Publications for the Methods

Publications associated with KBS LTER, GLBRC and LTAR projects. Click on the pdf link to get open access papers or to sign-in (free and immediate) to get other papers. Click on the data link to get formally published datasets (other datasets available as noted within the publications). Other ways to view KBS LTER publications can be accessed by the Research | Publications menu above.

Publications are also available on our KBS LTER Google Scholar page

2024

Guber, A. and A. Kravchenko. 2024.2-D soil zymography: Accounting for the spatial variation of pH. Rhizosphere 29:100862., DOI: 10.1016/j.rhisph.2024.100862

Kahmark, K., M. Jones, S. Bohm, N. Baker, and G. P. Robertson. 2024.Rainfall Manipulation Shelters for Agricultural Research. Kellogg Biological Station Long-term Ecological Research Special Publication. Zenodo https://doi.org/10.5281/zenodo.10607631 ., DOI: 10.5281/zenodo.10607631

McNamara Manning, K., J. Perrone, S. Petrycki, D. A. Landis, and C. A. Bahlai. 2024.Adapting to changing methodology in a long-term experiment. Ecosphere 15:e4951., DOI: 10.1002/ecs2.4951

2022

Pan, D., I. Gelfand, L. Tao, M. Abraha, K. Sun, X. Guo, J. Chen, G. P. Robertson, and M. A. Zondlo. 2022.A new open-path eddy covariance method for nitrous oxide and other trace gases that minimizes temperature corrections. Global Change Biology 28:1446-1457., DOI: 10.1111/gcb.15986

2021

Bahlai, C. A., E. R. White, J. D. Perrone, S. Cusser, and K. Stack Whitney. 2021.The broken window: An algorithm for quantifying and characterizing misleading trajectories in ecological processes. Ecological Informatics 64:101336., DOI: 10.1016/j.ecoinf.2021.101336

Belanger, M., C. Vizza, G. P. Robertson, and S. S. Roley. 2021.Quantifying and correcting for pre-assay CO2 loss in short-term carbon mineralization assays. SOIL 7:47-52., DOI: 10.5194/soil-7-47-2021

O'Neill, B., C. D. Sprunger, and G. P. Robertson. 2021.Do soil health tests match farmer experience? Assessing biological, physical, and chemical indicators in the Upper Midwest United States. Soil Science Society of America Journal 85:903-918., DOI: 10.1002/saj2.20233

Zhang, B., C. R. Penton, Z. Yu, C. Xue, Q. Chen, Z. Chen, C. Yan, Q. Zhang, M. Zhao, J. F. Quensen, and J. M. Tiedje. 2021.A new primer set for Clade I nosZ that recovers genes from a broader range of taxa. Biology and Fertility of Soils 57:523-531., DOI: 10.1007/s00374-021-01544-6

2020

Bramer, L. M., A. M. White, K. G. Stratton, A. M. Thompson, D. Claborne, K. Hofmockel, and L. A. McCue. 2020.ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data. PLOS Computational Biology 16:e1007654., DOI: 10.1371/journal.pcbi.1007654

Grace, P., T. J. van der Weerden, D. W. Rowlings, C. Scheer, C. Brunk, R. Kiese, K. Butterbach-Bahl, R. M. Rees, G. P. Robertson, and U. M. Skiba. 2020.Global Research Alliance N2O chamber methodology guidelines: Considerations for automated flux measurement. Journal of Environmental Quality 49:1126-1140., DOI: 10.1002/jeq2.20124

Kahmark, K., N. Millar, and G. P. Robertson. 2020.Static chamber method for measuring greenhouse gas fluxes. KBS LTER Special Publication. Zenodo http://doi.org/10.5281/zenodo.4630396., DOI: 10.5281/zenodo.4630396

Larimer, C. J., E. H. Denis, J. D. Suter, and J. J. Moran. 2020.Optical coherence tomography imaging of plant root growth in soil. Applied Optics 59:2474-2481., DOI: 10.1364/AO.384674

Lin, V. S., J. J. Rosnow, M. Y. McGrady, D. N. Smercina, J. R. Nuñez, R. S. Renslow, and J. J. Moran. 2020.Non-destructive spatial analysis of phosphatase activity and total protein distribution in the rhizosphere using a root blotting method. Soil Biology and Biochemistry 146:107820., DOI: 10.1016/j.soilbio.2020.107820

