Publications

  1. T. S. George, C. D. Giles, D. Menezes-Blackburn, L. M. Condron, A. C. Gama-Rodrigues, D. Jaisi, F. Lang, A. L. Neal, M. I. Stutter, D. S. Almeida, R. Bol, K. G. Cabugao, L. Celi, J. B. Cotner and G. Feng and others. "Organic Phosphorus in the Terrestrial Environment: A Perspective on the State of the Art and Future Priorities." Plant and Soil (2017)doi:10.1007/s11104-017-3391-x.
  2. Phillips, Katherine N., Casey M. Godwin, and James B. Cotner. "The Effects of Nutrient Imbalances and Temperature on the Biomass Stoichiometry of Freshwater Bacteria." Frontiers in Microbiology 8 (2017)doi:10.3389/fmicb.2017.01692.
  3. Jeyasingh, Punidan D, Jared M Goos, Seth K Thompson, Casey M Godwin, and James B Cotner. "Ecological Stoichiometry Beyond Redfield: An Ionomic Perspective on Elemental Homeostasis." Frontiers in Microbiology 8 (2017).
  4. Cotner, James B. 2016. ”Nitrogen Is Not a ‘House of Cards’." Environ Sci Technol 51, no. 1: doi:10.1021/acs.est.6b04890. http://dx.doi.org/10.1021/acs.est.6b04890.
  5. Godwin, Casey M, Emily A Whitaker, and James B Cotner. "Growth Rate and Resource Imbalance Interactively Control Biomass Stoichiometry and Elemental Quotas of Aquatic Bacteria." Ecology. doi:10.1002/ecy.1705.
  6. Ramstack Hobbs, Joy M, William O Hobbs, Mark B Edlund, Kyle D Zimmer, Kevin M Theissen, Natalie Hoidal, Leah M Domine, Mark A Hanson, Brian R Herwig, and James B Cotner. "The Legacy of Large Regime Shifts in Shallow Lakes.” Ecological Applications 26, no. 8 (2016): 2660-2674.
  7. Hall, Ed K, Don R Schoolmaster Jr, Andre M Amado, Edward G Stets, Jay T Lennon, Leah Domine, and Jim B Cotner. 2016. ”Scaling Relationships Among Drivers of Aquatic Respiration: From the Smallest to the Largest Freshwater Ecosystems." Inland Waters 6: 1-10.
  8. Pan, Tiffany, Kelsey Gladen, Elizabeth C Duncan, Sehoya Cotner, James B Cotner, Daniel C McEwen, and Brian D Wisenden. "Bold, Sedentary Fathead Minnows Have More Parasites." Zebrafish 13, no. 4 (2016): doi:10.1089/zeb.2015.1185.
  9. Staley, Christopher, Trevor J Gould, Ping Wang, Jane Phillips, James B Cotner, and Michael J Sadowsky. 2016. ”Sediments and Soils Act As Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River." Microbial ecology doi:10.1007/s00248-016-0729-5.
  10. Staley, Christopher, Trevor J Gould, Ping Wang, Jane Phillips, James B Cotner, and Michael J Sadowsky. 2015. ”High-throughput Functional Screening Reveals Low Frequency of Antibiotic Resistance Genes in DNA Recovered From the Upper Mississippi River.” Journal of Water and Health 13: 693-703.
  11. Staley, Christopher, Trevor J Gould, Ping Wang, Jane Phillips, James B Cotner, and Michael J Sadowsky. "Evaluation of Water Sampling Methodologies for Amplicon-based Characterization of Bacterial Community Structure." Journal of Microbiological Methods 114 (2015): doi:10.1016/j.mimet.2015.05.003.
  12. Zimmer, Kyle D., William O. Hobbs, Leah M. Domine, Brian R. Herwig, Mark A. Hanson, and James B. Cotner. "Uniform Carbon Fluxes in Shallow Lakes in Alternative Stable States." Limnol. Oceanogr. (2015): doi:10.1002/lno.10215.
