Jim Cotner
Phone Numbers
Office Address

1987 Upper Buford Circle
St. Paul, MN 55108
United States

James B.


Ecology, Evolution and Behavior

Microbial metabolism has changed the composition of the Earth, including the atmosphere, lakes and oceans over nearly four billion years of life on the planet. We examine how microbes affect aquatic environments, primarily freshwater, via their composition, metabolism and production of greenhouse gases such as carbon dioxide and methane. Our work uses ecological stoichiometry as a framework to help us understand the dynamics of microbes and the biogeochemical cycles of important elements such as carbon, nitrogen and phosphorus in lakes, ponds and streams.

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Research statement

I seek to understand the role of heterotrophic bacteria in regulating production versus decomposition in aquatic environments.

Because most organic carbon burial occurs in aquatic ecosystems, they are critical to carbon dynamics on Earth. Furthermore, because heterotrophic bacteria are the most numerous organisms on the planet, they play a critical role in carbon fluxes in lakes and the ocean. Most carbon passes through "the microbial loop" on the way to its ultimate fate, either as storage in sediments or respiration as carbon dioxide. The availability of inorganic nutrients, especially phosphorus (P), plays an important role in the regulation of carbon fluxes in aquatic ecosystems through its impact on bacteria. In the coastal ocean and eutrophic lakes (high P availability), relatively low quantities of primary production funnels through bacteria and the microbial loop, increasing nutrient and carbon availability to the remainder of the food web. This contrasts with most of the ocean and many oligotrophic (low P availability) lakes where bacteria, because of their high affinity for P, are the main biomass component and the most metabolically active part of the microbial loop. Consequently, if you would like to catch fish, you probably would not want to spend most of your time in the oligotrophic gyres of the open ocean or the middle of Lake Superior. Because of their critical metabolic function in the biosphere, bacteria have significant impacts on the geochemistry of soils, lakes, rivers and oceans, including cycling and food web dynamics of contaminants, such as mercury and PCB's.

I have examined microbial processes in a wide variety of habitats; pelagic and benthic, freshwater and marine, lotic and lentic, and natural and human-impacted systems. I am particularly interested in the impacts of humans on microbial functions in ecosystems and global biogeochemical processes.

Selected publications

Godwin, Casey Michael, and James B Cotner. "Stoichiometric Flexibility in Diverse Aquatic Heterotrophic Bacteria Is Coupled to Differences in Cellular Phosphorus Quotas." Frontiers in Microbiology 6 (2015): doi:10.3389/fmicb.

Godwin, Casey M, and James B Cotner.  Aquatic Heterotrophic Bacteria Have Highly Flexible Phosphorus Content and Biomass Stoichiometry.  The ISME journal (2015) doi:10.1038/ismej.2015.34.

Godwin CM, Cotner JB. 2014. Carbon:phosphorus homeostasis of aquatic bacterial assemblages is mediated by shifts in assemblage composition.  Aquat Microb Ecol 73:245-258.

Amado, André M, James B Cotner, Rose M Cory, Betsy L Edhlund, and Kristopher McNeill. "Disentangling the Interactions Between Photochemical and Bacterial Degradation of Dissolved Organic Matter: Amino Acids Play a Central Role." Microbial ecology (2014) doi:10.1007/s00248-014-0512-4.

Rocca, Jennifer D, Edward K Hall, Jay T Lennon, Sarah E Evans, Mark P Waldrop, James B Cotner, Diana R Nemergut, Emily B Graham, and Matthew D Wallenstein. "Relationships Between Protein-encoding Gene Abundance and Corresponding Process Are Commonly Assumed Yet Rarely Observed." The ISME journal (2014)doi:10.1038/ismej.2014.252.

Bellinger, Brent J, Benjamin A S Van Mooy, James B Cotner, Helen F Fredricks, Claudia R Benitez-Nelson, Jo Thompson, Anne Cotter, Michael L Knuth, and Casey M Godwin. "Physiological Modifications of Seston in Response to Physicochemical Gradients Within Lake Superior." Limnology and Oceanography 59, no. 3 (2014): doi:10.4319/lo.2014.59.3.1011.

Small, Gaston E, James B Cotner, Jacques C Finlay, Rebecca A Stark, and Robert W Sterner.  2014. Nitrogen Transformations at the Sediment–water Interface Across Redox Gradients in the Laurentian Great Lakes. Hydrobiologia 731, no. 1 (2014): doi:10.1007/s10750-013-1569-7.

Staley, Christopher, Trevor J. Gould, Ping Wang, Jane Phillips, James B. Cotner, and Michael J. Sadowsky. "Core Functional Traits of Bacterial Communities in the Upper Mississippi River Show Limited Variation in Response to Land Cover." Frontiers in Microbiology 5 (2014)doi:10.3389/fmicb.2014.00414.

Staley, Christopher, Trevor J. Gould, Ping Wang, Jane Phillips, James B. Cotner, and Michael J. Sadowsky. Bacterial Community Structure Is Indicative of Chemical Inputs in the Upper Mississippi River. Frontiers in Microbiology 5 (2014)doi:10.3389/fmicb.2014.00524.