Veličković, D., V. S. Lin, A. Rivas, C. R. Anderton, and J. J. Moran. 2020.An approach for broad molecular imaging of the root-soil interface via indirect matrix-assisted laser desorption/ionization mass spectrometry. Soil Biology and Biochemistry 146:107804., DOI: 10.1016/j.soilbio.2020.107804

2019

Guo, J., J. F. Quensen, Y. Sun, Q. Wang, C. T. Brown, J. R. Cole, and J. M. Tiedje. 2019.Review, evaluation and directions for gene-targeted assembly for ecological analyses of metagenomes. Frontiers in Microbiology 10:957., DOI: 10.3389/fgene.2019.00957

Razavi, B. S., X. Zhang, N. Bilyera, A. Guber, and M. Zarebanadkouki. 2019.Soil zymography: Simple and reliable? Review of current knowledge and optimization of the method. Rhizosphere 11:100161., DOI: 10.1016/j.rhisph.2019.100161

2018

Lee-Cullin, J. A., J. P. Zarnetske, S. S. Ruhala, and S. Plont. 2018.Toward measuring biogeochemistry within the stream-groundwater interface at the network scale: An initial assessment of two spatial sampling strategies. Limnology and Oceanography: Methods 16:722-733., DOI: 10.1002/lom3.10277

Welshofer, K. B., P. L. Zarnetske, N. K. Lany, and L. A. Thompson. 2018.Open-top chambers for temperature manipulation in taller-stature plant communities. Methods in Ecology and Evolution 9:254-259., DOI: 10.1111/2041-210X.12863

2017

Dazzo, F. B. and Y. G. Yanni. 2017.Spatial ecology of microbial colonization intensity and behavior in rice rhizoplane biofilms analyzed by CMEIAS Bioimage Informatics software. Journal of Soil Science & Plant Health 1:1., DOI: 10.4172/JSPH.1000101

Ruhala, S. S. and J. P. Zarnetske. 2017.Using in-situ optical sensors to study dissolved organic carbon dynamics of streams and watersheds: A review. Science of The Total Environment 575:713-723., DOI: 10.1016/j.scitotenv.2016.09.113

Welshofer, K. B., P. L. Zarnetske , N. K. Lany, and L. A. Thompson. 2017.Data from: Open-top chambers for temperature manipulation in taller-stature plant communities. Dryad Digital Repository http://dx.doi.org/10.5061/dryad.2br8k., DOI: 10.5061/dryad.2br8k

2015

Dazzo, F. B., Y. Yanni, A. Jones, and A. Elsadany. 2015.CMEIAS bioimage informatics that define the landscape ecology of immature microbial biofilms developed on plant rhizoplane surfaces. AIMS Bioengineering 2:469-486., DOI: 10.3934/bioeng.2015.4.469

Ji, Z., K. J. Card, and F. B. Dazzo. 2015.CMEIAS JFrad: A digital computing tool to discriminate the fractal geometry of landscape architectures and spatial patterns of individual cells in microbial biofilms. Microbial Ecology 69:710-720., DOI: 10.1007/s00248-014-0495-1

Kravchenko, A. N. and G. P. Robertson. 2015.Statistical challenges in analyses of chamber-based soil CO2 and N2O emissions data. Soil Science Society of America Journal 79:200-211., DOI: 10.2136/sssaj2014.08.0325

Robertson, G. P. and S. K. Hamilton. 2015.Long-term ecological research in agricultural landscapes at the Kellogg Biological Station LTER site: conceptual and experimental framework. The Ecology of Agricultural Landscapes: Long-Term Research on the Path to Sustainability Pages 1-32,

Stoddard, S. F., B. J. Smith, R. Hein, B. R. Roller, and T. M. Schmidt. 2015.rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Research 43:D593-598., DOI: 10.1093/nar/gku1201

2014

Folland, I., D. Trione, and F. Dazzo. 2014.Accuracy of biovolume formulas for CMEIAS computer-assisted microscopy and body size analysis of morphologically diverse microbial populations and communities. Microbial Ecology 68:596-610., DOI: 10.1007/s00248-014-0410-9

Kravchenko, A. N., W. Negassa, A. K. Guber, and S. Schmidt. 2014.New approach to measure soil particulate organic matter in intact samples using X-ray computed microtomography. Soil Science Society of America Journal 78:1177-1185., DOI: 10.2136/sssaj2014.01.0039

