statistical procedures such as randomized complete block design (RCBD). Using spatial analyses (SA) that take into account spatial variability between plots has a potential for faster and more efficient detection of soil C differences. We hypothesize that for variables with strong spatial continuity, such as total soil C, accurate spatial variability assessment can be obtained even in relatively small experiments. Thus, SA can significantly improve the statistical efficiency of even these experiments. The objective of this study is to test this hypothesis by comparing performances of RCBD analysis and SA for simulated small-sized experiments where soil C is the response variable. Total soil C data collected from 11 field sites at the Long-Term Ecological Research (LTER) experiment in Michigan were used as an input for simulated experiments. Performance of SA depended on the strength of spatial correlation in soil C and was found to be related to topographical diversity of the experimental sites. In the sites with more diverse topography and stronger spatial correlation of soil C the SA produced lower standard errors for treatment means than those of the RCBD analysis (8 out of 11 sites). In two sites with the flattest topography and weak spatial correlation, SA did not have advantages over RCBD. Kravchenko, A. N., G. P. Robertson, S. S. Snapp, and A. J. M. Smucker. 2006. Using spatial variability information for improved estimates of soil carbon. Agronomy Journal 98: 823-829.

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2006 Lack of information about the spatial variability of soil C in different management systems limits accurate extrapolation of C sequestration findings to large scales. The objectives of this study were to: (i)describe and quantify variability of total C in three management systems, chisel-plow (CT) and no-till (NT) with conventional chemical inputs and a chisel-plow organic management practice with cover crops (CT-cover) 15 yr after conversion from conventional management;(ii) assess the strengths of spatial correlation in the three studied systems; and (iii) evaluate contributions of topography and texture to the overall total C variability and its spatial components. The data were collected at 12 60 by 60 m plots at the Long Term Ecological Research site, Kellogg Biological Station, MI. The data consisted of elevation measurements taken on a 2 by 5 m grid and a total of 1160measurements of total C, sand, silt, and clay contents taken from the0- to 5-cm depth. Overall variability of total C in NT was more than four times greater than in CT, and in CT-cover the variability was more than two times greater than CT. Spatial correlation of total C was the strongest in NT, followed by CT-cover, and then by CT. Stronger spatial structures in NT and CT-cover were found to form in response to topographical and texture gradients. Effects of texture were largely associated with topographical effects; however, even when topography was controlled for, texture still substantially contributed to explaining total C variability. Kravchenko, A. N., G. P. Robertson, X. Hao, and D. G. Bullock. 2006. Management practice effects on surface total carbon: Difference in spatial variability patterns. Agronomy Journal 98: 1559-1568.

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2006 Kurzman, A. L. 2006. Changes in major solute chemistry as water infiltrates soils: Comparisons between managed agroecosystems and unmanaged vegetation. Zoology. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

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2006 We analyzed the communities of soil basidiomycetes in agroecosystems that differ in tillage history at the Kellogg Biological Station Long-Term Ecological Research site near Battle Creek, Michigan. The approach combined soil DNA extraction through a bead-beating method modified to increase recovery of fungal DNA, PCR amplification with basidiomycete-specific primers, cloning and restriction fragment length polymorphism screening of mixed PCR products, and sequencing of unique clones. Much greater diversity was detected than was anticipated in this habitat on the basis of culture-based methods or surveys of fruiting bodies. With "species" defined as organisms yielding PCR products with 99% identity in the 5' 650 bases of the nuclear large-subunit ribosomal DNA, 241 "species" were detected among 409 unique basidiomycete sequences recovered. Almost all major clades of basidiomycetes from basidiomycetous yeasts and other heterobasidiomycetes through polypores and euagarics (gilled mushrooms and relatives) were represented, with a majority from the latter clade. Only 24 of 241 "species" had 99% or greater sequence similarity to named reference sequences in GenBank, and several clades with multiple "species" could not be identified at the genus level by phylogenetic comparisons with named sequences. The total estimated "species" richness for this 11.2-ha site was 367 "species" of basidiomycetes. Since >99% of the study area has not been sampled, the accuracy of our diversity estimate is uncertain. Replication in time and space is required to detect additional diversity and the underlying community structure. Lynch, M. D., and R. G. Thorn. 2006. Diversity of basidiomycetes in Michigan agricultural soils. Applied and Environmental Microbiology 72: 7050-7056.

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2006 Mueller, F., A. J. M. Smucker, and R. Horn. 2006. From micro-pores to ecosystems: Ecological gradients as components of environmental analysis and management. Proceedings of the International Soil Tillage Research Organization (ISTRO) 17: 1640-1641.

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2006 Simulations of dispersal across computer- generated neutral landscapes have generated testable predictions about the relationship between dispersal success and landscape structure. Models predict a threshold response in dispersal success with increasing habitat fragmentation. A threshold is defined as an abrupt, disproportionate decline in dispersal success at a certain proportion of habitat in the landscape. To identify potential empirical threshold responses in invasion success to landscape structure, we quantified the relationship between progression of the gypsy moth (Lymantriadispar) invasion wave front across Michigan (1985–1996) and the structure of the Michigan landscape using two indices of invasion success and six landscape metrics. We also examined the effect of scale of analysis and choice of land cover characterization on our results by repeating our analysis at three scales using two different land cover maps. Contrary to simulation model predictions, thresholds in invasion success did not correspond closely with thresholds in landscape structure metrics. Increased variation in invasion success indices at smaller scales of analysis also suggested that invasion success should be studied atlarger spatial extents (‡75km2) than would be appropriate for characterizing individual dispersal events. The predictions of individual dispersal models across neutral landscapes may have limited applications for the monitoring and management of vagile species with excellent dispersal capabilities such as the gypsy moth. Nessledge, G. M., B. A. Maurer, and S. H. Gage. 2006. Gypsy moth response to landscape structure differs from neutral model predictions: Implications for invasion monitoring. Bio Invasions: DOI 10.1007/s/10530-006-9061-1.

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2006 The literature was reviewed and analyzed to determine the feasibility of using a combination of acid hydrolysis and CO2-C release during long-term incubation to determine soil organic carbon (SOC) pool sizes and mean residence times (MRTs). Analysis of 1100 data points showed the SOC remaining after hydrolysis with 6 M HCl ranged from 30 to 80% of the total SOC depending on soil type, depth, texture, and management. Nonhydrolyzable carbon (NHC) in conventional till soils represented 48% of SOC; no-till averaged 56%, forest 55%, and grassland 56%. Carbon dates showed an average of 1200 yr greater MRT for the NHC fraction than total SOC. Long-term incubation, involving measurement of CO2 evolution and curve fitting, measured active and slow pools. Active-pool C comprised 2 to 8% of the SOC with MRTs of days to months; the slow pool comprised 45 to 65% of the SOC and had MRTs of 10 to 80 yr. Comparison of field 14C and 13C data with hydrolysis�incubation data showed a high correlation between independent techniques across soil types and experiments. There were large differences in MRTs depending on the length of the experiment. Insertion of hydrolysis/incubation derived estimates of active (Ca), slow (Cs), and resistant pools (Cr) into the DAYCENT model provided estimates of daily field CO2 evolution rates. These were well correlated with field CO2 measurements. Although not without some interpretation problems, acid hydrolysis' laboratory incubation is useful for determining SOC pools and fluxes especially when used in combination with associated measurements. Paul, E. A., S. J. Morris, R. T. Conant, and A. F. Plante. 2006. Does the acid hydrolysis incubation method measure meaningful soil organic carbon pools? Soil Science Society of America Journal 70: 1023-1035.

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2006 Previously available primer sets for detecting anaerobic ammonium-oxidizing (anammox) bacteria are inefficient, resulting in a very limited database of such sequences, which limits knowledge of their ecology. To overcome this limitation, we designed a new primer set that was 100% specific in the recovery of 700-bp 16S rRNA gene sequences with >96% homology to the "Candidatus Scalindua" group of anammox bacteria, and we detected this group at all sites studied, including a variety of freshwater and marine sediments and permafrost soil. A second primer set was designed that exhibited greater efficiency than previous primers in recovering full-length (1,380-bp) sequences related to "Ca. Scalindua," "Candidatus Brocadia," and "Candidatus Kuenenia." This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anammox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments. Penton, C. R., A. H. Devol, and J. M. Tiedje. 2006. Molecular evidence for the broad distribution of anammox in freshwater and marine sediments. Applied and Environmental Microbiology 72: 6829-6832.

549

2006 Hydropneumatic root separation from field soil collects organic non-root residues. This study compares manual cleaning to electronic cleaning with image analysis of carrot roots from field experiments. Washed and stained very fine roots of carrots (diameter 0.15 mm) were video-recorded by using a high-resolution robotic camera system. Fibrous root lengths and widths of roots from samples grown in fine sand (n = 160) and organic soils (n = 150) were determined by automated image processing of video-recorded images. During video-recording, some non-root residue remained with the extracted fine roots, especially in samples from organic soils, where residue materials comprised partially decomposed straw and peat. In computerized image analysis, materials with length-to-width ratios of =3:1 were deemed non-root debris and discarded electronically. The 3:1 length-to-width ratio was chosen for distinguishing long thin root images from short organic residues. Results show that more non-root residue was recovered by image analysis than was recorded by dry weight estimation after manual cleaning. Length, surface area and volume averaged 15%, 18% and 24% of non-root residue in the manually fully cleaned samples (residue estimation 0%, i.e. no visible debris recorded visually) of fine sand soils (n = 80). Length, surface area, and volume averaged 20%, 25% and 33% (r = 0.55, p < 0.0001), respectively, of non-root residue in the organic soil samples with residues <10% (g residues/g roots and residues) (n = 71). Both root and residue densities were higher at soil depths of 0 - 25 cm than in deeper subsoils, where the percentages of discarded residue were highest. Electronic non-root separation effectively eliminated short and partially decomposed organic material that was hardly visible or otherwise difficult and time-consuming to remove manually. Pietola, L., and A. J. M. Smucker. 2006. Elimination of non-root residue by image analysis of very fine roots. Computers and Electronics in Agriculture 53: 92-97.

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2006 Robertson, G. P., and A. S. Grandy. 2006. Soil system management in temperate regions. Pages 27-39 in N. Uphoff, A. S. Ball, E. Fernandes, H. Herren, O. Husson, M. Laing, C. Palm, J. Pretty, P. Sanchez, N. Snanginga, and J. Thies, eds. Biological Approaches to Sustainable Soil Systems. CRC Press, Taylor and Francis Group, Boca Raton, Florida, USA.

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2006 While specialists are thought to be well adapted to their resources, generalists are thought to be a jack of-all-trades but master of none. However, few studies have examined how selection by multiple resources influences the evolution of morphnological traits in generalists. As most plants are dependent upon pollinators for reproduction, pollinators are important, and often essential, plant resources. I examined the degree of generalization in wild radish (Raphanus raphanistrum) nd how selection by multiple pollinators influences adaptation to each toxon individually, both within and among populations. Although previous studies of generalization in plant-pollination systems have focused primarily on estimates of species richness, pollinators exhibit great variation in visitation rates. I found that diversity indices, which take into account both species richness and evenness, provide a more useful estimate of pollinator generalization. I characterized generalization in the pollinator assemblage of the widespread agricultural weed, wild radish, and studied how pollinators differed in their selection on several floral traits. Although wild radish is effectively pollinated by at least 14 pollinator genera, few of these taxa actually selected on floral traits. My findings suggest that wild radish is able to adapt to a subset of its pollinators without trading off the ability to effectively use other taxa. Finally, I examined how selection and drift have contributed to differentiation of floral and phonological traits of wild radish by comparing estimates of population differentiation in quantitative traits (Qst) to population differentiation in allele frequencies (Fst). I found that differences in most floral traits among populations can be explained by drift alone. I also found that life history traits such as ovule number and flowering time were under strong divergent selection across populations, suggesting life history traits may have been important in colonization and adaptation to new habitats. Overall, my results indicate that wild radish has successfully evolved to use many pollinators to effect reproduction, that it can adapt to a subset of these pollinators without trading off the ability to use others effectively, and that its success as a generalist my be one reason for its successful invasion in many non-native environments. Sahli, H. F. 2006. Generalization in plant pollination systems and its effect on floral evolution within and among populations of wild radish (Raphanus raphanistrum). Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

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2006 Despite the development of diversity indices in community ecology that incorporate both richness and evenness, pollination biologists commonly use only pollinator richness to estimate generalization. Similarly, while pollination biologists have stressed the utility of pollinator importance, incorporating both pollinator abundance and effectiveness, importance values have not been included in estimates of generalization in pollination systems. In this study, we estimated pollinator generalization for 17 plant species using Simpson’s diversity index, which includes richness and evenness. We compared these estimates with estimates based on only pollinator richness, and compared diversity estimates calculated using importance data with those using only visitation data. We found that pollinator richness explains only 57–65% of the variation in diversity, and that, for most plant species, pollinator importance was determined primarily by differences in visitation rather than by differences in effectiveness. While simple richness may suffice for broad comparisons of pollinator generalization, measures that incorporate evenness will provide a much more accurate understanding of generalization. Although incorporating labor-intensive measurements of pollinator effectiveness are less necessary for broad surveys, effectiveness estimates will be important for detailed studies of some plant species. Unfortunately, at this point it is impossible to predict a priori which species these are Sahli, H. F., and J. K. Conner. 2006. Characterizing ecological generalization in plant-pollination systems. Oecologia 148: 365-372.

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2006 A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists' inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology. Schmidt, T. M. 2006. The maturing of microbial ecology. International Microbiology 9: 217-223

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2006 A trait-based community assembly approach to weed management may enhance our understanding of how weed communities respond to specific management practices and increase the utility of weed management based on ecological principles. Therefore, identifying management practices that operate as assembly filters and the species traits upon which they act is an important first step in developing a more predictive weed science. Here, I report results from a 3-yr investigation of the effects of timing of annual tillage (spring vs. fall) on the annual assembly of arable weed communities. The timing of tillage had consistent and dramatic effects on the composition of weed communities; spring tillage led to weed communities dominated by early emerging spring annual forbs and C4 grasses, and fall tillage led to communities dominated by later-emerging forbs and C3 grasses. Traits determining a species' susceptibility to tillage time likely include germination syndrome and life cycle, both of which influence how species respond to changes in soil resource levels and light availability driven by seasonal disturbance regime. Manipulating the timing of tillage and other major soil disturbances may therefore be an important tool for managers interested in influencing community composition or targeting species with similar germination and life-history traits. Smith, R. G. 2006. Timing of tillage is an important filter on the assembly of weed communities. Weed Science 54: 705-712.

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2006 The dynamics of soil seed banks in crop rotations of corn, soybean, and winter wheat were investigated to determine whether weed seed inputs associated with the winter wheat phases of the rotation were present in the readily germinable fraction of the seed bank in subsequent phases. Two studies were conducted, each in chisel-plowed systems. In one study, we compared seed banks in plots after 8 yr of corn grown continuously and with rotation that included winter wheat and soybean. A second study followed seed bank composition and abundance for 3 yr in plots that were planted to corn and soybean in successive years after planting to winter wheat. Seed banks were measured by direct germination in a heated greenhouse. In the first study, seed banks in plots planted to continuous corn (never planted to winter wheat) and the corn phase of the rotation (winter wheat planted 3 yr earlier) did not differ in species composition or abundance despite significant differences in seed banks in plots that had been planted to winter wheat the previous season. In the second study, seed bank abundance and composition in plots planted to winter wheat in 2001 rapidly changed after planting of corn and soybean in 2002 and 2003, respectively. Data from the two experiments suggest that seed banks in annual row crops experience rapid change in composition and abundance and can be strongly influenced by the most recent crop. This could limit our ability to infer longer term trends associated with changes in management practices from studies of soil seed banks Smith, R. G., and K. L. Gross. 2006. Rapid change in the germinable fraction of the weed seed bank in crop rotations. Weed Science 54: 1094-1100.