  13. Godwin, Casey Michael, and James B Cotner. 2015. ”Stoichiometric Flexibility in Diverse Aquatic Heterotrophic Bacteria Is Coupled to Differences in Cellular Phosphorus Quotas." Frontiers in Microbiology 6: doi:10.3389/fmicb.
  14. Godwin, Casey M, and James B Cotner. 2015. Aquatic Heterotrophic Bacteria Have Highly Flexible Phosphorus Content and Biomass Stoichiometry. The ISME Journal doi:10.1038/ismej.2015.34.
  15. Staley, Christopher, Dylan Johnson, Trevor J Gould, Ping Wang, Jane Phillips, James B Cotner, and Michael J Sadowsky. 2015. ”Frequencies of Heavy Metal Resistance Are Associated with Land Cover Type in the Upper Mississippi River." The Science of the Total Environment 511: doi:10.1016/j.scitotenv.2014.12.069.
  16. 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.
  17. Staley, Christopher, Trevor J Gould, Ping Wang, Jane Phillips, James B Cotner, and Michael J Sadowsky. 2015. ”Species Sorting and Seasonal Dynamics Primarily Shape Bacterial Communities in the Upper Mississippi River." The Science of the Total Environment 505: doi:10.1016/j.scitotenv.2014.10.012.
  18. Amado, André M, James B Cotner, Rose M Cory, Betsy L Edhlund, and Kristopher McNeill. 2014. ”Disentangling the Interactions Between Photochemical and Bacterial Degradation of Dissolved Organic Matter: Amino Acids Play a Central Role." Microbial Ecology doi:10.1007/s00248-014-0512-4.
  19. 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. 2014. ”Relationships Between Protein-encoding Gene Abundance and Corresponding Process Are Commonly Assumed Yet Rarely Observed." The ISME Journal. doi:10.1038/ismej.2014.252.
  20. 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. 2014. ”Physiological Modifications of Seston in Response to Physicochemical Gradients Within Lake Superior." Limnology and Oceanography 59, no. 3: doi:10.4319/lo.2014.59.3.1011.
  21. 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.
  22. Staley, Christopher, Trevor J. Gould, Ping Wang, Jane Phillips, James B. Cotner, and Michael J. Sadowsky. 2014. ”Core Functional Traits of Bacterial Communities in the Upper Mississippi River Show Limited Variation in Response to Land Cover." Frontiers in Microbiology 5 doi:10.3389/fmicb.2014.00414.
  23. 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. 2014. Frontiers in Microbiology 5 doi:10.3389/fmicb.2014.00524.
  24. Winemiller, Kirk O, Carmen G Montaña, Daniel L Roelke, James B Cotner, JoséVicente Montoya, Luzmila Sanchez, Maria Mercedes Castillo, and Craig A Layman. 2014. ”Pulsing Hydrology Determines Top-down Control of Basal Resources in a Tropical River-floodplain Ecosystem." Ecological Monographs 84: 621-635.
  25. 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: 1147-1158.
  26. 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: doi:10.4319/lom.2013.11.316.
  27. 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.
  28. 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: 7222-7229.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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
  34. Cory, R M, K McNeill, J B Cotner, A Amado, J M Purcell, and A G Marshall. 2010. Singlet Oxygen in the Coupled Photochemical and Biochemical Oxidation of Dissolved Organic Matter. Environmental Science & Technology 44: 3683-3689.
  35. Tranvik, L.J., J.A. Downing, J.B. Cotner and others. 2009. Lakes and reservoirs as regulators of carbon cycling and climate. Limnology and Oceanography 54: 2298-2314.
  36. Cotner, J.B., J. Kenning and J.T. Scott. 2009. The microbial role in littoral zone biogeochemical processes: Why Wetzel was right. Verh. Internat. Verein. Limnol. 30 (6): 981-984.