Winemiller, Kirk O, Carmen G Montaña, Daniel L Roelke, James B Cotner, JoséVicente Montoya, Luzmila Sanchez, Maria Mercedes Castillo, and Craig A Layman. "Pulsing Hydrology Determines Top-down Control of Basal Resources in a Tropical River-floodplain Ecosystem." Ecological Monographs (2014).

Staley, Christopher, Tatsuya Unno, Trevor J Gould, Bruce Jarvis, Jane Phillips, James B Cotner, and Michael J Sadowsky. 2013. Application of Illumina Next-generation Sequencing to Characterize the Bacterial Community of the Upper Mississippi River. Journal of Applied Microbiology 115, no. 5 (2013): 1147-1158.

Hobbs, WO, DR Engstrom, SP Scottler, KD Zimmer, and JB Cotner. 2013. Estimating Modern Carbon Burial Rates in Lakes Using a Single Sediment Sample. Limnology and Oceanography-Methods 11 (2013): doi:10.4319/lom.2013.11.316.

T. Crews, J. Cotner and C. McCreary. 2013. Cultural beliefs, values, and the biogeochemical cycling of P, Chapter 7 in K. Wyant, J. Corman, and J.J. Elser (eds.), Phosphorus, Food, and Our Future, Oxford University Press, New York, USA (in press).

Peterson, Britt M, Ann M McNally, Rose M Cory, John D Thoemke, James B Cotner, and Kristopher McNeill. 2012. Spatial and Temporal Distribution of Singlet Oxygen in Lake Superior. Environmental science & technology 46, no. 13 (2012): 7222-7229.

Theissen, Kevin M, William O Hobbs, Joy M Ramstack Hobbs, Kyle D Zimmer, Leah M Domine, James B Cotner, and Shinya Sugita.  2012. The Altered Ecology of Lake Christina: A Record of Regime Shifts, Land-use Change, and Management From a Temperate Shallow Lake. The Science of the Total Environment 433: doi:10.1016/j.scitotenv.2012.06.068.
Scott, J.T., J.B. Cotner and T.M. LaPara. 2012. Variable stoichiometry and homeostatic regulation of bacterial biomass elemental composition. Frontiers in Aquatic Microbiology 3 (42) 1-8; doi: 10.3389/fmicb.2012.00042. 

Cotner, James B, and Edward K Hall. "Comment on "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus"." Science 332, no. 6034 (2011): doi:10.1126/science.1201943.

Kolka, R. K.; Mitchell, C.P.J.; Jeremiason, J. D.; Hines, N. A.; Grigal, D. F.; Engstrom, D. R.; Coleman-Wasik, J.K.; Nater, E. A.; Swain, E.B.; Monson, B. A.; Fleck, J. A.; Johnson, B.; Almendinger, J. E.; Branfireun, B. A.; Brezonik, P.L.; Cotner, J.B. 2011. Mercury cycling in peatland watersheds. In “Kolka, R.K.; Sebestyen, S. .;  Verry, E. S.; Brooks, K.N., eds. Peatland biogeochemistry and watershed hydrology at the Marcell Experimental Forest. Boca Raton, FL: CRC Press: 349-370.

Cotner J.B., E.K. Hall, T. Scott  and M. Heldal. 2010. Freshwater bacteria are stoichiometrically flexible with a nutrient composition similar to seston. Front. Microbio. doi: 10.3389/fmicb.2010.00132
Biddanda, B., M. Ogdahl, and J.B. Cotner. 2000. Contribution of heterotrophic bacteria to planktonic biomass and respiration in lakes and the ocean. Submitted to Limnology and Oceanogra

Cotner, J.B. 1999. Heterotrophic bacterial growth and nutrient limitation in large, oligotrophic lakes and oceans. VerhInternatVereinLimnol. (In press)

Cotner, J.B., J.W. Ammerman, E.R. Peele, and E. Bentzen. 1997. Nutrient-limited bacterioplankton growth in the Sargasso Sea. Aquatic Microbial Ecology 13:141-149.

Cotner, J.B., W.S. Gardner, J.R. Johnson, R.H. Sada, J.F. Cavaletto, and R.T. Heath. 1995. Effects of zebra mussels (Dreissena polymorpha) on bacterioplankton: Evidence for both size-selective consumption and growth stimulation. Journal of Great Lakes Research 21:514-528.

Cotner, J.B., Jr. and W.S. Gardner. 1993. Heterotrophic bacterial mediation of ammonium and dissolved free amino acid fluxes in the Mississippi River plume. Marine Ecology Progress Series 93:75-87.

Cotner, J.B., Jr. and R.G. Wetzel. 1992. Uptake of dissolved inorganic and organic phosphorus compounds by phytoplankton and bacterioplankton. Limnology and Oceanography 37:232-243.


Ph.D., University of Michigan, Ann Arbor, 1990