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2006 The effects of crop rotation and management system on annual variability in weed communities and crop yields were assessed in a 4-yr study in Michigan. Variability of the weed community and corn yields were assessed using the coefficient of variation (CV) and a multivariate dissimilarity index (Bray-Curtis) that accounted for changes in both weed species abundance and composition. The treatments included two rotations: continuous corn and a corn-corn-soybean-wheat rotation, and two management systems: conventional (CONV) and organic-based (ORG). Weed biomass was significantly higher in the ORG system; however, there was no effect of crop rotation on weed biomass or number of weed species in a treatment (species richness). Annual variability in weed community composition and structure was affected by both crop rotation and management system and was highest in the ORG rotation. In contrast to the weed community, variability in corn yield was highest in the least-diverse cropping system (CONV monoculture), despite that system having a more constant weed community. Corn yield in the ORG rotation was not significantly different from that in the CONV monoculture. Results of this study suggest that management aimed at increasing cropping system diversity may have additional effects on weed communities and crop yields beyond those commonly reported, and these may have important implications for the development of more efficient and sustainable weed and crop management practices. Smith, R. G., and K. L. Gross. 2006. Weed community and corn yield variability in diverse management systems. Weed Science 54: 106-113.

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2006 Stewart, C. E. 2006. Soil carbon saturation: A new model of soil organic matter stabilization and turnover. Ph.D. Dissertation, Colorado State University, Ft. Collins, Colorado, USA.

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2006 Stres, B., and J. M. Tiedje. 2006. New frontiers in soil microbiology: How to link structure and function of microbial communities? Pages 1-22 in P. Nannipieri and K. Smalla, eds. Soil Biology, Nucleic Acids and Proteins in Soil. Springer Verlag, Berlin, Heidelberg, Germany

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2006 The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 ± 1.2, 32.5 ± 0.6, and 35.6 ± 1.4 for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 ± 4.2) was similar to that produced during hydroxylamine oxidation (33.5 ± 1.2) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 ± 1.7), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens 0.6 ± 1.9 and 0.5 ± 1.9, respectively) were similar to those during nitrate reduction (0.5 ± 1.9 and 0.5 ± 0.6, respectively), indicating no influence of either substrate on site preference. Site preferences of 33 and 0 are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O. Sutka, R. L., N. E. Ostrom, P. H. Ostrom, J. A. Breznak, H. Gandhi, A. J. Pitt, and F. Li. 2006. Distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundences. Applied and Environmental Microbiology 72: 638-644.

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2006 The concept of ecosystem services (ES) provides a transformative lens for thinking about the relation between humankind and nature. The lens is especially revealing when applied to agriculture, the most widespread managed ecosystem on the planet. ES are defined as "the conditions and processes through which natural ecosystems, and the species that make them up, sustain and fulfill human life" (Daily 1997). By focusing on what ecosystems do for humans, the ES concept invites analysis of what humans do to ecosystems and why they do it. Agriculture (including planted forests) conventionally supplies food, fiber, and fuel "provisioning services" in ES parlance (Millennium Ecosystem Assessment 2005). Farmers also help to maintain the natural "supporting" ES that make agriculture productive, such as pollination, biological pest regulation, and soil nutrient renewal. In theory, the same managed ecosystems that provide these marketed products could produce other types of ES if suitable incentives existed. The broad class of "regulation ES" covers climate regulation, water purity, surface water flows, groundwater levels, and waste absorption and breakdown. All of these offer benefits that are poorly captured by current markets, yet which managed agricultural and forest ecosystems could potentially provide. The same is true for the provision of habitat for wild species and the cultural, recreational, and informational ES. In fact, compared to more natural ecosystems, agriculture and forestry have much readier potential to expand their supply of currently nonmarketed ES for three reasons: (1) much is known about biophysical input-output relationships in the system, (2) there exist precedents for economic incentives that could induce greater ES supply, and (3) the past performance of agriculture suggests strong capability to supply goods and services in response to attractive incentives. The rest of this paper expands on these themes by exploring the history of public awareness and reaction to ES linked to agriculture, some precedents for inducing farmers to supply a different product mix, the existing research base on agriculture as viewed from an ES perspective, and research needs in order to augment the provision of currently nonmarketed ES from agricultural lands. Swinton, S. M., F. Lupi, G. P. Robertson, and D. A. Landis. 2006. Ecosystem services from agriculture: Looking beyond the usual suspects. American Journal of Agricultural Economics 88: 1160-1166.

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2006 Thorn, R. G., M.-A. Lachance, and J. Scott. 2006. Methods for studying terrestrial fungal ecology and diversity in C. A. Reddy, T. J. Beveridge, J. A. Breznak, L. Snyder, T. M. Schmidt, and G. A. Marzluf, eds. Methods for General and Molecular Microbiology. American Society for Microbiology Press, Washington, DC.

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2006 Wiangwang, N. 2006. Hyperspectral data modeling for water quality studies in Michigan's inland lakes. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

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2006 Davis, A., K. Renner, C. Sprague, L. Dyer, and D. Mutch, eds. 2005. Integrated Weed Management: One Year's Seeding. Michigan State University Extension Bulletin E-2931, East Lansing, Michigan, USA.

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2005 Weed seedbanks have been studied intensively at local scales, but to date, there have been no regional-scale studies of weed seedbank persistence. Empirical and modeling studies indicate that reducing weed seedbank persistence can play an important role in integrated weed management. Annual seedbank persistence of 13 summer annual weed species was studied from 2001 through 2003 at eight locations in the north central United States and one location in the northwestern United States. Effects of seed depth placement, tillage, and abiotic environmental factors on seedbank persistence were examined through regression and multivariate ordinations. All species examined showed a negative relationship between hydrothermal time and seedbank persistence. Seedbank persistence was very similar between the two years of the study for common lambsquarters, giant foxtail, and velvetleaf when data were pooled over location, depth, and tillage. Seedbank persistence of common lambsquarters, giant foxtail, and velvetleaf from October 2001 through 2002 and October 2002 through 2003 was, respectively, 52.3% and 60.0%, 21.3% and 21.8%, and 57.5% and 57.2%. These results demonstrate that robust estimates of seedbank persistence are possible when many observations are averaged over numerous locations. Future studies are needed to develop methods of reducing seedbank persistence, especially for weed species with particularly long-lived seeds. Davis, A. S., J. Cardina, F. Forcella, G. B. Johnson, G. Kegode, J. L. Lindquist, E. C. Luschei, K. A. Renner, C. K. Sprague, and M. M. Williams. 2005. Environmental factors affecting seedbank persistence of 13 annual weeds across the U.S. corn belt. Weed Science 53: 296-306.

2005 Characterizing the long-term effect of agricultural management systems on weed communities will aid in developing sustainable weed management practices. Weed seedbanks and aboveground biomass were measured within a corn-soybean-wheat crop sequence from 1990 through 2002 at Hickory Corners, MI. Four management systems were compared: conventional (CONV; full rates of N fertilizer and herbicides, moldboard tillage), no till (NT; same as CONV with no primary tillage), reduced input (RI; reduced rates of N fertilizer and herbicides, moldboard tillage, mechanical weed control, wheat underseeded with red clover), and organic (ORG; same as RI but no synthetic inputs). Multivariate ordinations of weed seedbanks showed a divergence of the CONV and NT systems from the RI and ORG systems. The CONV and NT seedbanks were dominated by grass species (mainly fall panicum and large crabgrass), whereas the RI and ORG systems were dominated by common lambsquarters and common chickweed. Within a single growing season, weed seedbanks in the RI and ORG systems were positively correlated with weed biomass whereas seedbanks in the CONV and NT system had little predictive value. Weed biomass from 1990 through 2002 showed a strong association of grass weed species with the corn phase of the CONV and NT system and common lambsquarters and redroot pigweed with the corn and soybean phases of the RI and ORG systems. Weed biomass diversity measures were negatively correlated with soybean yields in RI and ORG and wheat yields in NT, RI, and ORG. It is not clear whether crops were less competitive in the NT, RI, and ORG treatments, allowing new weed species to enter the plots, or whether less effective weed management in the NT, RI, and ORG treatments resulted in increased species richness, causing reduced crop yields. Mechanistic studies are needed to elucidate the relationship between weed community diversity and crop performance. Davis, A. S., K. Renner, and K. L. Gross. 2005. Weed seedbank and community shifts in a long-term cropping systems experiment. Weed Science 53: 296-306.

2005 Translational power is the cellular rate of protein sysnthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is highter among rapidly growing microbes, and lower among slowly growing microbes. One facter known to affect translational power is biased use of synonymous codons. The correlation within an organism between expression level and degree of codon bias among genes of Escherichia coli and other bacteria capable of rapid growht is commonly attributed to selection for high translational power. Conversely, the absence of such a correlation is some slowlyh growing microbes has been interpreted as the absence of selection for tanslational power. Because codon bias caused by translational selection varies between rapidly growing and slowly growing microbes, we investigated whether observed differences in translational power among microbes could be explained entirely by differences in the degree of codon bias. Although the data are not availabe to estimate the effect of codon bias in other species, we developed an empirically-based mathematical model to compare the translation rate of E. colil to the ttranslation rate of a hypothetical strain which differs from E. coli only by lacking codon bias. Dethlefsen, L., and T. M. Schmidt. 2005. Differences in codon bias cannot explain differences in translational power among microbes. BMC Bioinformatices 6: 3.

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2005 Remotely sensed data can aid in estimating biophysical variables of corn (Zea mays L.). This study identifies spectral wavelengths, spectral vegetation indices (SVIs), and timing needed for estimating yield and leaf area index (LAI) for corn. Canopy reflectance (460-810 nm range) was measured periodically in 1999 and 2000 within a field study varying N and irrigation management for corn. Corn grain yield was strongly related to canopy reflectance for either individual wavelengths or for SVIs, reaching an optimum (R-2 > 0.9) at R5 dent stage in both years. Green reflectance based on simple ratio (green simple ratio index, GSRI) had the highest R-2, lowest RMSE, and most consistent slope and intercept between years. In contrast, LAI was best predicted by normalized difference vegetation index (NDVI) (RSME = 0.426) while green normalized difference vegetation index (GNDVI) performed poorly (RMSE = 0.604). Corn grain yield in this study was best predicted at stage R5 using the green simple ratio index. Elwadie, M., F.J. Pierce, and J. Qi. 2005. Remote sensing of corn canopy dynamics and biophysical variables estimation. Agronomy Journal 97: 99-105.

2005 Despite mycologists interest in its unique spore-dispersal mechanism, systematic studies of the genus Sphaerobolus have received little attention. In our previous work multiple gene genealogies indicated the existence of three divergent lineages in the genus Sphaerobolus, each representing a phylogenetic species. Macro- and micromorphological analyses of colony and fruit-body characters presented here confirmed that these three phylogenetic species correspond to two known species, S. iowensis and S. stellatus, and a newly discovered species. In addition, an expanded gene genealogical analysis is presented for the three species. The new species, named Sphaerobolus ingoldii Geml, Davis et Geiser, is described based on both molecular and morphological data. In addition, while S. iowensis previously had been reported in only two localities, we found that it is as common as or more common than S. stellatus in North America. Despite the considerable amount of DNA polymorhism found in all species, nested clade analyses of S. iowensis and S. stellatus indicated little phylogeographic structure in either species, perhaps due to heavy movement mediated by human activities. Geml, J., D. D. Davis, and D. M. Geiser. 2005. Systematics of the genus Sphaerobolus based on molecular and morphological data, with the description of Sphaerobolus ingoldii sp. nov. Mycologia 97: 680-694.

2005 Carbon sequestration and greenhouse gas abatement in soils are two of a limited number of rapidly-deployable, high impact CO2 stabilization options now available to policy makers. Among agricultural management options, eliminating tillage may have the broadest mitigation potential because it alters emissions of all three biogenic greenhouse gases. No-till soil management in the U.S, although increasing, however, continues to be rotated with tillage because of perceptions that no-till limits N availability and decreases yields. This raises questions about the permanence of stored C, which has been identified as the fundamental challenge to terrestrial C sequestration. In this dissertation I address the ecological processes underlying soil organic matter permanence and the ecosystem and agronomic consequences of long-term no-till. In the first series of experiments, reported in Chapter 2, I determined aggregate-associated soil C pools in ten ecosystems on the same soil series along a management intensity gradient. I also assess the degree to which C is protected by aggregates using size and density fractionation techniques coupled with long-term mineralization assays of crushed and intact aggregates. Active pool C increases when 2000-8000 pm aggregates were broken into microaggregates (<250 p.m) ranged from 18% in conventional agriculture to 59% in alfalfa. Potential release of whole-soil labile C from physical protection following macroaggregate destruction was seven to nine-fold greater in successional systems than conventional agriculture. In the second set of experiments, reported in Chapter 3-5, I cultivated a never-previously cultivated field and minimized plant community changes to look at soil disturbance free from the influence of other agricultural management practices. I infer soil C permanence from responses of aggregate-protected soil organic matter, enzyme activities that reflect soil microbial activity, and trace gas fluxes. I, therefore, attempt to advance our ability to predict tillage effects on soils by understanding the basic ecological processes controlling soil's response to disturbance. Cultivation immediately reduced 2000-8000 pm aggregates to levels commonly found in agricultural soils tilled > 50 years. The destruction of aggregates released particulate C from protected microsites and limited the incorporation of aboveground C into new aggregates. This lead to a series of biogeochemical transformations I term an aggregate cascade. Microbial activity and N cycling increase, substantially increasing fluxes of both nitrous oxide and carbon dioxide. Growing plants can modify the effects of tillage on N availability and N20 flux but have little effect on aggregation or CO2 emissions. This cascade is accelerated by increased soil temperature and other environmental changes following decomposition that promote decomposition. In chapter 6, I report on an analysis of data from the till and no-till treatments of the KBS LTER and conclude that over 12 years there were no yield declines or environmental consequences (e.g. increased N20 emissions) associated with no-till. This work was performed in collaboration with classmates in a graduate seminar. My results show that cultivation immediately destabilizes physical and microbial processes related to C and N retention in soils. I also demonstrate that no-till cropping can be practiced with no yield or environmental trade-offs. Together, these results demonstrate the importance and feasibility of protecting no-till soils from periodic cultivation. Grandy, A. S. 2005. Ecosystem consequences of soil aggregation following soil disturbance. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

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2005 Cover crop roots and shoots release carbon and nitrogen compounds in situ during their decomposition. Depending upon the season, these C and N compounds may be sequestered, the C may be respired or the N may be leached below the root zone. A field study was established to identify the contributions of cover crop root and shoot N to different regions within aggregates in the Ap horizon of a Kalamazoo loam soil. Fall-planted rye plants (Secale cerealeL.) were labeled the next May with foliar applications of solutions containing 99% atom (15NH4)2SO4. Isotopic enrichment of soil aggregates ranging from 2.0 to 4.0, 4.0±6.3 and 6.3±9.5 mm across was determined following plant residue applications. Concentric layers of aggregates were removed from each aggregate by newly designed meso soil aggregate erosion (SAE) chambers. Non-uniform distributions of total N and recently derived rye N in soil macroaggregates, across time, suggested that the formations and functions of macroaggregates are very dynamics processes and soil aggregates influence where N is deposited. Early in the season, more 15N migrated to the interior regions of the smallest aggregates, 2-4 mm across, but it was limited to only surfaces and transitional regions of the larger aggregates, 6.3±9.3 mm across. Exterior layers of aggregates between 6.0 and 9.5 mm retained 1.6% of the N derived from roots in July 1999, which was three times more than their interior regions. This was slightly greater than the % Nderived from shoot. One month later, as the maize root absorption of N increased rapidly, % N derived from roots and % N derived from shoot were nearly equal in exterior layers and interior regions of soil aggregates. This equilibrium distribution may have been from either greater diffusion of N within the aggregates and/or maize root removal form aggregate exteriors. Results supported that most of roots grew preferentially around surfaces of soil aggregates rather than through aggregates. Cover crop roots contributed as much N as cover crop shoots to the total soil N pool. Subsequent crops use N from the most easily accessible zones of soil structure, which are surfaces of larger soil aggregates. Therefore maintaining active plant roots and aggregated soil structure in the soil enhances N sequestration and maximize soil N availability. These studies suggest that the rapid and perhaps bulk flow of soil N solutions may bypass many of the central regions of soil aggregates, resulting in greater leaching losses. Kavdir, Y., and A. J. M. Smucker. 2005. Soil aggregate sequestration of cover crop root and shoot-derived nitrogen. Plant and Soil 272: 263-276.