Necpálová, M., R. P. Anex, A. N. Kravchenko, L. J. Abendroth, S. J. Del Grosso, W. A. Dick, M. J. Helmers, D. Herzmann, J. G. Lauer, E. D. Nafziger, J. E. Sawyer, P. C. Scharf, J. S. Strock, and M. B. Villamil. 2014.What does it take to detect a change in soil carbon stock? A regional comparison of minimum detectable difference and experiment duration in the north central United States. Journal of Soil and Water Conservation 69:517-531., DOI: 10.2489/jswc.69.6.517

Ogle, S. M., P. R. Adler, F. J. Breidt, S. Del Grosso, A. Franzluebbers, M. Liebig, B. Linquist, G. P. Robertson, M. Schoeneberger, J. Six, C. van Kessel, R. Venterea, and T. West. 2014.Chapter 3: Quantifying greenhouse sources and sinks in cropland and grazing land systems. Quantifying greenhouse gas fluxes in agriculture and forestry: methods for entity-scale inventory. Technical Bulletin Number 1939 Pages 3.1-141,

Woltz, J. M. and D. A. Landis. 2014.Comparison of sampling methods of Aphis glycines predators across the diel cycle. Journal of Applied Entomology 138:475-484., DOI: 10.1111/jen.12106

2013

Burgin, A. J., S. K. Hamilton, W. Gardner, and M. McCarthy. 2013.Nitrate reduction, denitrification, and dissimilatory nitrate reduction to ammonium in wetland sediments. Methods in biogeochemistry of wetlands Pages 519-537, DOI: 10.2136/sssabookser10.c28

Dazzo, F. B., K. J. Klemmer, R. Chandler, and Y. G. Yanni. 2013.In situ ecophysiology of microbial biofilm communities analyzed by CMEIAS computer-assisted microscopy at single-cell resolution. Diversity 5:426-460., DOI: 10.3390/d5030426

Dazzo, F. B. and S. Gantner. 2013.In situ calling distances and high population independent N-acylhomoserine lactone-mediated communication on plant root surfaces. Molecular microbial ecology of the rhizosphere, Volume 2 Pages 785-789, DOI: 10.1002/9781118297674.ch74

Dazzo, F. B. and Y. G. Yanni. 2013.CMEIAS: an improved computing technology for quantitative image analysis of root colonization by Rhizobacteria in situ at single-cell resolution. Molecular microbial ecology of the rhizosphere, Volume 2 Pages 733-742, DOI: 10.1002/9781118297674.ch69

Dazzo, F. B. and C. Gross. 2013.CMEIAS Quadrat Maker: A digital software tool to optimize grid dimensions and produce quadrat images for landscape ecology spatial analysis. Journal of Ecosystems & Ecography 3:136., DOI: 10.4172/2157-7625.1000136

Millar, N., G. P. Robertson, A. Diamant, R. J. Gehl, P. R. Grace, and J. P. Hoben. 2013.Quantifying N2O emissions reductions in US agricultural crops through N fertilizer rate reduction. ,

2012

Dazzo, F. B. 2012.CMEIAS-aided microscopy of the spatial ecology of individual bacterial interactions involving cell-to-cell communication within biofilms. Sensors 12:7047-7062., DOI: 10.3390/s120607047

Grieshop, M. J., B. P. Werling, K. Buehrer, J. Perrone, R. Isaacs, and D. A. Landis. 2012.Big brother is watching: Studying insect predation in the age of digital surveillance. American Entomologist 58:172-182., DOI: 10.1093/ae/58.3.172

Kasten, E. P., S. H. Gage, J. Fox, and W. Joo. 2012.The remote environmental assessment laboratory's acoustic library: An archive for studying soundscape ecology. Ecological Informatics 12:50-67., DOI: 10.1016/j.ecoinf.2012.08.001

Millar, N., G. P. Robertson, A. Diamant, R. J. Gehl, P. R. Grace, and J. P. Hoben. 2012.Methodology for quantifying nitrous oxide (N2O) emissions reductions by reducing nitrogen fertilizer use on agricultural crops. ,

2011

Smemo, K. A., N. E. Ostrom, M. R. Opdyke, P. H. Ostrom, S. Bohm, and G. P. Robertson. 2011.Improving process-based estimates of N2O emissions from soil using temporally extensive chamber techniques and stable isotopes. Nutrient Cycling in Agroecosystems 91:145-154., DOI: 10.1007/s10705-011-9452-2