  37. Hall, E.K., A.R. Dzialowski, S. M. Stoxen, and J.B. Cotner. 2009. The effect of temperature on the coupling between phosphorus and growth in natural bacterioplankton communities. Limnology and Oceanography 54: 880-889.
  38. Cory, R.M., J.B. Cotner and K. McNeill. 2009. Quantifying interactions between singlet oxygen and aquatic fulvic acids. Environmental Science and Technology 43: 718-723.
  39. Boreen, A. L., B. L. Edhlund, J. B. Cotner, and K. McNeill. 2008. Indirect photodegradation of dissolved free amino acids: The contribution of singlet oxygen and the differential reactivity of DOM from various sources. Environmental Science and Technology 42: 5492-5498.
  40. Zhang, Z., N. D. Pendse, K. N. Phillips, J. B. Cotner, and A. Khodursky. 2008. Gene expression patterns of sulfur starvation in Synechocystis sp PCC 6803. BMC Genomics 9.
  41. Waples, J.T., B. Eadie, J.V. Klump, M. Squires, J. Cotner, and G. McKinley. 2008. The Laurentian Great Lakes in Halles, B. Continental Margins: A synthesis and planning workshop. Report of the North American Continental Margins Working Group for the U.S. Carbon Cycle Scientific Steering Group and Interagency Working Group. U.S. Carbon Cycle Science Program, Washington, DC, 110 pp.
  42. Stets, E.G., and J.B. Cotner. Littoral zones as sources of biodegradable dissolved organic carbon in lakes. Canadian Journal of Fisheries and Aquatic Science 65 :2454-2460.
  43. Kerfoot, W. C., JW Budd, SA Green, JB Cotner, BA Biddanda, DJ Schwab and HA Vanderploeg. 2008. Doughnut in the desert: Late-winter production pulse in southern Lake Michigan. Limnology and Oceanography 53: 589-604.
  44. Johengen, T.H., B.A. Biddanda and J. B. Cotner. Stimulation of Lake Michigan plankton by sediment resuspension and river runoff. 2008. Journal of Great Lakes Research 34: 213-227.
  45. Hall, E.K., C. Neuhauser and J.B. Cotner. 2008. Toward a mechanistic understanding of how natural bacterial communities respond to changes in temperature in aquatic ecosystems. ISME Journal 2: 471-481.
  46. Stets, E.G. and J.B. Cotner. 2008. The influence of dissolved organic carbon on bacterial phosphorus uptake and bacteria-phytoplankton dynamics in two Minnesota lakes. Limnology and Oceanography 53: 137-147.
  47. Hall, E. K.; Cotner, J. B. 2007. Interactive effect of temperature and resources on carbon cycling by freshwater bacterioplankton communities. Aquatic Microbial Ecology 49: 35-45.
  48. Amado, A.M., J.B. Cotner, A.L. Suhett, F. de A. Esteves, V. F. Farjalla. 2007. Contrasting interactions among dissolved organic carbon substrates for photochemical and microbial degradation processes in aquatic ecosystems. Aquatic Microbial Ecology 49: 25-34.
  49. Cotner, J. B., J. V. Montoya, D. L. Roelke, and K. O. Winemiller. 2006. Seasonally variable riverine production in the Venezuelan llanos. Journal of the North American Benthological Society 25: 171-184.
  50. Montoya, J. V., D. L. Roelke, K. O. Winemiller, J. B. Cotner, and J. A. Snider. 2006. Hydrological seasonality and benthic algal biomass in a Neotropical floodplain river. Journal of the North American Benthological Society 25: 157-170.
  51. Roelke, D. L., J.B. Cotner and others 2006. Optically determined sources of allochthonous organic matter and metabolic characterizations in a tropical oligotrophic river and associated lagoon. Journal of the North American Benthological Society 25: 185-197.
  52. Winemiller, K. O., J. V. Montoya, D. L. Roelke, C. A. Layman, and J. B. Cotner. 2006. Seasonally varying impact of detritivorous fishes on the benthic ecology of a tropical floodplain river. Journal of the North American Benthological Society 25: 250-262.