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2005 Alfalfa (Medicago sativa L.) contributes 430 million kg N year(-1) to the US Corn-Belt soils, according to a 1991 survey. Minimizing leaching losses from these very large N inputs requires a better understanding of the specific root dynamics that relate to the shoot-borne nitrates which have been reported to develop throughout many soil profiles. The objective of the present study was to determine the impact of decaying alfalfa roots on nitrate inputs to soils and on soil hydraulic conductivity properties which affect nitrate leaching. An experiment was initiated in 1994 and data for this report were taken from research on a Kalamazoo loam soil (fine-loamy, mixed, mesic Typic Hapludalf) at the KBS/LTER (long-term ecological research) site in southwestern Michigan, during the period from 1996 through 1997. Soil extractable nitrate (NO3-N) and ammonium (NH4-N) were monitored to soil depths of 150 cm and soil soluble NO3-N and NH4-N were monitored by suction lysimeters to the depth of 65 cm. Saturated hydraulic conductivity (K-sat) of soil was measured by the double-ring infiltrometer method. Following glyphosate termination of the alfalfa stands, nitrate-N released from mineralized alfalfa roots plus shoots totaled 75 kg ha(-1). Alfalfa roots generated 36 kg ha(-1) and alfalfa shoots generated 39 kg ha(-1) which accumulated in the Ap horizons from April to July in 1997. The presence of decaying alfalfa roots in the profile quadrupled Ksat values as compared to bare fallow soils. Nitrates released from decomposing alfalfa roots combined with root-enhanced hydraulic conductivities dramatically increased NO3-N leaching following the termination of alfalfa stands. NO3-N leaching to deeper horizons approached 83 kg ha(-1) in root treatments and 144 kg ha(-1) in the root plus shoot treatments during the period from April to December, following alfalfa termination. Our data suggest that under temperate climate such as that of Michigan, groundwater contamination by nitrates can be reduced by terminating alfalfa stands immediately before spring-planting of the subsequent row crop, which can absorb the large quantities of N leaking from decomposing shoots and roots of the legume. (c) 2005 Elsevier B.V. All rights reserved. Kavdir, Y., D. P. Rasse, and A. J. M. Smucker. 2005. Specific contributions of dacaying alfalfa roots to nitrate leaching in a Kalamazoo loam soil. Agriculture, Ecosystems, and Environment 109: 97-106.

2005 The quantitative characterization of spatiotemporal variability in crop grain yields is an important component for successful precision-agriculture applications. The objective of this study was to analyze and quantify effects of management practices, topographical features, and weather conditions on spatial variability of crop yields. A one-factor randomized complete block design experiment with six replications was established at the Long Term Ecological Research site in southwest Michigan in 1988. The treatments used in this study were two treatments with conventional chemical inputs (chisel plow and no-till) and two organic-based chisel-plowed treatments with a winter leguminous cover crop (low chemical input and zero chemical input). The data consisted of corn (Zea mays L.), soybean [Glycine max (L.) Merr.], wheat (Triticum aestivum L.) yields collected via combine monitors from 1996 to 2001. We observed that stressful conditions, regardless of the stress origin, were associated with increase in the overall yield variability (coefficient of variation) as well as the small-scale yield variability (variogram values at short lag distances and variogram slopes near the origin) with yields probably being more sensitive to the small-scale variations in growth conditions due to soil and microtopographical differences. Coefficients of variation were as high as 45% in years with low precipitation and as low as 14% in years with above-average precipitation. During the years with low precipitation, both the coefficients of variation and the small-scale variability were often significantly higher in the zero chemical input treatment than in the treatments that received fertilizer inputs. The coefficients of variation and the small-scale variability parameters also tended to be higher in corn stressed by antagonism from previous wheat crop in the no-till treatment. Kravchenko, A. N., G. P. Robertson, K. D. Thelen, and R. R. Harwood. 2005. Management, topographical, and weather effects on spatial variability of crop grain yields. Agronomy Journal 97: 514-523.

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2005 Annual crop fields typically are simple habitats dominated by a few plant species where pesticides play a major role in managing weed and insect infestations. Recently, there has been significant interest in the potential to reduce reliance on pesticides by manipulating plant species and communities to benefit natural enemies of insects and weeds. Such efforts aim to enhance natural enemy impact by providing appropriate food, shelter, and hosts, and efforts typically are accomplished by manipulation of plant species, populations, or communities. Habitat management is generally viewed as an important factor in maintaining stable insect and natural enemy populations in agricultural systems and may have a similar function in increasing weed seed predation. Crop and noncrop habitats provide resources to natural enemies either directly through floral nectar and Pollen, indirectly by increased host or prey availability, or through emergent properties of the habitat such as by moderating the microclimate. These critical resources for natural enemies can be provided in agricultural ecosystems at several scales: within fields, at field margins, or as a component of the larger landscape. Because individual natural enemy species may require quite specific resources at different times and spatial scales, not all attempts to manipulate habitat diversity are equally effective. We review the role of plant resources, including weeds, in supporting natural enemy communities and provide case studies of how varying plant diversity at different spatial scales can influence the effectiveness of biological control in agricultural landscapes. Landis, D. A., F. D. Menalled, A. C. Costamagna, and T. K. Wilkinson. 2005. Manipulating plant resources to enhance beneficial arthropods in agricultural landscapes. Weed Science 53: 902-908.

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2005 The relationship between nitrous oxide (N2O) flux and N availability in agricultural ecosystems is usually assumed to be linear, with the same proportion of nitrogen lost as N2O regardless of input level. We conducted a 3-year, high-resolution N fertilizer response study in southwest Michigan USA to test the hypothesis that N2O fluxes increase mainly in response to N additions that exceed crop N needs. We added urea ammonium nitrate or granular urea at nine levels (0-292 kg N ha(-1)) to four replicate plots of continuous maize. We measured N2O fluxes and available soil N biweekly following fertilization and grain yields at the end of the growing season. From 2001 to 2003 N2O fluxes were moderately low (ca. 20 g N2O-N ha(-1) day(-1)) at levels of N addition to 101 kg N ha(-1), where grain yields were maximized, after which fluxes more than doubled (to > 50 g N2O-N ha(-1) day(-1)). This threshold N2O response to N fertilization suggests that agricultural N2O fluxes could be reduced with no or little yield penalty by reducing N fertilizer inputs to levels that just satisfy crop needs. McSwiney, C. P., and G. P. Robertson. 2005. Non-linear response of N2O flux to incremental fertilizer addition in a continuous maize (Zea mays sp.) cropping system. Global Change Biology 11: 1712-1719.

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2005 Mercader, R., and J. M. Scriber. 2005. Phenotypic plasticity in host selection in adult tiger swallowtail butterflies, Papilio glaucus (Lepidptera: Papilionidae). Pages 25-57 in T. N. Ananthakrishnan, ed. Insects and Phenotypic Plasticity. IHB, Oxford, England, UK.

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2005 Morris, S. J., and G. P. Robertson. 2005. Linking function between scales of resolution. Pages 13-26 in J. Dighton, P. V. Oudemans, and J. F. White, eds. The Fungal Community, 3rd Ed. Marcel Dekker, New York, New York, USA.

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2005 When appraising the impact of food and fiber production systems on the composition of the Earth's atmosphere and the 'greenhouse' effect, the entire suite of biogenic greenhouse gases - carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) - needs to be considered. Storage of atmospheric CO2 into stable organic carbon pools in the soil can sequester CO2 while common crop production practices can produce CO2, generate N2O, and decrease the soil sink for atmospheric CH4. The overall balance between the net exchange of these gases constitutes the net global warming potential (GWP) of a crop production system. Trace gas flux and soil organic carbon (SOC) storage data from long-term studies, a rainfed site in Michigan that contrasts conventional tillage (CT) and no-till (NT) cropping, a rainfed site in northeastern Colorado that compares cropping systems in NT, and an irrigated site in Colorado that compares tillage and crop rotations, are used to estimate net GWP from crop production systems. Nitrous oxide emissions comprised 40-44% of the GWP from both rain-fed sites and contributed 16-33% of GWP in the irrigated system. The energy used for irrigation was the dominant GWP source in the irrigated system. Whether a system is a sink or source of CO2, i.e. net GWP, was controlled by the rate of SOC storage in all sites. SOC accumulation in the surface 7.5 cm of both rainfed continuous cropping systems was approximately 1100 kg CO2 equivalents ha(-1) y(-1). Carbon accrual rates were about three times higher in the irrigated system. The rainfed systems had been in NT for > 10 years while the irrigated system had been converted to NT 3 years before the start of this study. It remains to be seen if the C accrual rates decline with time in the irrigated system or if N2O emission rates decline or increase with time after conversion to NT. Mosier, A. R., A. D. Halvorson, G. A. Peterson, G. P. Robertson, and L. Sherrod. 2005. Measurement of net global warming potential in three agroecosystems. Nutrient Cycling in Agroecosystems 7: 67-76.

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2005 A number of experiments have addressed how increases in nitrogen availability increase the productivity and decrease the diversity of plant communities. We lack, however, a rigorous mechanistic understanding of how changes in abundance of particular species combine to produce changes in community productivity and diversity. Single experiments cannot provide insight into this issue because each species occurs only once per experiment, and each experiment is conducted in only one location; thus, it is impossible from single experiments to determine whether responses of particular species are consistent across environments or dependent on the particular environmental context in which the experiment was conducted. To address this issue, we assembled a dataset of 20 herbaceous species that were each represented in at least 6 different fertilization experiments and tested whether responses were general across experiments. Of the 20 species, one consistently increased in relative abundance and five consistently decreased across replicate experiments. A partially-overlapping group of 8 species displayed responses to nitrogen that varied predictably among experiments as a function of geographic location, neighboring species, or a handful of other community characteristics (ANPP, precipitation, species richness, relative abundance of focal species in control plots, and community composition). Thus, despite modest replication and a limited number of predictor variables, we were able to identify consistent patterns in response of 10 out of 20 species across multiple experiments. We conclude that the responses of individual species to nitrogen addition are often predictable, but that in most cases these responses are functions of the abiotic or biotic environment. Thus, a rigorous understanding of how plant species respond to nitrogen addition will have to consider not only the traits of individual plant species, but also aspects of the communities in which those plants live. Pennings, S. C., C. M. Clark, E. E. Cleland, S. L. Collins, L. Gough, K. L. Gross, D. G. Milchunas, and K. N. Suding. 2005. Do individual plant species show predictable responses to nitrogen addition across multiple experiments? Oikos 110: 547-555.

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2005 Field biologists and ecologists are starting to open new avenues of inquiry at greater spatial and temporal resolution, allowing them to "observe the unobservable" through the use of wireless sensor networks. Sensor networks facilitate the collection of diverse types of data (from temperature to imagery and sound) at frequcnt intervals - even multiple times per second - over large areas, allowing ecologists and field biologists to engage in intensive and expansive sampling and to unobtrusively collect new types of data. Moreover, real-time data flows allow researchers to react rapidly to events, thus extending the laboratory to the field. We review some existing uses of wireless sensor networks, identify possible areas of application, and review the underlying technologies in the hope of stimulating additional use of this promising technology to address the grand challenges of environmental science. Porter, J. H., P. Arzberger, H.-W. Braun, P. Bryant, S. H. Gage, T. Hansen, P. Hanson, C.-C. Lin, F.-P. Lin, T. K. Kratz, W. Michener, S. Shapiro, and T. Williams. 2005. Wireless sensor networks for ecology. BioScience 7: 561-572.

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2005 Studies on the occurrence and effects of specular reflection in midinfrared spectra of soils have shown that distortions due to specular reflection occur for both organic (humic acid) and non-organic fractions (carbonates, silica, ashed fraction of soil). The results explain why the spectra of CaCO3 in limed soils do not match published spectra and offer an explanation as to why the presence of inorganic C interferes with the development of calibrations for organic C. These results may also have implications for the use of mid-infrared spectra for quantitative and qualitative analysis of soils. For example, libraries of spectra collected by means other than diffuse reflectance would be largely useless for comparing mineral spectra to soil spectra. To obtain the best results with forages and grains, it is necessary to develop separate calibrations for different products, but this has not seemed to be a problem for diverse sets of soil samples with C contents of 0 to 5%. Mid-infrared calibrations have also appeared to be more robust than the corresponding near-infrared calibrations in that fewer outliers are found. However, the results discussed here indicate that at least for some soil types (e. g., large differences in mineralogy or C contents), separate calibrations may be necessary. Reeves, J. B. I., B. A. Francis, and S. K. Hamilton. 2005. Specular reflection and diffuse reflectance spectroscopy of soils. Applied Spectroscopy 59: 39-46.

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2005 The Kalamazoo River (Michigan, USA) has six run-of-the-river dams. The two hydropower reservoirs' residence times vary from 2 up to 11 days during the year. The four decommissioned impoundments residence times vary from a quarter of day to 1.5 days during the year. Inflows and outflows for the two hydropower reservoirs were sampled weekly in order to quantify the roles of reservoirs as sinks or transformers for nutrients. Three longitudinal river surveys from Morrow Lake inflow to Lake Allegan outflow were conducted at varying discharges. Special emphasis was placed on above and below Plainwell, Otsego, Allegan City and Trowbridge decommissioned impoundments. Despite their spatial proximity, a Total Maximum Daily Load for phosphorus (P) was deemed necessary for Lake Allegan to control summer algal blooms, whereas Morrow Lake lacks nuisance summer algal blooms. Lake Allegan outflow waters exhibited potential silica and nitrogen limitation in the late summer while Morrow Lake did not, which may explain the undesirable algal blooms in Lake Allegan. The longer residence time allows phytoplankton to build up to undesirable levels within Lake Allegan, but not in Morrow Lake. High algal abundance was observed in the Lake Allegan inflow, which may have resulted from Morrow Lake's algae transported downstream, or new algal biomass build-up as the river passed through semi-impounded reaches; the results reported here support the latter hypothesis. Reid, N. 2005. Biogeochemical impacts of major reservoirs on the Kalamazoo River. Zoology. MS. Thesis, Michigan State University, East Lansing, Michigan, USA.

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2005 Robertson, G. P. 2005. Biogenic trace gas emissions from terrestrial ecosystems: The need for full-cost accounting mitigation strategies. Proceedings of the 2005 International Plant Nutrition Conference, Beijing, China, PRC.