Wang, W., A. N. Kravchenko, A. J. Smucker, and M. L. Rivers. 2011.Comparison of image segmentation methods in simulated 2D and 3D microtomographic images of soil aggregates. Geoderma 162:231-241., DOI: 10.1016/j.geoderma.2011.01.006

2010

Dazzo, F. B. 2010.CMEIAS digital microscopy and quantitative image analysis of microorganisms. Microscopy: Science, Technology, Applications and Education Vol 2, Pages 1083-1090,

Gross, C. A., C. Reddy, and F. B. Dazzo. 2010.CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution. Microbial Ecology 59:400-414., DOI: 10.1007/s00248-009-9616-7

2009

Kravchenko, A. N., M. A. Martin, A. J. Smucker, and M. L. Rivers. 2009.Limitations in determining multifractal spectra from pore–solid soil aggregate images. Vadose Zone Journal 8:220-226., DOI: 10.2136/vzj2008.0008

Lee, Z. M., C. Bussema, and T. M. Schmidt. 2009.rrnDB: Documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Research 37:D489-D493., DOI: 10.1093/nar/gkn689

2008

Mason, R., P. Roe, M. Towsey, J. Zhang, J. Gibson, and S. Gage. 2008.Towards an acoustic environmental observatory. Fourth IEEE International Conference on eScience, 2008 Pages 135-142, DOI: 10.1109/eScience.2008.16

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., DOI: 10.1016/j.mimet.2008.07.017

2007

Dazzo, F. B., M. Schmid, and A. Hartmann. 2007.Immunofluorescence microscopy and fluorescence in situ hybridization combined with CMEIAS and other image analysis tools for soil- and plant-associated microbial autecology. Manual of Environmental Microbiology, 3rd Ed. Pages 712-733,

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 of Washington 109:359-365.,

Thorn, R. G., J. Scott, and M. A. Lachance. 2007.Methods for studying terrestrial fungal ecology and diversity. Methods for General and Molecular Microbiology, 3rd Ed. Pages 929-951,

2006

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., DOI: 10.1111/j.1574-6941.2005.00037.x

Pietola, L. and A. J. Smucker. 2006.Elimination of non-root residue by image analysis of very fine roots. Computers and Electronics in Agriculture 53:92-97.,

Stres, B. and J. M. Tiedje. 2006.New frontiers in soil microbiology: How to link structure and function of microbial communities?. Soil Biology: Nucleic Acids and Proteins in Soil Vol 8, Pages 1-22,

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 abundances. 72:638-644.,

2005

Porter, J. H., P. Arzberger, H. -. 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.,

2004

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

Reddy, C. K. and F. B. Dazzo. 2004.Computer-assisted segmentation of bacteria in color micrographs. Microscopy & Analysis 18:5-7.,

2002

McDermott, T. R. and F. B. Dazzo. 2002.Use of fluorescent antibodies for studying the ecology of soil- and plant-associated microbes. Manual of Environmental Microbiology Pages 615-626,

2001

Bergsma, T. T., N. E. Ostrom, M. Emmons, and G. P. Robertson. 2001.Measuring simultaneous fluxes from soil of N2O and N2 in the field using the 15N-Gas "Nonequilibrium" technique. Environmental Science and Technology 35:4307-4312., DOI: 10.1021/es010885u

Liu, J., F. B. Dazzo, O. Glagoleva, B. Yu, and A. Jain. 2001.CMEIAS: A computer-aided system for the image analysis of bacterial morphotypes in microbial communities. Microbial Ecology 41:173-194.,

1999

Bledsoe, C. S., T. J. Fahey, F. P. Day, and R. W. Reuss. 1999.Measurement of static root parameters: biomass, length, and distribution in the soil profile. Pages 413-436,

Boone, R. D., D. F. Grigal, P. Sollins, R. J. Ahrens, and D. E. Armstrong. 1999.Soil sampling, preparation, archiving, and quality control. Pages 3-28,

Coleman, D. C., J. M. Blair, E. T. Elliott, and D. H. Wall. 1999.Soil invertebrates. Pages 349-377,

Elliott, E. T., J. W. Heil, E. F. Kelly, and H. C. Monger. 1999.Soil structural and other physical properties. Pages 74-85,

Fahey, T., C. S. Bledsoe, F. Day, R. Ruess, and A. J. Smucker. 1999.Fine root production and demography. Standard Soil Methods for Long-Term Ecological Research Pages 437-455,

