KBS LTER Publications

Publications associated with KBS LTER. 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.

  • 2019

    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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3814)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3749)
  • 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.

    abstract + pdf abstract pdf data (https://lter.kbs.msu.edu/pub/3639)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3732)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3592)
  • 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.

    abstract + pdf abstract pdf data (https://lter.kbs.msu.edu/pub/3649)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3558)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3451)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3419)
  • 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. Pages 1-32 in S. K. Hamilton, J. E. Doll, and G. P. Robertson, eds. The Ecology of Agricultural Landscapes: Long-Term Research on the Path to Sustainability. Oxford University Press, New York, New York, USA.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3457)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3448)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3394)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3384)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3599)
  • 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. Pages 3.1-141 in M. Eve, D. Pape, M. Flugge, R. Steele, D. Man, M. Riley-Gilbert, and S. Biggar, eds. Quantifying greenhouse gas fluxes in agriculture and forestry: methods for entity-scale inventory. Technical Bulletin Number 1939. Office of the Chief Economist, U.S. Department of Agriculture, Washington, D.C., USA.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3366)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3292)
  • 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. Pages 519-537 in R. D. Delaune, R. Reddy, C. J. Richardson, and P. Megonigal, eds. Methods in biogeochemistry of wetlands. Soil Science Society of America, Madison, Wisconsin, USA.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3142)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3239)
  • Dazzo, F. B. and S. Gantner. 2013. In situ calling distances and high population independent N-acylhomoserine lactone-mediated communication on plant root surfaces. Pages 785-789 in F. DeBruijn, ed. Molecular microbial ecology of the rhizosphere, Volume 2. J Wiley & Sons, Hoboken, New Jersey.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3159)
  • 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. Pages 733-742 in F. de Bruijn, ed. Molecular microbial ecology of the rhizosphere, Volume 2. J Wiley & Sons, Hoboken, New Jersey.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3158)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3495)
  • 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. Verified Carbon Standard, Washington, DC, USA.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3262)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3156)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3236)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3445)
  • 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. American Carbon Registry, Winrock International, Little Rock, Arkansas, USA.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3263)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3088)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3125)
  • 2010

    Dazzo, F. B. 2010. CMEIAS digital microscopy and quantitative image analysis of microorganisms. Vol 2, Pages 1083-1090 in A. Mendez-Vilas and J. Diaz, eds. Microscopy: Science, Technology, Applications and Education. Formatex Research Center Microscopy Book Series #4, Badajoz, Spain.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2152)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2144)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2187)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2185)
  • 2008

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

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2246)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2242)
  • 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. Pages 712-733 in J. L. Garland, C. Hurst, D. Lipson, A. L. Mills, L. Stezenbach, and R. C. Crawford, eds. Manual of Environmental Microbiology, 3rd Ed.. American Society for Microbiology, Washington, DC.

  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2296)
  • Thorn, R. G., J. Scott, and M. A. Lachance. 2007. Methods for studying terrestrial fungal ecology and diversity. Pages 929-951 in E. A. Paul, ed. Methods for General and Molecular Microbiology, 3rd Ed.. Elsevier Academic Press, Oxford, UK.

  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2399)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2368)
  • Stres, B. and J. M. Tiedje. 2006. New frontiers in soil microbiology: How to link structure and function of microbial communities? Vol 8, Pages 1-22 in P. Nannipieri and K. Smalla, eds. Soil Biology: Nucleic Acids and Proteins in Soil. Springer Verlag, Heidelberg, Germany.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2354)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2350)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2433)
  • 2004

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

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2513)
  • Reddy, C. K. and F. B. Dazzo. 2004. Computer-assisted segmentation of bacteria in color micrographs. Microscopy & Analysis 18:5-7.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2489)
  • 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 Manual of Environmental Microbiology. American Society for Microbiology Press, Washington, DC, USA.

  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2658)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2639)
  • 1999

    Fahey, T., C. S. Bledsoe, F. Day, R. Reuss, and A. J. Smucker. 1999. Fine root production and demography. Pages 437-455 in G. P. Robertson, C. S. Bledsoe, D. C. Coleman, and P. Sollins, eds. Standard Soil Methods for Long-Term Ecological Research. Oxford University Press, New York, New York, USA.

  • Groffman, P. M., E. A. Holland, D. D. Myrold, G. P. Robertson, and X. Zou. 1999. Denitrification. Pages 272-290 in G. P. Robertson, C. S. Bledsoe, D. C. Coleman, and P. Sollins, eds. Standard Soil Methods for Long-Term Ecological Research. Oxford University Press, New York, New York, USA.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2738)
  • Holland, E. A., G. P. Robertson, J. Greenberg, P. Groffman, R. Boone, and J. Gosz. 1999. Soil CO2, N2O, and CH4 Exchange. Pages 185-201 in G. P. Robertson, C. S. Bledsoe, D. C. Coleman, and P. Sollins, eds. Standard Soil Methods for Long-Term Ecological Research. Oxford University Press, New York, New York, USA.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2736)
  • Sinsabaugh, R. L., M. J. Klug, H. P. Collins, P. E. Yeager, and S. O. Peterson. 1999. Characterizing soil microbial communities. Pages 318-348 in G. P. Robertson, C. S. Bledsoe, D. C. Coleman, and P. Sollins, eds. Standard Soil Methods for Long-Term Ecological Research. Oxford University Press, New York, New York.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2713)
  • 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. Pages 89-105 in G. P. Robertson, C. S. Bledsoe, D. C. Coleman, and P. Sollins, eds. Standard Soil Methods for Long-Term Ecological Research. Oxford University Press, New York, New York.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2711)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2799)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2772)
  • 1997

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

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2779)
  • Johnson, L. B. and S. H. Gage. 1997. Landscape approaches to the analysis of aquatic ecosystems. Freshwater Biology 37:113-132.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2829)
  • 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.

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/2865)
  • 1994

    Holben, W. E. 1994. Isolation and purification of bacterial DNA from soil. Pages 727-751 in R. Weaver, P. Bottomly, and S. Angle, eds. Methods of Soil Analysis Part 2. Microbiological and Biochemical Properties. Soil Science Society of America, Madison, Wisconsin, USA.

  • 1993

    Klug, M. J. and J. M. Tiedje. 1993. Response of microbial communities to changing environmental conditions: chemical and physiological approaches. Pages 371-374 in R. Guerrero and C. Pedros-Alio, eds. Trends in Microbial Ecology. Spanish Society for Microbiology, Barcelona, Spain.

  • 1990

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

    abstract + pdf abstract pdf (https://lter.kbs.msu.edu/pub/3033)
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