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2005 Agriculture meets a major human need and both affects and depends on all other life support systems. Current trends point to continued human population growth and ever higher levels of consumption as the global economy expands. This will stress the capacity of agriculture to meet food needs without further sacrificing the environmental integrity of local landscapes and the global environment. Agriculture's main challenge for the coming decades will be to produce sufficient food and fiber for a growing global population at an acceptable environmental cost. This challenge requires an ecological approach to agriculture that is largely missing from current management and research portfolios. Crop and livestock production systems must be managed as ecosystems, with management decisions fully informed of environmental costs and benefits. Currently, too little is known about important ecological interactions in major agricultural systems and landscapes and about the economic value of the ecosystem services associated with agriculture. To create agricultural landscapes that are managed for multiple services in addition to food and fiber will require integrative research, both ecological and socioeconomic, as well as policy innovation and public education. Robertson, G. P., and S. M. Swinton. 2005. Reconciling agricultural productivity and environmental integrity: A grand challenge for agriculture. Frontiers in Ecology and the Environment 3: 38-46.

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2005 Ecological theory regarding the role of species diversity in the functioning of terrestrial ecosystems may have important implications for the design and management of agricultural systems that are less reliant on inputs of synthetic chemical fertilizers and pesticides for fertility and pest control. However, much of the evidence supporting the importance of diversity in ecosystem function comes from grassland systems where biotic conditions and disturbance regimes differ from those in most managed systems. Furthermore, agricultural studies that purport to demonstrate the impacts of crop diversity on crop yields and pest regulation are often confounded with applications of chemical fertilizers and pesticides. My research aims to understand how ecological theory regarding the role of diversity in ecosystem function can be used to predict weed and crop yield response to increasing crop diversity. I examined the relationships between row-crop diversity and ecosystem functions related to weed population regulation and crop productivity in two long-term experimental agroecosystems. The first system compared corn grown in continuous monoculture and in rotation with soybean and winter wheat under two input management systems: conventional and organic-based. The second system was an experimental manipulation of crop diversity with no external chemical inputs of fertilizer or herbicides. Crop diversity was manipulated by growing corn, soybean, and winter wheat continuously and in two and three-crop rotations and with either no, one, or two cover crops annually. Weed communities and crop yield both varied in response to these treatments. In the first system, weed communities were most variable from year to year in the organic rotation, while corn yield variability was highest in the least diverse cropping system (conventional monoculture). In the diversity experiment, crop diversity had relatively little effect on the abundance or composition of weeds. Cover crops in wheat had strong suppressive effects on weeds in both continuous wheat grown in monocultures and in rotation with corn and soybean, while cover crops had little effect on weed abundance or species composition in corn and soybean. In contrast to the effect on weed communities, crop diversity had large effects on crop productivity. Corn yields varied across the diversity treatments and in the most diverse treatments were comparable to those in conventionally managed systems in the region. The positive effect of crop diversity on yields in corn was driven by increased soil N that was related to the number of legume species in the rotation (red clover and soybean). Soybean yields were also higher in rotations with higher crop diversity, while winter wheat yields were unaffected by the number of crops in the rotation. These results suggest that increasing crop diversity can have significant impacts on crop yields, particularly in corn, and may decrease the need for intensive chemical management by suppressing weeds during phases of the rotation that are conducive to high cover crop growth (i.e. winter wheat) and by increasing soil nitrogen and the competitive advantage of crops over weeds. Smith, R. G. 2005. Agroecosystem diversity: impacts on weed communities and crop yield. PhD Dissertation, Michigan State University, East Lansing, Michigan, USA.

474

2005 Understanding how communities of important soil invertebrates vary with land use may lead to the development of more sustainable land-use strategies. We assessed the abundance and species composition of earthworm communities across six replicated long-term experimental ecosystems that span a gradient in agricultural land-use intensity. The experimental systems include a conventional row-crop agricultural system, two lower-intensity row-crop systems (no-till and tilled organic input), an early successional old-field system, a 40–60 years old coniferous forest plantation, and an old-growth deciduous forest system. Earthworm populations varied among systems; they were lowest in the most intensively managed row-crop system (107 m−2) and coniferous forest (160 m−2); intermediate in the old-field (273 m−2), no-till (328 m−2) and tilled organic (344 m−2) cropping systems; and highest in the old-growth deciduous forest system (701 m−2). Juvenile Aporrectodea species were the most common earthworms encountered in intensively managed systems; other species made up a larger proportion of the community in less intensively managed systems. Earthworm community biomass and species richness also varied and were lowest in the conventional row-crop system and greatest in the old-growth forest system. These results suggest that both land-use intensity and land-use type are strong drivers of the abundance and composition of earthworm communities in agricultural ecosystems. Smith, R. G., C. P. McSwiney, A. S. Grandy, P. Suwanwaree, R. M. Snider, and G. P. Robertson. 2008. Diversity and abundance of earthworms across an agricultural land-use intensity gradient. Soil & Tillage Research 100: 83-88.

597

2005 A field study was conducted to determine if earthworm activity would affect the abundance and composition of weed seed banks in annual row-crops. The abundance of weed seeds in surface-deposited earthworm casts was determined in continuous monocultures and rotations that included corn, soybean, and winter wheat, with or without cover crop. Casts were collected weekly over the growing season and the weed seed content determined by direct germination in a heated greenhouse. Weed seed composition in surface casts was compared to that in the seed bank (0-5 cm) and soil surface by the same method. Earthworm cast production varied temporally and among crops and was higher in winter wheat compared to corn or soybean. The effect of crop rotation on cast production was significant only in soybean, with the highest production in monocultures compared to three-crop rotations. Weed seed densities were significantly higher in casts collected from winter wheat than corn or soybean. Comparisons of the composition and relative abundance of seeds in earthworm casts with the surface soil layer and seed batik suggest that earthworms contribute to redistribution of weed seeds over the growing season. (c) 2005 Elsevier B.V. All rights reserved. Smith, R. G., K. L. Gross, and S. Januchowski. 2005. Earthworms and weed seed distribution in annual crops. Agriculture, Ecosystems, and the Environment 108: 363-367.

184

2005 Human activities have increased N availability dramatically in terrestrial and aquatic ecosystems. Extensive research demonstrates that local plant species diversity generally declines in response to nutrient enrichment, yet the mechanisms for this decline remain unclear. Based on an analysis of >900 species responses from 34 N-fertilization experiments across nine terrestrial ecosystems in North America, we show that both trait-neutral and trait-based mechanisms operate simultaneously to influence diversity loss as production increases. Rare species were often lost because of soil fertilization, randomly with respect to traits. The risk of species loss due to fertilization ranged from >60% for the rarest species to 10% for the most abundant species. Perennials, species with N-fixing symbionts, and those of native origin also experienced increased risk of local extinction after fertilization, regardless of their initial abundance. Whereas abundance was consistently important across all systems, functional mechanisms were often system-dependent. As IN availability continues to increase globally, management that focuses on locally susceptible functional groups and generally susceptible rare species will be essential to maintain biodiversity. Suding, K. N., S. L. Collins, L. Gough, C. Clark, E. E. Cleland, K. L. Gross, D. G. Milchunas, and S. Pennings. 2005. Functional- and abundance-based mechanisms explain diversity loss due to N fertilization. PNAS 102: 4387-4392.

194

2005 Methane oxidation in well-aerated soils is a significant global sink for atmospheric methane. We examined the effects of soil disturbance (simulated tillage) and N-fertilizer additions on methane oxidation in old-growth forest, mid-successional, and no-till maize ecosystems in southwest Michigan, USA. We found highest oxidation rates in forest sites (about 30 mu g CH4-C m(-2) h(-1) on average), with average rates in successional and agricultural sites about 75 and 12% of this, respectively. In the forest and successional sites a one-time N-fertilizer addition (100 kg NH4NO3-N ha(-1)) significantly suppressed oxidation for the several weeks that inorganic N pools were elevated. There was no effect of fertilizer addition in the agricultural site, where available N was already high and oxidation rates low. Soil disturbance by itself had no detectable effect on fluxes in any of the sites. Results confirm the overriding importance of elevated N for suppressing CH4 oxidation in managed and unmanaged ecosystems, and suggest further that recovery of CH4 suppression following agriculture is related to slow-changing soil properties such as soil organic matter composition or microbial community structure. Suwanwaree, P., and G. P. Robertson. 2005. Methane oxidation in forest, successional, and no-till agricultural ecosystems: Effects of nitrogen and soil disturbance. Soil Science Society of America Journal 69: 1722-1729.

197

2005 Swinton, S. M. 2005. As ecosystem services are demanded of agriculture, what of agricultural economists? Western Economics Forum 4: 21-23.

495

2005 Treseder, K. K., S. J. Morris, and M. F. Allen. 2005. The contribution of root exudates, symbionts, and detritus to carbon sequestration in the soil. Pages 145-162 in R. W. Zobel and S. F. Wright, eds. Roots and Soil Management - Interactions between Roots and Soil. American Society of Agronomy, Madison, Wisconsin.

500

2005 Anaerobic microbial processes play particularly important roles in the biogeochemical functions of wetlands, affecting water quality, nutrient transport, and greenhouse gas fluxes. This study simultaneously examined nitrate and sulfate removal rates in sediments of five southwestern Michigan wetlands varying in their predominant water sources from ground water to precipitation. Rates were estimated using in situ push-pull experiments, in which 500 mL of anoxic local ground water containing ambient nitrate and sulfate and amended with bromide was injected into the near-surface sediments and subsequently withdrawn over time. All wetlands rapidly depleted nitrate added at ambient ground water concentrations within 5 to 20 h, with the rate dependent on concentration. Sulfate, which was variably present in porewaters, was also removed from injected ground water in all wetlands, but only after nitrate was depleted. The sulfate removal rate in ground water-fed wetlands was independent of concentration, in contrast to rates in precipitation-fed wetlands. Sulfate production was observed in some sites during the period of nitrate removal, suggesting that the added nitrate either stimulated sulfur oxidation, possibly by bacteria that can utilize nitrate as an oxidant, or inhibited sulfate reduction by stimulating denitrification. All wetland sediments examined were consistently capable of removing nitrate and sulfate at concentrations found in ground water and precipitation inputs, over short time and space scales. These results demonstrate how a remarkably small area of wetland sediment can strongly influence water quality, such as in the cases of narrow riparian zones or small isolated wetlands, which may be excluded from legal protection. Whitmire, S. L., and S. K. Hamilton. 2005. Rapid removal of nitrate and sulfate by freshwater wetland sediments. Journal of Environmental Quality 34: 2062-2071.

203

2005 Bills, G. F., M. Christensen, M. Powell, and G. Thorn. 2004. Saprobic soil fungi. Pages 271-302 in G. M. Mueller, G. F. Bills, and M. S. Foster, eds. Biodiversity of Fungi: Inventory and Monitoring Methods. Elsevier Academic Press, Amsterdam, The Netherlands.

295

2004 Bird, G. W., R. R. Harwood, J. E. Sanchez, M. F. Berney, J. Smeenk, and J. J. Smith. 2004. Role of nematodes in nutrient cycling. Phytopathology 94: S129.

303

2004 Brewer, E. A. 2004. Impacts of Calcium and Nitrogen on Carbon Stabilization in Soils of an Afforested Red Pine Stand. MS Thesis, Bradley University, Peoria, Illinois.

306

2004 Caldeira, K., M. G. Morgan, D. Baldocchi, P. G. Brewer, C. T. A. Chen, G.-J. Nabuurs, N. Nakicenovic, and G. P. Robertson. 2004. A portfolio of carbon management options. Pages 103-130 in C. B. Field and M. R. Raupach, eds. The Global Carbon Cycle. Island Press, Washington, DC, USA.

310

2004 Council for Agricultural Science and Technology (CAST). 2004. Climate Change and Greenhouse Gas Mitigation: Challenges and Opportunities for Agriculture. Task Force Report No. 141, Council for Agricultural Science and Technology (CAST), Ames, Iowa, USA.

321

2004 Dazzo, F. B. 2004. Applications of quantitative microscopy in studies of plant surface microbiology. Pages 503-550 in A. Varma, L. Abbott, D. Werner, and R. Hampp, eds. Plant Surface Microbiology. Springer Verlag, Germany.

326

2004 Dazzo, F. B. 2004. New CMEIAS image analysis software for computer-assisted microscopy of microorganisms and their ecology. Microscopy Today 12: 18-23.

328

2004 Dazzo, F. B. 2004. Production of anti-microbial antibodies and their utilization in studies of microbial autecology by immunofluorescence microscopy and in situ CMEIAS image analysis. Pages 911-932 in G. A. Kowalchuk, F. deBruijn, I. Head, A. Akkermans, and J. Elsas, eds. Molecular Microbial Ecology Manual, 2nd ed. Kluwer, Dordrecht, The Netherlands.

327

2004 Carbon (C) can be sequestered in the mineral soil after the conversion of intensively cropped agricultural fields to more extensive land uses such as afforested and natural succession ecosystems. Three land-use treatments from the long-term ecological research site at Kellogg biological station in Michigan were compared with a nearby deciduous forest. Treatments included a conventionally tilled cropland, a former cropland afforested with poplar for 10 years and an old field (10 years) succession. We used soil aggregate and soil organic matter fractionation techniques to isolate C pools that (1) have a high potential for C storage and (2) accumulate C at a fast rate during afforestation or succession. These fractions could serve as sensitive indicators for the total change in C content due to land-use changes. At the mineral soil surface (0-7 cm), afforesting significantly increased soil aggregation to levels similar to native forest. However, surface soil (0-7 cm) C did not follow this trend: soil C of the native forest site (22.9 t C ha(-1)) was still significantly greater than the afforested (12.6 t C ha(-1)) and succession (15.4 t C ha(-1)) treatments. However, when the 0-50 cm soil layer was considered, no differences in total soil C were observed between the cropland and the poplar afforested system, while the successional system increased total soil C (0-50 cm) at a rate of 0.786 t C ha(-1) yr(-1). Afforested soils sequestered C mainly in the fine intra-aggregate particulate organic matter (POM) (53-250 mum), whereas the successional soils sequestered C preferentially in the mineral-associated organic matter and fine intra-aggregate POM C pools. De Gryze, S., J. Six, K. Paustian, S. J. Morris, E. A. Paul, and R. Merckx. 2004. Soil organic carbon pool changes following land use conversions. Global Change Biology 10: 1120-1132.

2004 Stoichiometric analyses can be used to investigate the linkages between N and C cycles and how these linkages influence biogeochemistry at many scales, from components of individual ecosystems up to the biosphere. N-specific NH4+ uptake rates were measured in eight streams using short-term N-15 tracer additions, and C to N ratios (C:N) were determined from living and non-living organic matter collected from ten streams. These data were also compared to previously published data compiled from studies of lakes, ponds, wetlands, forests, and tundra. There was a significant negative relationship between C:N and N-specific uptake rate; C:N could account for 41% of the variance in N-specific uptake rate across all streams, and the relationship held in five of eight streams. Most of the variation in N-specific uptake rate was contributed by detrital and primary producer compartments with large values of C:N and small values for N-specific uptake rate. In streams, particulate materials are not as likely to move downstream as dissolved N, so if N is cycling in a particulate compartment, N retention is likely to be greater. Together, these data suggest that N retention may depend in part on C:N of living and non-living organic matter in streams. Factors that alter C:N of stream ecosystem compartments, such as removal of riparian vegetation or N fertilization, may influence the amount of retention attributed to these ecosystem compartments by causing shifts in stoichiometry. Our analysis suggests that C:N of ecosystem compartments can be used to link N-cycling models across streams. Dodds, W. K., E. Marti, J. L. Tank, J. Pontius, S. K. Hamilton, N. B. Grimm, W. B. Bowden, W. H. McDowell, B. J. Peterson, H. M. Valett, J. R. Webster, and S. Gregory. 2004. Carbon and nitrogen stoichiometry and nitrogen cycling in streams. Oecologia 140: 458-467

2004 Ecologists attempt to establish general principles from a vast range of organizational, spatial, and temporal scales (Belovsky et al. 2004). The process of developing generalities in ecology involves two approaches often not addressed in introductory science courses: inductive and deductive. One way of thinking about this is to consider the inductive approach as examining particular cases and deriving general conclusions or rules from them, and the deductive approach as using generalities to make specific predictions that can then be tested. In this issue of Frontiers, Knapp et al. (pp 483-91) underline the need for general principles or "rules" in ecology, and research that tests the predictive limits of those rules. The rules illustrated in this article are based on long-term studies from the Konza prairie and Sevilleta Long-Term Ecological Research (LTER) sites. Existing data from savanna grasslands in South Africa are used to test rules derived from Konza studies of grassland responses to fire. Ebert-May, D., K. S. Williams, E. P. Weber, J. Hodder, and D. Luckie. 2004. Practicing scientific inquiry: what are the rules? Frontiers in Ecology and the Environment 2: 492-493.