Grigal, D. F., J. C. Bell, R. A. Ahrens, R. D. Boone, E. F. Kelly, H. C. Monger, and P. Sollins. 1999.Site and landscape characterization for ecological studies. Pages 29-54,

Groffman, P. M., E. A. Holland, D. D. Myrold, G. P. Robertson, and X. Zou. 1999.Denitrification. Standard Soil Methods for Long-Term Ecological Research Pages 272-290,

Harmon, M. E., K. J. Nadelhoffer, and J. M. Blair. 1999.Measuring decomposition, nutrient turnover, and stores in plant litter. Pages 202-240,

Harmon, M. E. and K. Lajtha. 1999.Analysis of detritus and organic horizons for mineral and organic constituents. Pages 143-165,

Holland, E. A., G. P. Robertson, J. Greenberg, P. Groffman, R. Boone, and J. Gosz. 1999.Soil CO2, N2O, and CH4 Exchange. Standard Soil Methods for Long-Term Ecological Research Pages 185-201,

Jarrell, W. M., D. E. Armstrong, D. F. Grigal, E. F. Kelly, H. C. Monger, and D. A. Wedin. 1999.Soil water and temperature status. ,

Johnson, N. C., T. E. O'Dell, and C. S. Bledsoe. 1999.Methods for ecological studies of mycorrhizae. Pages 378-412,

Lajtha, K., C. T. Driscoll, W. M. Jarrell, and E. T. Elliott. 1999.Soil phosphorus: characterization and total element analysis. Pages 115-142,

Lajtha, K., W. M. Jarrell, D. W. Johnson, and P. Sollins. 1999.Collection of soil solution. Pages 166-184,

Myrold, D. D., R. Reuss, and M. J. Klug. 1999.Dinitrogen fixation. Standard Soil Methods for Long-Term Ecological Research Pages 241-257,

Paul, E. A., D. Harris, M. Klug, and R. Ruess. 1999.The determination of microbial biomass. Standard Soil Methods for Long-Term Ecological Research Pages 291-317,

Sinsabaugh, R. L., M. J. Klug, H. P. Collins, P. E. Yeager, and S. O. Peterson. 1999.Characterizing soil microbial communities. Standard Soil Methods for Long-Term Ecological Research Pages 318-348,

Sollins, P., C. Glassman, E. A. Paul, C. Swanston, K. Lajtha, J. Heil, and T. E. Elliott. 1999.Soil carbon and nitrogen pools and fractions. Standard Soil Methods for Long-Term Ecological Research Pages 89-105,

1998

Ambus, P. and G. P. Robertson. 1998.Automated near-continuous measurement of carbon dioxide and nitrous oxide fluxes from soil. Soil Science Society of America Journal 62:394-400., DOI: 10.2136/sssaj1998.03615995006200020015x

Kemner, K. M., W. Yun, Z. Cai, B. Lai, H. R. Lee, D. G. Lengnini, W. Rodriguez, J. Jastrow, R. M. Miller, S. T. Pratt, M. A. Schnnegurt, C. F. Kulpa, and A. J. Smucker. 1998.Using X-ray microprobes for environmental research. Proceedings of the International Society for Optical Engineering 3449:45-54., DOI: 10.1117/12.330354

1997

Harris, D., R. P. Voroney, and E. A. Paul. 1997.Measurement of microbial biomass N:C by chloroform fumigation-incubation. Canadian Journal of Soil Science 77:507-514., DOI: 10.4141/S96-064

Johnson, L. B. and S. H. Gage. 1997.Landscape approaches to the analysis of aquatic ecosystems. Freshwater Biology 37:113-132., DOI: 10.1046/j.1365-2427.1997.00156.x

1996

Eash, N. S., P. D. Stahl, T. B. Parkin, and D. L. Karlen. 1996.A simplified method for extraction of ergosterol from soil. Soil Science Society of America Journal 60:468-471., DOI: 10.2136/sssaj1996.03615995006000020018x

1994

Holben, W. E. 1994.Isolation and purification of bacterial DNA from soil. Methods of Soil Analysis Part 2. Microbiological and Biochemical Properties Pages 727-751,

1993

Klug, M. J. and J. M. Tiedje. 1993.Response of microbial communities to changing environmental conditions: chemical and physiological approaches. Trends in Microbial Ecology Pages 371-374,

1990

Smucker, A. J. 1990.Quantification of root dynamics in agroecological systems. Remote Sensing Reviews 5:237-248., DOI: 10.1080/02757259009532132