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2004 Stable isotope enrichment experiments offer a potentially powerful way to examine the base of aquatic food webs, but interpretation of the data from these experiments may be confounded by problems such as selective ingestion/assimilation of bulk food sources by consumers, variable tracer enrichment over time, and the failure of consumers to approach isotopic equilibrium with the tracer in their diets over the course of the experiment. Our study examined data from a stable isotope addition experiment in which N-15-labeled NH4+ was added to a midwestern US stream. A compartment model was used to provide insights into the kinetics of N-15 uptake and release from algae, heterotrophic microbes colonizing detritus, and invertebrate consumers. The model accounted for temporal variation in the degree of isotopic enrichment and did not require the assumption of isotopic eqilibrium between consumers and their diets. The importance of instream production (i.e., growth of algae and microbes within the study reach during the experiment) relative to allochthonous and upstream inputs was similar to38 to 50% for heptageniids and Psephenus, 10 to 20% for Orconectes propinquus, Gammarus, hydropsychids, and larval Stenelmis, and <10% for the filter-feeding Similium and the unionid mussel Pleurobema sintoxia. The alternative choices of algae or heterotrophic microbes as the basis of consumer diets made little difference in these estimates, even though the microbes became more IN-enriched than the algae because microbes had higher turnover rates. These results were subject to a number of caveats, and guidelines for experimental design are suggested for future studies to help address some of these problems. Hamilton, S. K., J. L. Tank, D. F. Raikow, E. Siler, N. J. Dorn, and N. Leonard. 2004. The role of in-stream vs. allochthonous N in stream food webs: Modeling the results of a nitrogen isotope addition experiment. Journal of the North American Benthological Society 23: 429-448.

2004 Kavdir, Y., and A. J. M. Smucker. 2004. Effects of rye roots and shoots on soil aggregate erosion rate. Journal of Harran Uni. Agr. Fac. 8: 29-32.

374

2004 We examined the effects of fertilization and gypsy moth defoliation of hybrid poplar (Populus X canadensis Moench 'Eugenei') on ectomycorrhizal (ECM) and arbuscular mycorrhizal (AM) fungal colonization, ECM richness, and ECM composition in the summers of 1997 and 1998. The factorial experiment included two levels of defoliation (defoliated and control) and fertilization (100 kg N.ha(-1) and control). Gypsy moth (Lymantria dispar L.) populations were manipulated to obtain defoliation in the summer of 1996, 1997, and 1998; fertilization subplots were fertilized with NH4NO3 (100 kg N.ha(-1)) in the spring of these years. There were no significant effects of defoliation on ECM or AM colonization in either year; there was a significant (p less than or equal to 0.05) decline in AM colonization in fertilized plots in 1997 and a significant interaction between defoliation and fertilization effects on ECM colonization in 1997. In the nondefoliated plots, ECM fungal colonization increased, whereas AM colonization decreased because of fertilization. In the defoliated plots, neither ECM nor AM colonization was affected by fertilization. ECM community composition and richness were unchanged by any treatment. The small and transient effects of defoliation and fertilization on poplar AMs and ECMs demonstrate the tolerance of these early-successional trees to defoliation and their ability to rapidly use high levels of available nitrogen. Kosola, K. R., D. M. Durall, G. P. Robertson, D. I. Dickmann, D. Parry, C. A. Russell, and E. A. Paul. 2004. Resilience of mycorrhizal fungi on defoliated and fertilized hybrid poplars. Canadian Journal of Botany 82: 671-680.

104

2004 Landis, D. A., T. B. Fox, and A. C. Costamagna. 2004. Impact of multicolored Asian lady beetle as a biological control agent. American Entomologist 50: 153-155.

382

2004 Lynch, M. D. J. 2004. Species richness and composition of soil Basidiomycota. MS Thesis, University of Western Ontario, London, Ontario, Canada.

387

2004 Menalled, F., and D. A. Landis. 2004. Conservation of ground beetles in annual crops. Pages 593-595 in J. Capinera, ed. Encyclopedia of Entomology. Kluwer Academic Press, Dordrecht, The Netherlands.

393

2004 Menalled, F. D., D. A. Landis, and L. E. Dyer. 2004. Research and extension supporting ecologically based IPM systems. Journal of Crop Improvement 11: 153-174.

396

2004 We measured denitrification and total nitrate uptake rates in a small stream (East Fork of Walker Branch in eastern Tennessee) using a new field N-15 tracer addition and modeling approach that quantifies these rates for entire stream reaches. The field experiment consisted of an 8-h addition of 99 atom% (KNO3)-N-15 and a conservative solute tracer. Two 15N tracer addition experiments were performed on consecutive days, the first under ambient NO concentrations (23 mug N L-1) and the second with a NO3- addition of approximately 500 mug N L-1. We fit first-order NO3- uptake and two-box denitrification models to the longitudinal measurements of tracer N-15 in dissolved NO3-, N-2, and N2O in stream water to determine rates. Total NO; uptake rates were 0.028 m(-1) (0.32 mug N m(-2) s(-1)) and 0.01 m(-1) (1.6 mug N m(-2) s(-1)) under ambient NO3- and with NO3- addition, respectively. Denitrification rates were 0.0046 m(-1) (uncertainty range of 0.002 to 0.008 m(-1)) and 9 x 10(-5) m(-1) (uncertainty range of 3 x 10(-5) to 21 x 10(-5) m(-1)) under ambient NO3- and with NO3- addition, respectively. Denitrification resulted almost exclusively in N-2 production (>99%) and comprised about 16% (+/-10%) of total NO3- uptake rate under ambient NO3- concentrations and about 1% (+/-1%) of total NO3- uptake rate with NO3- addition. Denitrification rate expressed on a mass flux basis was about 12 mumol m(-2) h(-1) under ambient NO3- concentrations, a value within the range reported for other streams with low NO3- concentrations. Mullholland, P. J., H. M. Valett, J. R. Webster, S. A. Thomas, L. N. Cooper, S. K. Hamilton, and B. J. Peterson. 2004. Stream denitrification and total nitrate uptake rates measured using a field 15N tracer addition approach. Limnology and Oceanography 49: 809-820.

127

2004 Digital micrographs of micro-organisms in their natural habitats are highly complex, posing major challenges for image processing and advanced analysis [1]. This image complexity is further exacerbated when the microbes have been stained with general colored dyes to increase their contrast and visualization, or with specific chromophores linked to molecular probes that reveal unique cellular components or specific biochemical activities on their surface or interior. Depending on the stain used, the color of the microbes in the digital image can provide useful information on their in-situ biochemical, physiological, ecological and phylogenetic characteristics without the need for their laboratory cultivation. Thus, color images of microbes can contain large amounts of very useful information so long as the foreground objects of interest can be accurately segmented and analyzed. Herein lies the problem: the pixels that comprise the microbial objects of interest typically have a variable color range and therefore these foreground objects cannot be accurately defined using color segmentation routines whose operation is based on isolation of pixels with a single RGB value. The goal of our work summarized here is to develop a system that can semi-automate the segmentation of multicolored foreground microbes so they can be analyzed accurately in digitized color images that also contain complex and usually noisy backgrounds [2,3]. The system described here is a component of CMEIAS (Center for Microbial Ecology image Analysis System) whose combined purpose is to strengthen microscopybased approaches for understanding microbial ecology. Reddy, C. K., and F. B. Dazzo. 2004. Computer-assisted segmentation of bacteria in color micrographs. Microscopy & Analysis 18: 5-7.

610

2004 Robertson, G. P. 2004. Abatement of nitrous oxide, methane, and the other non-CO2 greenhouse gases: The need for a systems approach. Pages 493-506 in C. B. Field and M. R. Raupach, eds. The Global Carbon Cycle. Island Press, Washington, DC, USA.

441

2004 Agriculture’s contribution to radiative forcing is principally through its historical release of carbon in soil and vegetation to the atmosphere and through its contemporary release of nitrous oxide (N2O) and methane (CH4). The sequestration of soil carbon in soils now depleted in soil organic matter is a well-known strategy for mitigating the buildup of CO2 in the atmosphere. Less well-recognized are other mitigation potentials. A full-cost accounting of the effects of agriculture on greenhouse gas emissions is necessary to quantify the relative importance of all mitigation options. Such an analysis shows nitrogen fertilizer, agricultural liming, fuel use, N2O emissions, and CH4 ﬂuxes to have additional signiﬁcant potential for mitigation. By evaluating all sources in terms of their global warming potential it becomes possible to directly evaluate greenhouse policy options for agriculture. A comparison of temperate and tropical systems illustrates some of these options. Robertson, G. P., and P. R. Grace. 2004. Greenhouse gas fluxes in tropical and temperate agriculture: The need for a full-cost accounting of global warming potentials. Environment, Development and Sustainability 6:51-63.

161

2004 Environmental research in agriculture is today largely reactive, focused on problems at small scales and conducted within narrow disciplinary boundaries. This approach has worked to abate a number of environmental problems created by agriculture, but it has not provided effective solutions for many of the most recalcitrant ones. Furthermore, the approach fails to position agriculture to deliver new environmental benefits that the public and policymakers increasingly demand. A new vision is needed for environmental research in agriculture-one that is anticipatory; promotes long-term, systems-level research at multiple scales; better incorporates important interactions between the biophysical and social sciences; and provides for the proper evaluation of deployed solutions. Achieving this vision will require major changes in funding strategies, in institutional reward structures, and in policies that presently inhibit collaborations across disciplinary and institutional boundaries. It is, nevertheless, time to act. Robertson, G. P., J. C. Broome, E. A. Chornesky, J. R. Frankenberger, P. Johnson, M. Lipson, J. A. Miranowski, E. D. Owens, D. Pimentel, and L. A. Thrupp. 2004. Rethinking the vision for environmental research in U.S. agriculture. BioScience 54: 61-65.

156

2004 Large-scale outbreaks of defoliating insects are common in temperate forests. These outbreaks are thought to be responsible for substantial cycling of nitrogen (N), and its loss from the system. Gypsy moth (Lymantria dispar) populations within poplar plots were manipulated over 2 years so that the ecosystem-wide consequences of catastrophic defoliation on N cycling could be examined. The quantities of N in leaf litter-fall, ammonia volatilization and soil N pools were estimated across the two seasons. Defoliated leaf biomass was estimated from experimentally derived approximate digestibility factors and added to the mass of senesced leaf to determine total annual leaf production. Throughout the growing season the defoliation treatment peaked at about 40% in year 1 and 100% in year 2. Rapid regrowth after defoliation meant that only 45% of the annual leaf biomass was consumed in the defoliation treatment in year 2, while control plots suffered about 20% consumption each year. In each year, defoliated plots produced 20% more leaf biomass and N than the controls, a phenomenon attributed to compensatory photosynthesis. No substantial losses of N via ammonia volatilization, nitrous oxide emission or nitrate leaching were observed. Neither was there any sustained or substantial gain in the soils microbial biomass or inorganic N pools. These observations suggest that the defoliated poplars were able to compete with soil microbes and N loss mechanisms for soil N as it became available, thereby ameliorating the effects of defoliation on soil nitrogen cycling. We conclude from this study that the N mineralized from defoliation residues was conserved in this plantation ecosystem. Russell, C. A., K. R. Kosola, E. A. Paul, and G. P. Robertson. 2004. Nitrogen cycling in poplar stands defoliated by insects. Biogeochemistry 68: 365-381.

163

2004 The discovery of the soybean aphid, Aphis glycines Matsumura, in U.S. soybean production systems in 2000 has provided a unique opportunity to study the interaction of a new invader with existing natural enemy communities. One research thrust has been examining the role of predators in soybean aphid dynamics in the Midwest. We discuss the roles of predatory arthropods in field crops and set forth a conceptual model that we have followed to identify key predators in the soybean aphid system. We identify Orius insidiosus (Say) and Harmonia axyridis (Pallas) as potentially key predators and show our findings on their phenology in soybean fields and their impact on soybean aphid population dynamics. Finally, we discuss how this information can be used in integrated pest management programs for soybean aphid and point to gaps in our knowledge where future studies are needed. Rutledge, C. E., R. J. O'Neil, T. B. Fox, and D. A. Landis. 2004. Soybean aphid predators and their use in IPM. Annals of the Entomological Society of America 97: 240-248.

164

2004 In this study, we investigated the impact of cropping system management on C and N pools, crop yield, and N leaching in a long-term agronomic experiment in Southwest Michigan. Four management types, conventional (CO), integrated fertilizer (IF), integrated compost (IC), and transitional organic (TO) were applied to two crop sequences, a corn (Zea mays L.)-corn-soybean [Glycine mar (L.) Merr.]-wheat (Triticum aestivum L.) rotation and continuous corn, which were grown with and without cover crops in the IF, IC, and TO managements. Using compost as a fertility source and reducing the use of herbicides and other chemicals resulted in long-term changes in soil organic matter pools such TO greater than or equal to IC > IF greater than or equal to CO for total C and N and for the labile C and N measured through aerobic incubations at 70 and 150 d. Mineralizable N varied within the rotation, tending to increase after soybean and decrease after corn production in all systems. Corn yield was closely associated with 70-d N mineralization potential, being greatest for first-year corn with cover and least for continuous corn without cover under all management types. Although the TO and IC systems produced the lowest yield for second-year or continuous corn, the combination of soybean and wheat plus red clover (Trifolium pratense L.) always supported high yield for first-year corn. Fall nitrate level and nitrate leaching were higher for commercially fertilized corn than for any other crop or for compost-amended corn. Sanchez, J. E., R. R. Harwood, T. C. Willson, K. Kizilkaya, J. Smeenk, E. Parker, E. A. Paul, B. D. Knezek, and G. P. Robertson. 2004. Integrated agricultural systems: Managing soil carbon and nitrogen for productivity and environmental quality. Agronomy Journal 96: 769-775.

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2004 Management programs for major forest defoliators such as gypsy moths or forest tent caterpillars, and crop pests such as the European corn borer have shifted from broad-spectrum insecticides to more environmentally benign microbial pesticides such as Bacillus thuringiensis (foliage sprays and transgenic toxin expression in plant tissues). Phytochemically resistant host plants and natural enemies have been used as alternative pest management strategies (including generalist tachinid ﬂies such as Compsilura, viruses, microsporidians, and fungi), but all of these have some non-target impacts, as described from literature review. A sequence of lab and ﬁeld studies were conducted to determine non-target impacts on native Lepidoptera in North America. The conclusions reached are that a decision not to spray Bt pesticides (i.e. to allow defoliation and natural pest outbreaks to run their course) could be as bad or worse for non-target Lepidoptera as the microbial insecticides would be. The important concept that must be maintained is that all pest management programs have some risk of negative non-target impacts, but it is the magnitude and relative importance that will remain the most critical issue for environmental impacts and pest management. Scriber, J. M. 2004. Non-target impacts of forest defoliator management options: Decision for no spraying may have worse impacts on non-target Lepidoptera that Bacillus thuringiensis insecticides. Journal of Insect Conservation 8: 241-261.

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2004 Smith, J. J. 2004. Impacts of soil ecosystem disturbance on nematode community structure. MS Thesis, Dept. of Entomology, Michigan State University, East Lansing, Michigan, USA.

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2004 The classification of agricultural tillage systems has proven challenging in the past using traditional classification methods due to the similarity of spectral reflectance signatures of soils and senescent crop residues. In this study, five classification methods were examined to determine the most suitable classification algorithm for the identification of no-till (NT) and traditional tillage (TT) cropping methods: minimum distance (MD), Mahalanobis distance, Maximum Likelihood (ML), spectral angle mapping (SAM), and the cosine of the angle concept (CAC). A Landsat ETM+ image acquired over southern Michigan and northern Indiana was used to test these classification methods. Each classification method was validated with 293 ground truth sampling locations collected commensurate with the satellite overpass. Classification accuracy was then assessed using error matrix analysis, Kappa statistics, and tests for statistical significance. The results indicate that of the classification routines examined, the two spectral angle methods were superior to the others. The cosine of the angle concept algorithm outperformed all the other classification routines for tillage practice identification and mapping, yielding an overall accuracy of 97.2% (Kappa = 0.959). (C) 2004 Elsevier Inc. All rights reserved. South, S. R., J. Qi, and D. P. Lusch. 2004. Optimal classification methods for mapping agricultural tillage practices. Remote Sensing of Environment 91: 90-97.

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2004 An integrative approach was used to obtain pure cultures of previously uncultivated members of the divisions Acidobacteria and Verrucomicrobia from agricultural soil and from the guts of wood-feeding termites. Some elements of the cultivation procedure included the following: the use of agar media with little or no added nutrients; relatively long periods of incubation (more than 30 days); protection of cells from exogenous peroxides; and inclusion of humic acids or a humic acid analogue (anthraquinone disulfonate) and quorum-signaling compounds (acyl homoserine lactones) in growth media. The bacteria were incubated in the presence of air and in hypoxic (1 to 2% O-2 [vol/vol]) and anoxic atmospheres. Some bacteria were incubated with elevated concentrations of CO2 (5% [vol/vol]). Significantly more Acidobacteria were found on isolation plates that had been incubated with 5% CO2. A simple, high-throughput, PCR-based surveillance method (plate wash PCR) was developed. This method greatly facilitated detection and ultimate isolation of target bacteria from as many as 1,000 colonies of nontarget microbes growing on the same agar plates. Results illustrate the power of integrating culture methods with molecular techniques to isolate bacteria from phylogenetic groups under-represented in culture. Stevenson, B. S., S. A. Eichorst, J. T. Wertz, and T. M. Schmidt. 2004. New strategies for cultivation and detection of previously uncultured microbes. Applied and Environmental Microbiology 70: 4748-4755.

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2004 The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions. nosZ gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RELP). The total nosZ RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total nosZ profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify nosZ identity. The sequence diversity of nosZ clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct nosZ RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for nosZ RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of nosZ clones into an interleaved Michigan soil cluster whose cultured members are alpha-Proteobacteria. Only four nosZ sequences from cultivated soil and one from the native soil were related to sequences found in gamma-Proteobacteria. Sequences from the native field formed a distinct, closely related cluster (D-mean = 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (D-mean = 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of nosZ sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community. Stres, B., I. Mahne, G. Avgustin, and J. M. Tiedje. 2004. Nitrous oxide reductase (nosZ) gene fragments differ between native and cultivated Michigan soils. Applied and Environmental Microbiology 70: 301-309.

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2004 There is increasing interest in developing better predictive tools and a broader conceptual framework to guide the restoration of degraded land. Traditionally, restoration efforts have focused on re-establishing historical disturbance regimes or abiotic conditions, relying on successional processes to guide the recovery of biotic communities. However, strong feedbacks between biotic factors and the physical environment can alter the efficacy of these successional-based management efforts. Recent experimental work indicates that some degraded systems are resilient to traditional restoration efforts owing to constraints such as changes in landscape connectivity and organization, loss of native species pools, shifts in species dominance, trophic interactions and/or invasion by exotics, and concomitant effects on biogeochemical processes. Models of alternative ecosystem states that incorporate system thresholds and feedbacks are now being applied to the dynamics of recovery in degraded systems and are suggesting ways in which restoration can identify, prioritize and address these constraints. Suding, K. N., K. L. Gross, and G. Houseman. 2004. Alternative states and positive feedbacks in restoration ecology. Trends in Ecology & Evolution 19: 46-53.

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2004 Bird, G. W. 2003. Role of integrated pest management and sustainable development. Pages 73-85 in K. S. Maredia, D. Dakouo, and D. Mota-Sanchez, eds. Integrated Pest Management in the Global Arena. CABI Publishing, Cambridge, Massachusetts, USA.

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2003 The hypothesis that soil light fraction and heavy fraction harbor distinct eubacterial communities and have differing numbers and sizes of bacterial cells was tested in three agronomic cropping systems. This hypothesis would imply that these soil fractions are distinct microbial habitats. Shoot residue and rhizosphere soil were also included in the analysis. Terminal restriction fragment length polymorphism (T-RFLP) of 16S ribosomal DNA was used to assay eubacterial community structure. T-RFLP profiles were affected by both soil fraction and cropping system, accounting for 35–50% of the variance in the profiles. T-RFLP profiles separated samples into two distinct eubacterial habitats: soil heavy fraction, which includes the mineral particles and associated humified organic matter, and soil light fraction/shoot residue and rhizosphere, which includes particulate soil organic matter. Differences were not based on organic C content of fractions alone; T-RFLP profiles were also differentiated by cropping system and by rhizosphere versus light fraction/shoot residue. Heavy fraction communities had the least amount of random variability in T-RFLP profiles, resulting in the clearest cropping system effects, while rhizosphere and shoot residue communities were the most variable. Profiles from organically managed corn soil were more variable than for either conventionally managed corn or alfalfa. The log number of bacterial cells per gram fraction was affected by soil fraction but not cropping system, being highest in the light fraction. The percentage of cells >0.18 μm3 was also greater in the light fraction than in other fractions. While bacterial cell density was generally correlated with C content of the soil fraction, heavy fraction did have a significantly greater number of cells per μg C than other soil fractions. The results show that habitat diversity in soil, related both to the amounts and types of organic matter, as well as other potential factors, are important in maintaining the high soil bacterial species diversity and evenness that is found in soil. Blackwood, C. B. 2003. Eubacterial community structure and population size within the soil light fraction, rhizosphere, and heavy fraction of several agricultural systems. Soil Biology and Biochemistry 35: 1245-1255.

2003 Terminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacterial communities. These samples included soil collected from three regions of the United States, soil fractions derived from three agronomic field treatments, soil samples taken from within one meter of each other in an alfalfa field, and replicate laboratory bioreactors. Cluster analysis by Ward's method and by the unweighted-pair group method using arithmetic averages (UPGMA) were compared. Ward's method was more effective at differentiating major groups within sets of profiles; UPGMA had a slightly reduced error rate in clustering of replicate profiles and was more sensitive to outliers. Most replicate profiles were clustered together when relative peak height or Hellinger-transformed peak height was used, in contrast to raw peak height. Redundancy analysis was more effective than cluster analysis at detecting differences between similar samples. Redundancy analysis using Hellinger distance was more sensitive than that using Euclidean distance between relative peak height profiles. Analysis of Jaccard distance between profiles, which considers only the presence or absence of a terminal restriction fragment, was the most sensitive in redundancy analysis, and was equally sensitive in cluster analysis, if all profiles had cumulative peak heights greater than 10,000 fluorescence units. It is concluded that T-RFLP is a sensitive method of differentiating between microbial communities when the optimal statistical method is used for the situation at hand. It is recommended that hypothesis testing be performed by redundancy analysis of Hellinger-transformed data and that exploratory data analysis be performed by cluster analysis using Ward's method to find natural groups or by UPGMA to identify potential outliers. Analyses can also be based on Jaccard distance if all profiles have cumulative peak heights greater than 10,000 fluorescence units. Blackwood, C. B., T. Marsh, S.-H. Kim, and E. A. Paul. 2003. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Applied and Environmental Microbiology 69: 926-932.

2003 Soil microbial communities are integrally involved in biogeochemical cycles and their activities are crucial to the productivity of terrestrial ecosystems. Despite the importance of soil microorganisms, little is known about the distribution of microorganisms in the soil or the manner in which microbial community structure responds to changes in land management. We investigated the structure of microbial communities in the soil over two years in a series of replicated plots, that included, cultivated fields, fields abandoned from cultivation and fields with no history of cultivation. Microbial community structure was examined by monitoring the relative abundance of ribosomal RNA (rRNA) from seven of the most common bacterial groups in soil (the Alpha and Beta Proteobacteria, Actinobacteria, Cytophagales, Planctomycetes, Verrucomicrobia and the Acidobacteria) and the Eukarya. These data reveal that soil microbial communities are dynamic, capable of significant change at temporal scales relative to seasonal events. However, despite temporal change in microbial community structure, the rRNA relative abundance of particular microbial groups is affected by the local environment such that recognizable patterns of community structure exist in relation to field management. Buckley, D. H., and T. M. Schmidt. 2003. Diversity and dynamics of microbial communities in soils from agroecosystems. Environmental Microbiology 5: 441-452.

2003 Increases in the concentrations of greenhouse gases, carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and halocarbons in the atmosphere due to human activities are associated with global climate change. The concentration of N2O has increased by 16% since 1750. Although the atmospheric concentration of N2O is much smaller (314 ppb in 1998) than of CO2 (365 ppm), its global warming potential ( cumulative radiative forcing) is 296 times that of the latter in a 100-year time horizon. Currently, it contributes about 6% of the overall global warming effect but its contribution from the agricultural sector is about 16%. Of that, almost 80% of N2O is emitted from Australian agricultural lands, originating from N fertilisers (32%), soil disturbance (38%), and animal waste (30%). Nitrous oxide is primarily produced in soil by the activities of microorganisms during nitrification, and denitrification processes. The ratio of N2O to N-2 production depends on oxygen supply or water-filled pore space, decomposable organic carbon, N substrate supply, temperature, and pH and salinity. N2O production from soil is sporadic both in time and space, and therefore, it is a challenge to scale up the measurements of N2O emission from a given location and time to regional and national levels. Estimates of N2O emissions from various agricultural systems vary widely. For example, in flooded rice in the Riverina Plains, N2O emissions ranged from 0.02% to 1.4% of fertiliser N applied, whereas in irrigated sugarcane crops, 15.4% of fertiliser was lost over a 4-day period. Nitrous oxide emissions from fertilised dairy pasture soils in Victoria range from 6 to 11 kg N2O-N/ ha, whereas in arable cereal cropping, N2O emissions range from < 0.01% to 9.9% of N fertiliser applications. Nitrous oxide emissions from soil nitrite and nitrates resulting from residual fertiliser and legumes are rarely studied but probably exceed those from fertilisers, due to frequent wetting and drying cycles over a longer period and larger area. In ley cropping systems, significant N2O losses could occur, from the accumulation of mainly nitrate-N, following mineralisation of organic N from legume-based pastures. Extensive grazed pastures and rangelands contribute annually about 0.2 kg N/ha as N2O (93 kg/ha per year CO2-equivalent). Tropical savannas probably contribute an order of magnitude more, including that from frequent fires. Unfertilised forestry systems may emit less but the fertilised plantations emit more N2O than the extensive grazed pastures. However, currently there are limited data to quantify N2O losses in systems under ley cropping, tropical savannas, and forestry in Australia. Overall, there is a need to examine the emission factors used in estimating national N2O emissions; for example, 1.25% of fertiliser or animal- excreted N appearing as N2O (IPCC 1996). The primary consideration for mitigating N2O emissions from agricultural lands is to match the supply of mineral N ( from fertiliser applications, legume-fixed N, organic matter, or manures) to its spatial and temporal needs by crops/pastures/trees. Thus, when appropriate, mineral N supply should be regulated through slow-release (urease and/or nitrification inhibitors, physical coatings, or high C/N ratio materials) or split fertiliser application. Also, N use could be maximised by balancing other nutrient supplies to plants. Moreover, non-legume cover crops could be used to take up residual mineral N following N-fertilised main crops or mineral N accumulated following legume leys. For manure management, the most effective practice is the early application and immediate incorporation of manure into soil to reduce direct N2O emissions as well as secondary emissions from deposition of ammonia volatilised from manure and urine. Current models such as DNDC and DAYCENT can be used to simulate N2O production from soil after parameterisation with the local data, and appropriate modification and verification against the measured N2O emissions under different management practices. In summary, improved estimates of N2O emission from agricultural lands and mitigation options can be achieved by a directed national research program that is of considerable duration, covers sampling season and climate, and combines different techniques ( chamber and micrometeorological) using high precision analytical instruments and simulation modelling, under a range of strategic activities in the agriculture sector. Dalal, R. C., W. Wang, G. P. Robertson, and W. J. Parton. 2003. Nitrous oxide emission from Australian agricultural lands and mitigation options: a review. Australian Journal of Soil Research 41: 165-195

2003 Management practices that influence the quantity of C inputs returned to the soil from cropping systems and compost applications alter subsequent biotic activity broadly, contribute to seasonal fluctuations in nutrient dynamics, and may increase C sequestration. The effects of crop rotations and compost applications on soil-C sequestration and decompostion, and the turnover time of C-4-derived corn C were assessed via changes in the C content and C-13 values of particulate organic matter (POM) and total soil organic C (SCIC). The majority of organic inputs entered the POM fraction, defined as the sand-sized soil separates remaining on a 53-mum sieve after removal of residues (>2 mm), dispersion in 5% sodium polyphosphate, and 12 h of shaking. Before the application of compost to soil, 85% of the C in the compost material was classified as PCIM. Measurements of POM-C in the soil were 45% higher and SOC was 16% greater where compost was applied in place of N fertilizer. Addition of compost to POM-C diminished the value of POM as an indicator of short-term changes in nutrient dynamics. However, POM-C remaining from compost applications made during the period 1993 to 1997 may be an indicator of enhanced macroaggregate stability: improved soil tilth and the retention of soil C and N. The turnover time of C4-derived C in the POM fraction was 11 years compared with 22 years in SOC. The presence of compost C did not affect the turnover time of corn-derived C. High cropping intensity and chisel plow management increased C sequestration relative to the preceding alfalfa management. Fortuna, A. M., E. A. Paul, and R. R. Harwood. 2003. The effects of compost and crop rotations on carbon turnover and the particulate organic matter fraction. Soil Science 168: 434-444.

2003 Nitrification potential is the maximum capacity of a soil's population of nitrifying bacteria to transform NH4+-N to NO3--N. Time of season and the effect of several management practices on nitrification potentials were measured via an amended slurry method, shaken for 24 h at 25 degreesC. Management strategies that reduce potential nitrification rates without limiting plant N uptake may increase the ratio of plant biomass to plant N content (PB:N), the aboveground net primary production (ANPP) per unit of N in ANPP, and decrease the amount of NO3- available for leaching, and/or conversion to N2O. Sites were located in Hickory Corners, MI, USA, on Haplic Luvisols. Management practices included: substitution of compost for N fertilizer, use of a rotation in place of continuous maize and the addition of cover crops. A previously tilled, successional grassland was used as a contrast to agricultural managements. Where N fertilizer was applied, nitrification potential increased in late May and again in late August-October. The seasonal pattern was similar but less pronounced where compost was applied. Nitrification rates were 4.2 times greater than that of the successional site when N fertilizer was applied. Use of N fertilizer increased nitrification potentials 1.5 times above treatments where compost was applied during 1998 and 1999 in the 6th and 7th years of the rotation. In some instances, nitrification potentials could be correlated with in situ NO3--N measurements. Average PB:Ns in the fertilizer management were greater or equivalent to the successional grassland site. Compost increased PB:N above that of N fertilizer. Utilization of compost decreased nitrification potentials, maintained yields, and increased PB:N. The crop N content was lower when compost was applied. Thus, grain and stover quality may be lowered and need to be monitored. (C) 2003 Elsevier Science B.V. All rights reserved. Fortuna, A. M., R. R. Harwood, G. P. Robertson, J. W. Fisk, and E. A. Paul. 2003. Seasonal changes in nitrification potential associated with application of N fertilizer and compost in maize systems of southwest Michigan. Agriculture, Ecosystems and the Environment 97: 285-293.

2003 The uniformity, low cost and ease of application associated with inorganic fertilizers have diminished the use of organic nutrient sources. Concern for food safety, the environment and the need to dispose of animal and municipal wastes have focused attention on organic sources of N such as animal-derived amendments, green manures, and crop rotations. Managing organic N sources to provide sufficient N for crop growth requires knowledge of C and N decomposition over several years, particularly where manure and compost are applied. We report a comparison of compost and chemical fertilizer, use of a corn-corn-soybean-wheat rotation compared to continuous corn and the use of cover crops. Nitrogen (150d) and C incubations (317 d) were conducted to determine the effect of cropping system and nutrient management on: N mineralization potential (NMP), the mineralizable organic N pool (N.), the mean residence time (MRT) of No, C mineralization (C-min), and soil organic carbon (SOC) pool sizes and fluxes. Compost applications over 6 y increased the resistant pool of C by 30% and the slow pool of C by 10%. The compost treatment contained 14% greater soil organic C than the fertilizer management. Nitrogen was limiting on all compost treatments with the exception of first year corn following wheat fallow and clover cover crop. The clover cover crop and wheat-fallow increased inorganic N in both nutrient managements. We recommend that growers adjust their N fertilizer recommendation to reflect the quantity and timing of N mineralized from organic N sources and the N immobilization that can be associated with compost or other residue applications. Proper management of nutrients from compost, cover crops and rotations can maintain soil fertility and increase C sequestration. Published by Elsevier Science Ltd. Fortuna, A. M., R. R. Harwood, K. Kizilkaya, and E. A. Paul. 2003. Optimizing nutrient availability and potential carbon sequestration in an agroecosystem. Soil Biology and Biochemistry 35: 1005-1013.

2003 Gage, S. H. 2003. Climate variability in the North Central Region: Characterizing drought severity patterns. Pages 56-73 in D. Greenland, D. Goodin, and R. Smith, eds. Climate Variability and Ecosystem Response at Long Term Ecological Research Sites. Oxford University Press, Oxford, UK.

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2003 Grace, P. R., M. C. Jain, L. W. Harrington, and G. P. Robertson. 2003. Long-term sustainability of the tropical and subtropical rice and wheat system: An environmental perspective. Pages 27-43 in J. K. Ladha, J. E. Hill, J. M. Duxbury, R. K. Gupta, and R. J. Buresh, eds. Improving the Productivity and Sustainability of Rice-Wheat System: Issues and Impacts. American Society of Agronomy Special Publication 65, Madison, Wisconsin, USA.

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2003 Holdaway-Dopp, H. A. 2003. Changes in microbial community responses to gradients of carbon, nitrogen, and wetting cycles in ceoncentric layers of soil macro-aggregates. MS Theses, Michigan State University, East Lansing, Michigan, USA.

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2003 Population models indicate that managing agroecosystems to reduce weed seed survival in soil seedbanks has the potential to decrease weed populations. A series of bioassays was conducted in soil collected from the Long Term Ecological Research site at the Kellogg Biological Station in Hickory Corners, MI. We determined the effect of 1) contrasting agricultural management, 2) burial method, 3) surface sterilization, and 4) mechanical damage to seed coats on the proportion of weed seeds surviving a 28 d incubation in soil at 25 C and 330 kPa matric potential. Weed species included common lambsquarters (Chenopodium album), field pennycress (Thaspi arvense), giant foxtail (Setaria faberi), kochia (Kochia scoparia), velvetleaf (Abutilon theophrasti), and yellow foxtail (Setaria glauca). Each of the four factors studied significantly (P < 0.05) affected weed seed survival. Seed survival rates of both giant foxtail and velvetleaf were 10 to 20% lower in conventionally managed soils than in soils managed with low, or no, chemical inputs. Burying seeds in mesh bags, a common experimental practice, increased velvetleaf seed mortality due to an increase in fatal germination, but had the opposite effect on giant foxtail seeds. Surface sterilization of the seed coat with 5% bleach for 5 minutes decreased velvetleaf seed survival by 7%, but increased giant foxtail seed survival by 40%. Survival of all six weed species was reduced by mechanical damage to the seed coat, with large declines in velvetleaf and kochia seed survival (77 and 83%, respectively). The wide range of weed seed survival rates in response to altered abiotic and biotic conditions holds promise for the development of agricultural management practices that reduce weed seed survival in soil seedbanks. Ianuzzi, James (REU Student), Adam Davis, and Karen Renner. 2003. Factors Affecting Weed Seed Survival in Soil Seedbanks.

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2003 Arbuscular mycorrhizal (AM) fungi are integral components of grasslands because most plants are associated with interconnected networks of AM hyphae. Mycorrhizae generally facilitate plant uptake of nutrients from the soil. However, mycorrhizal associations are known to vary in their mutualistic function, and there is currently no metric that links AM functioning with fungal colonization of roots. Mycorrhizal structures differ in their physiological and ecological functioning, so changes in AM allocation to intraradical (inside roots) and extraradical (in soil) structures may signal shifts in mycorrhizal function. We hypothesize that the functional equilibrium model applies to AM fungi and that fertilization should reduce allocation to arbuscules, coils, and extraradical hyphae, the fungal structures that are directly involved in nutrient acquisition and transfer to plants. This study compared AM responses to experimental N enrichment at five grasslands distributed across North America. Samples were collected from replicated N-enriched (and some P-enriched) and control plots throughout the growing season for three years. Intraradical AM structures were measured in over 1400 root samples, extraradical hyphal density was measured in over 590 soil samples, and spore biovolume was analyzed in over 400 soil samples. There were significant site X N interactions for spore biovolume, extraradical hyphae, intraradical hyphae, and vesicles. Nitrogen enrichment strongly decreased AM structures at Cedar Creek, the site with the lowest soil N:P, and it increased AM structures at Konza Prairie, the site with the highest soil N:P. As predicted by the functional equilibrium model, in soils with sufficient P, relative allocation to arbuscules, coils, and extraradical hyphae was generally reduced by N enrichment. Allocation to spores and hyphae was most sensitive to fertilization. At the mesic sites, this response was associated with a shift in the relative abundance of Gigasporaceae within AM fungal communities. This study demonstrates that N enrichment impacts mycorrhizal allocation across a wide range of grassland ecosystems. Such changes are important because they suggest an alteration in mycorrhizal functioning that, in turn, may impact plant community composition and ecosystem function. Johnson, N. C., D. L. Rowland, L. Corkidi, L. M. Egerton-Warburton, and E. B. Allen. 2003. Nitrogen enrichment alters mycorrhizal allocation at five mesic to semiarid grasslands. Ecology 84: 1895-1908.

2003 McKeown, C. H. 2003. Quantifying the roles of competition and niche separation in native and exotic cocconellids, and the changes in the community in response to an exotic prey species. Entomology. MS. Thesis, Michigan State University, East Lansing, Michigan, USA.

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2003 Menalled, F., M. Liebman, and K. Renner. 2003. The ecology of weed seed predation in herbaceous crop systems in D. Batish, ed. Handbook of Sustainable Weed Management. The Haworth Press, Binghampton, New York, USA.

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2003 Interpretation of soil organic C (SOC) dynamics depends heavily on analytical methods and management systems studied. Comparison of data from long-term corn (Zea mays)-plot soils in Eastern North America showed mean residence times (MRTs) of SOC determined by C-14 dating were 176 times those measured with C-13 abundance following a 30-yr replacement Of C-3 by C-4 plants on the same soils. However, MRTs of the two methods were related (r(2) = 0.71). Field C-13 MRTs of SOC were also related (R-2 = 0.55 to 0.85) to those measured by (CO2)-C-13 evolution and curve fitting during laboratory incubation. The strong relations, but different MRTs, were interpreted to mean that the three methods sampled different parts of a SOC continuum. The SOC of all parts of this continuum must be affected by the same controls on SOC dynamics for this to occur. Methods for site selection, plant biomass, soil sampling and analysis were tested on agricultural, afforested-agriculture, and native forest sites to determine the controls on SOC dynamics. Soil-C changes after afforestation were -0.07 to 0.55 Mg C ha(-1) yr(-1) on deciduous sites and -0.85 to 0.58 Mg C ha(-1) yr(-1) under conifers. Soil N changes under afforestation ranged from -0.1 to 0.025 Mg N ha(-1) yr(-1). Ecosystem N accumulation was -0.09 to 0.08 Mg N ha(-1) yr(-1). Soil C and N sequestration but not plant biomass were related to soil Ca, Mg, and K contents. Comparative, independent assays of long-term plots provides information for concept testing and the confidence necessary for decision-makers determining C-cycle policies. Paul, E. A., S. J. Morris, J. Six, K. Paustian, and E. G. Gregorich. 2003. Interpretation of soil carbon and nitrogen dynamics in agricultural and afforested soils. Soil Science Society of America Journal 67: 1620-1628.

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2003 Pitt, A. J. 2003. Isotopomer effects associated with nitrification and denitrification: Implications for the global nitrous oxide cycle. MS. Thesis, Michigan State University, East Lansing, Michigan, USA.

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2003 We examined the impacts on U.S. agriculture of transient climate change as simulated by 2 global general circulation models focusing on the decades of the 2030s and 2090s. We examined historical shifts in the location of crops and trends in the variability of U.S. average crop yields, finding that non-climatic forces have likely dominated the north and westward movement of crops and the trends in yield variability. For the simulated future climates we considered impacts on crops, grazing and pasture, livestock, pesticide use, irrigation water supply and demand, and the sensitivity to international trade assumptions, finding that the aggregate of these effects were positive for the U.S. consumer but negative, due to declining crop prices, for producers. We examined the effects of potential changes in El Nino/Southern Oscillation (ENSO) and impacts on yield variability of changes in mean climate conditions. Increased losses occurred with ENSO intensity and frequency increases that could not be completely offset even if the events could be perfectly forecasted. Effects on yield variability of changes in mean temperatures were mixed. We also considered case study interactions of climate, agriculture, and the environment focusing on climate effects on nutrient loading to the Chesapeake Bay and groundwater depletion of the Edward's Aquifer that provides water for municipalities and agriculture to the San Antonio, Texas area. While only case studies, these results suggest environmental targets such as pumping limits and changes in farm practices to limit nutrient run-off Would need to be tightened if current environmental goals were to be achieved under the climate scenarios we examined. Reilly, J., F. Tubiello, B. A. McCarl, D. Abler, R. Darwin, K. Fuglie, S. Hollinger, R. C. Izaurralde, S. Jagtag, J. Jones, L. Mearns, D. Ojima, E. A. Paul, K. Paustian, S. Riha, N. Rosenberg, and C. Rosenzweig. 2003. U.S. agriculture and climate change: New results. Climatic Change 57: 43-69.

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2003 Scriber, J. M., A. Stump, and M. Deering. 2003. Hybrid zone ecology and tiger swallowtail trait clines in North America. Pages 367-391 in C. Boggs, W. Watt, and P. Erlich, eds. Ecology and Evolution Taking Flight: Butterflies as Model Study Systems. University of Chicago Press, Chicago, Illinois, USA.

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2003 Smeenk, J. P. 2003. The impacts of continuous corn and a corn-soybean-wheat rotation grown under various management schemes on nitrate leaching, soil physical characteristics and net returns. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

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2003 Smucker, A. J. M. 2003. Root carbon contributions to soil aggregate formation and function. Pages 421-426 in J. Abe, ed. Roots: The Dynamic Interface between Plants and the Earth. Kluwer Academic Publishers, The Netherlands.

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2003 Smucker, A. J. M., C. J. Dell, and D. Santos. 2003. Tillage modifications of carbon sequestration within soil aggregates. Proceedings of the 16th International Conference of ISTRO: 1157-1159.

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2003 South, S. R. 2003. Identification and mapping of agricultural tillage methods utilizing remotely sensed data. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

487

2003 Methane oxidation-in aerobic upland soils is an important sink for annually increasing atmospheric methane. The methane oxidation capacity of soil may be declining due to the conversion of natural forest to other uses. I investigate methane oxidation along a gradient of soil disturbance from mature old-growth forest to agricultural fields. I found that soils in the mature deciduous forest oxidize substantially more CH4 than mid-successional forest and no-till agricultural fields. A single application of 100 kg N fertilizer per hectare significantly decreased CH4 oxidation rates in both mature deciduous forest and mid-successional communities but had no effects in agricultural fields, which already had low oxidation rates. In contrast, a 10 cm depth plowing did not show a significant detectable effect on soil CH4 consumption in any soils. Additionally, lower levels of N fertilization (30 kg N ha-1) significantly affected CH4 oxidation in coniferous forest, but not in deciduous forest nor in mid-successional communities. Methane oxidation significantly differed among soil depths. In deciduous forest soil cores incubated in the laboratory, CH4 uptake was highest at 5-10 cm depth whereas there were no significant differences with depth (0-5, 5-10, 10-20, and 20-30 cm) in coniferous forest, in a mid-successional community, nor in no-till agricultural soils. Organic and conventional corn-corn-soybean-wheat management systems also had similar average soil CH4 uptake rates. Nevertheless, CH4 oxidation significantly differed among crops, such that organic corn had the highest rates of oxidation while organic soybean and wheat had the lowest rates. Rates in conventionally managed corn, soybean, and wheat crops were similar and intermediate. Soil methane oxidation was not significantly correlated with CO2 emission. Soil nitrate and ammonium were weak indicators of changes of CH4 oxidation among land use types and soil depths. Nitrification potential was also a good indicator of CH4 oxidation rates. Results suggest a major effect of agricultural management on CH4 oxidation in terrestrial ecosystems, with reductions in oxidation capacity related more to changes in nitrogen availability than physical soil disturbance itself. Low-level nitrogen additions (10 kg N ha-1), similar to rates of N-deposition, however, were not sufficient to reduce oxidation in undisturbed forests or mid-successional communities. Suwanwaree, P. 2003. Methane oxidation in terrestrial ecosystems: Patterns and effects of disturbance. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

492

2003 In a growing body of literature from a variety of ecosystems is strong evidence that various components of biodiversity have significant impacts on ecosystem functioning. However, much of this evidence comes from short-term, small-scale experiments in which communities are synthesized from relatively small species pools and conditions are highly controlled. Extrapolation of the results of such experiments to longer time scales and larger spatial scales-those of whole ecosystems-is difficult because the experiments do not incorporate natural processes such as recruitment limitation and colonization of new species. We show how long-term study of planned and accidental changes in species richness and composition suggests that the effects of biodiversity on ecosystem functioning will vary over time and space. More important, we also highlight areas of uncertainty that need to be addressed through coordinated cross-scale and cross-site research. Symstad, A. J., F. S. Chapin, D. H. Wall, K. L. Gross, L. F. Huenneke, G. G. Mittelbach, D. P. C. Peters, and D. G. Tilman. 2003. Long-term and large-scale perspectives on biodiversity-ecosystem functioning relationships. BioScience 53: 89-98.

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2003 1. The Lotic Intersite Nitrogen eXperiment (LINX) was a coordinated study of the relationships between North American biomes and factors governing ammonium uptake in streams. Our objective was to relate inter-biome variability of ammonium uptake to physical, chemical and biological processes. 2. Data were collected from 11 streams ranging from arctic to tropical and from desert to rainforest. Measurements at each site included physical, hydraulic and chemical characteristics, biological parameters, whole-stream metabolism and ammonium uptake. Ammonium uptake was measured by injection of N-15-ammonium and downstream measurements of N-15-ammonium concentration. 3. We found no general, statistically significant relationships that explained the variability in ammonium uptake among sites. However, this approach does not account for the multiple mechanisms of ammonium uptake in streams. When we estimated biological demand for inorganic nitrogen based on our measurements of in-stream metabolism, we found good correspondence between calculated nitrogen demand and measured assimilative nitrogen uptake. 4. Nitrogen uptake varied little among sites, reflecting metabolic compensation in streams in a variety of distinctly different biomes (autotrophic production is high where allochthonous inputs are relatively low and vice versa).5. Both autotrophic and heterotrophic metabolism require nitrogen and these biotic processes dominate inorganic nitrogen retention in streams. Factors that affect the relative balance of autotrophic and heterotrophic metabolism indirectly control inorganic nitrogen uptake. Webster, J. R., P. J. Mulholland, J. L. Tank, H. M. Valett, W. R. Dodds, B. J. Peterson, W. B. Bowden, C. N. Dahm, S. Findlay, S. V. Gregory, N. B. Grimm, S. K. Hamilton, S. L. Johnson, E. Marti, W. B. McDowell, J. L. Meyer, D. D. Morrall, S. A. Thomas, and W. M. Wollheim. 2003. Factors affecting ammonium uptake in streams - an inter-biome perspective. Freshwater Biology 48: 1329-1352.

202

2003 Biogeochemical transformations in wetlands impact water quality and nutrient transport across landscapes as well as greenhouse gas fluxes. Anaerobic microbial processes, such as denitrification and methanogenesis, play particularly important roles in the biogeochemical functions of wetlands. I explored the influence of anaerobic microbial processes on wetland biogeochemistry in surficial sediments of southwest Michigan wetlands. I examined porewater chemistry profiles in sediments of 12 wetlands to see if there was evidence for thermodynamic constraints on anaerobic microbial processes and to see if the wetland's water source impacted the porewater chemistry. Although the large spatial and temporal variability in porewater chemistry obscured patterns among wetlands, wetland porewaters were generally depleted in nitrate and sulfate relative to source waters, and the presence of sulfide in porewaters confirmed that sulfate reduction occurred at most sites. Porewater chemistry showed little relationship to water source. To further investigate anaerobic microbial decomposition in wetland sediments, I measured ambient rates of denitrification, sulfate reduction, iron reduction, methanogenesis and acetate turnover in three groundwater- and three precipitation-fed wetlands. Denitrification was not detected in any wetland. Iron reduction was measurable mainly in precipitation-fed wetlands, while sulfate reduction rates were greater in groundwater-fed wetlands than in precipitation-fed wetlands. Methanogenesis was measurable in all wetlands, with no differences between wetlands with contrasting water sources, indicating that methanogenesis was important irregardless of water source. Acetate turnover rates were comparable to those measured in other productive sediment environments. Push-pull experiments provided estimates of potential in-situ rates of denitrification and sulfate reduction. All wetlands examined showed the same potential to rapidly remove nitrate and removal was dependent on concentration. Sulfate was also taken up from injected groundwater in all wetlands, but only after nitrate was depleted. The sulfate reduction rates in groundwater-fed wetlands were independent of sulfate concentrations, while the rates in precipitation-fed wetlands were dependent on sulfate concentrations. Results from these studies indicate that water source can influence the biogeochemical functions of wetlands, but that other factors could influence anaerobic decomposition as well. Whitmire, S. 2003. Anaerobic biogeochemical functions of Michigan wetlands and the influence of water source. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

506

2003 The interaction between insect outbreaks and forest health or tree plantation management has been considered rarely from an experimental approach. From 1996-98, Agrawal et al experimentally created a gypsy moth outbreak that defoliated large plots of mature hybrid poplars, Populus xeuramericana, with half of the plots fertilized in a factorial design. They examined the mortality and regeneration of the coppiced trees in the following growing season. Agrawal, A. A., K. R. Kosola, and D. Parry. 2002. Gypsy moth defoliation and N fertilization affect hybrid poplar regeneration following coppicing. Canadian Journal of Forest Research 32: 1491-1495.

291

2002 We investigated the effects of recent moisture history on the relative production of N2O and N2 during denitrification in soil from cropped and successional ecosystems. The soils were pedogenically identical but had been managed differently for the past decade. Sieved soils were amended with nitrate, glucose, and water. Long-wet and short-wet incubations received 80 and 0%, respectively, of prescribed water 2 d before incubation and the rest just before incubation. The N2O and N2 production and N2O mole fraction (N2O/[N2O + N2]) were measured using acetylene inhibition. The N2 production and soil 15N enrichment were measured by 15N-gas evolution. The response of N2O mole fraction to moisture history differed by ecosystem. Mean N2O mole fraction in the successional system was about the same for long-wet and short-wet treatments (0.34 and 0.33, respectively). For the cropped system, however, the N2O mole fraction was 0.36 for the long-wet and 0.90 for the short-wet treatment. Thus, in the cropped system a much smaller proportion of end product was N2O if soil had been wet for 2 d. For N2 fluxes, the isotope method gave the same pattern (r = 0.92) but only about one-third the magnitude, suggesting that N2 derived from two distinct pools. Differences in response of N2O mole fraction for successional and cropped soils may be due to differences in microbial communities. Further knowledge of ecosystem differences with respect to N2O mole fraction and recent moisture history may improve modeled estimates of local and global N2O fluxes. Bergsma, T. T., G. P. Robertson, and N. E. Ostrom. 2002. Influence of soil moisture and land use history on denitrification end-products. Journal of Environmental Quality 31: 711-717.

2002 Buckley, D. H., and T. M. Schmidt. 2002. Exploring the diversity of soil - a microbial rainforest. Pages 183-208 in J. T. Staley and A. L. Reysenbach, eds. Biodiversity of Microbial Life: Foundation of Earth's Biosphere. Wiley, New York, New York, USA.

309

2002 Detailed studies of stream N uptake were conducted in a prairie reach and gallery forest reach of Kings Creek on the Konza Prairie Biological Station. Nutrient uptake rates were measured with multiple short-term enrichments of NO3- and NH4+ at constant addition rates in the spring and summer of 1998. NH4+ uptake was also measured with N-15-NH4+ tracer additions and short-term unlabeled NH4+ additions at 12 stream sites across North America. Concurrent addition of a conservative tracer was used to account for dilution in all experiments. NH4+ uptake rate per unit area (U-t) was positively correlated to nutrient concentration across all sites (r(2) = 0.41, log-log relationship). Relationships between concentration and U-t were used to determine whether the uptake was nonlinear (i.e., kinetic uptake primarily limited by the biotic capacity of microorganisms to accumulate nutrients) or linear (e.g., limited by mass transport into stream biofilms). In all systems, U-t was lower at ambient concentrations than at elevated concentrations. Extrapolation from uptake measured from a series of increasing enrichments could be used to estimate ambient U-t Linear extrapolation of U-t assuming the relationship passes through the origin and rates measured at 1 elevated nutrient concentration underestimated ambient U-t by similar to3-fold. Uptake rates were saturated under some but not all conditions of enrichment; in some cases there was no saturation up to 50 mumol/L. The absolute concentration at which U-t was saturated in Kings Creek varied among reaches and nutrients. Uptake rates of NH4+ at ambient concentrations in all streams were higher than would be expected, assuming U-t does not saturate with increasing concentrations. At ambient nutrient concentrations in unpolluted streams, U-t is probably limited to some degree by the kinetic uptake capacity of stream biota. Mass transfer velocity from the water column is generally greater than would be expected given typical diffusion rates, underscoring the importance of advective transport. Given the short-term spikes in nutrient concentrations that can occur in streams (e.g., in response to storm events), U-t may not saturate, even at high concentrations. Dodds, W. K., A. J. Lopez, R. D. Bowden, S. Gregory, N. B. Grimm, S. K. Hamilton, A. E. Hershey, E. Marti, W. H. McDowell, J. L. Meyer, D. D. Morrall, P. J. Mulholland, B. J. Peterson, J. T. Tank, H. M. Valett, J. R. Webster, and W. M. Wollheim. 2002. N uptake as a function of concentration in streams. Journal of the North American Benthological Society 21: 206-220.

2002 Elwadie, M. 2002. Spatial and temporal dynamics of nitrogen-water interactions in corn in Michigan. Ph.D. Dissertation, Michigan State University, East Lansing, Michigan, USA.

334

2002 The absolute amount of microbial biomass and relative contribution of fungi and bacteria are expected to vary among types of organic matter (OM) within a stream and will vary among streams because of differences in organic matter quality and quantity. Common types of benthic detritus [leaves, small wood, and fine benthic organic matter (FBOM)] were sampled in 9 small (1st-3rd order) streams selected to represent a range of important controlling factors such as surrounding vegetation, detritus standing stocks, and water chemistry. Direct counts of bacteria and measurements of ergosterol (a fungal sterol) were used to describe variation in bacterial and fungal biomass. There were significant differences in bacterial abundance among types of organic matter with higher densities per unit mass of organic matter on fine particles relative to either leaves or wood surfaces. In contrast, ergosterol concentrations were significantly greater on leaves and wood, confirming the predominance of fungal biomass in these larger size classes. In general, bacterial abundance per unit organic matter was less variable than fungal biomass, suggesting bacteria will be a more predictable component of stream microbial communities. For 7 of the 9 streams, the standing stock of fine benthic organic matter was large enough that habitat-weighted reach-scale bacterial biomass was equal to or greater than fungal biomass. The quantities of leaves and small wood varied among streams such that the relative contribution of reach-scale fungal biomass ranged from 10% to as much as 90% of microbial biomass. Ergosterol concentrations were positively associated with substrate C:N ratio while bacterial abundance was negatively correlated with C:N. Both these relationships are confounded by particle size, i.e., leaves and wood had higher C:N than fine benthic organic matter. There was a weak positive relationship between bacterial abundance and streamwater soluble reactive phosphorus concentration, but no apparent pattern between either bacteria or fungi and streamwater dissolved inorganic nitrogen. The variation in microbial biomass per unit organic matter and the relative abundance of different types of organic matter contributed equally to driving differences in total microbial biomass at the reach scale. Findlay, S., J. L. Tanks, S. Dye, H. M. Valett, P. J. Mulholland, W. H. McDowell, S. Johnson, S. K. Hamilton, J. A. Edmonds, W. K. Dodds, and W. B. Bowden. 2002. A cross-system comparison of bacterial and fungal biomass in detritus pools of headwater streams. Microbial Ecology 43: 55-66.

2002 Fox, T. B. 2002. Biological control of soybean (Aphis glycines Matsumura) aphid in Michigan. MS Thesis, Michigan State University, East Lansing, Michigan, USA.

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2002 Gage, S. H., J. R. Gosz, and W. Michener. 2002. Site to regional scaling. Pages 37-41 in A. Withey, W. Michener, and P. Tooby, eds. Scalable Information Networks for the Environment. San Diego Supercomputer Center, San Diego, California, USA.

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2002 Highbush blueberries (Vaccinium corymbosum L.) are long lived perennial plants that are grown on acidic Soils. The goal of this study was to determine how blueberry cultivation might influence the nitrification capacity of acidic soils by comparing the nitrification potential of blueberry soils to adjacent noncultivated forest soils. The net nitrification potential of blueberry and forest soils was compared by treating soils with N-15 enriched (NH4)(2)SO4, and monitoring nitrate (NO3--N) production during a 34-day incubation period in plastic bags at 18 degreesC. Net nitrification was also compared by an aerobic slurry method. Autotrophic nitrifiers were quantified by the most probable number method. Nitrate production from labeled ammonium ((NH4+)-N-15) indicated that nitrification was more rapid in blueberry soils than in forest soils from six of the seven study sites. Slurry nitrification assays provided similar results. Blueberry soils also contained higher numbers of nitrifying bacteria compared to forest soils. Nitrification in forest soils did not appear to be limited by availability of NH4+ substrate. Results suggest that blueberry production practices lead to greater numbers of autotrophic nitrifying bacteria and increased nitrification capacity, possibly resulting from annual application of ammonium containing fertilizers. Hanson, E. J., P. A. Throop, S. Serce, J. Ravenscroft, and E. A. Paul. 2002. Comparison of nitrification rates in blueberry and forest soils. American Journal of Horticulture Science 127: 136-142.

2002 Harris, C. K., and C. Bailey. 2002. Public preferences for a clean, green agricultural machine. Pages 31-42 in C. K. Harris, J. Molnar, T. Tomazic, and R. Wimberley, eds. The Social Risks of Agriculture: Americans Speak Out on Food. Praeger, New York, New York, USA.

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2002 Harris, C. K., J. Molnar, T. Tomazic, and R. Wimberley, eds. 2002. The Social Risks of Agriculture: Americans Speak Out on Food. Praeger, New York, New York, USA.

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2002 Harwood, R. R. 2002. Sustainable agriculture on a populous, industrialized landscape: Building ecosystem vitality and productivity. Pages 305-315 in R. Lal, D. Hansen, N. Uphoff, and S. Slack, eds. Food Security and Environmental Quality in the Developing World. CRC Press, Boca Raton, Florida, USA.

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2002 Kavdir, Y., and A. J. M. Smucker. 2002. Soil aggregate sequestration of cover crop root and shoot residue nitrogen. Pages 134-142. Proceedings of the International Conference on Sustainable Land Use and Management. Soil Science Society of Turkey, Turkey.

373

2002 Late-summer starch accumulation in fine roots of poplars (Populus x canadensis Moench.) defoliated by gypsy moth (Lymantria dispar L.) lagged behind that in fine roots of undefoliated trees. If starch concentration declines with age, defoliation-induced changes in root system age structure could be partly responsible for this difference. To test this hypothesis, we measured fine-root starch and soluble sugar concentrations in roots of known age from trees in defoliated and undefoliated plots. There was a significant interaction between the effects of defoliation and root type (white, brown, or dead) on fine root soluble sugar concentration because of the high concentration of soluble sugars in white roots from trees in undefoliated plots. Both root starch and soluble sugar concentrations were variable among individuals of each age class. The population frequency distributions for starch and soluble sugar concentrations were both right-skewed, and fit by exponential functions. These data are most consistent with direct defoliation effects on a labile and dynamic pool of carbohydrates in poplar fine roots, rather than indirect defoliation effects on root system age structure. Kosola, K. R., D. I. Dickmann, and D. Parry. 2002. Carbohydrates in individual poplar fine roots- effects of root age and defoliation. Tree Physiology 22:741-746.

106

2002 McDermott, T. R., and F. B. Dazzo. 2002. Use of fluorescent antibodies for studying the ecology of soil- and plant-associated microbes. Pages 615-626 in C. Hurst, R. C. Crawford, G. R. Knudsen, M. J. McInerney, and L. D. Stetzenbach, eds. Manual of Environmental Microbiology. American Society for Microbiology Press, Washington, DC, USA.

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2002 Morris, S. J., and E. A. Paul. 2002. Forest ecology and soil organic matter. Pages 109-125 in J. M. Kimble, R. A. Birdsey, R. Lal, R. F. Follett, and J. Heath, eds. The Potential of US Forest Soil to Sequester Carbon and Mitigate the Greenhouse Effect. CRC Press, Boca Raton, Florida, USA.

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2002