  53. Cotner, J.B., W. Makino, B.A. Biddanda. 2006. Temperature affects stoichiometry and biochemical composition of Escherichia coli. Microbial Ecology 52:26-33.
  54. Hudson, M. J., D. L. Swackhamer, and J. B. Cotner. 2005. Effect of microbes on contaminant transfer in the Lake Superior food web. Environmental Science & Technology 39: 9500-9508.
  55. Weider, L.J., Elser, J.J., Crease, T.J., Mateos, M., Cotner, J.B., and T.A. Markow. 2005. The functional significance of ribosomal(r)DNA variation: Impacts on the evolutionary ecology of organisms. Annual Review of Ecology, Systematics and Evolution 36: 219-242.
  56. Cotner, J B, B A Biddanda, W Makino, and T Stets. 2004. Organic Carbon Biogeochemistry of Lake Superior. Aquatic Ecosystem Health and Management 7: 451-464.
  57. Makino, W. and J.B. Cotner. 2004. Elemental stoichiometry of a heterotrophic bacterial community in a freshwater lake: Implications for growth- and resource-dependent variations. Aquatic Microbial Ecology 34:33-41.
  58. Cotner, J.B., M. Suplee, N. Chen and D. Shormann. 2004. Carbon and nutrient cycling in a hypersaline lagoon. Estuarine, Coastal and Shelf Science 59: 639-652.
  59. Bergstedt, M.S., M. Hondzo, and J.B. Cotner. 2004. The effects of small scale fluid motion on bacterial growth and respiration. Freshwater Biology 49: 28-40.
  60. Chen, C. S., L. X. Wang, R. B. Ji, J. W. Budd, D. J. Schwab, D. Beletsky, G. L. Fahnenstiel, H. Vanderploeg, B. Eadie, and J. Cotner. 2004. Impacts of suspended sediment on the ecosystem in Lake Michigan: A comparison between the 1998 and 1999 plume events. Journal of Geophysical Research-Oceans 109.
  61. Chen, C. S., L. X. Wang, J. H. Qi, H. D. Liu, J. W. Budd, D. J. Schwab, D. Beletsky, H. Vanderploeg, B. Eadie, T. Johengen, J. Cotner, and P. J. Lavrentyev. 2004. A modeling study of benthic detritus flux's impacts on heterotrophic processes in Lake Michigan. Journal of Geophysical Research-Oceans 109.
  62. Gardner, W.S., P. J. Lavrentyev, J. Cavaletto, M. McCarthy, B.J.Eadie, T. H. Johengen, and J.B. Cotner. 2004. The distribution and dynamics of nitrogen and microbial plankton in southern Lake Michigan during spring transition 1999-2000. Journal of Geophysical Research 109: Art. # C03007.
  63. Elser, J.J., K. Acharya, M. Kyle, J. Cotner, W. Makino, T. Markow, T. Watts, S. Hobbie, W. Fagan, J. Schade, and R.W. Sterner. 2003. General conditions for coupling of growth-RNA-phosphorus stoichiometry in diverse biota. Ecology Letters 6: 936-943.
  64. Ammerman, J.W., R.R. Hood, D.A. Case and J.B. Cotner. 2003. Phosphorus Deficiency in the Atlantic: An Emerging Paradigm in Oceanography. Eos: 84: 165, 170.
  65. Biddanda, B.A., and J.B. Cotner. 2003. Dual effect of sunlight on the bioavailability of limnetic dissolved organic matter and its role in the aquatic carbon cycle. Journal of Great Lakes Research 29: 228-241.
  66. Makino, W., J.B. Cotner, R.W. Sterner, and J.J. Elser. 2003. Are bacteria more like plants or animals? Growth rate and substrate dependence of bacterial C:N:P stoichiometry, Functional Ecology 17: 121-130.
  67. Woods, H.A., W. Makino, J.B. Cotner, S. Hobbie, J. F. Harrison, K. Acharya, J. J. Elser. 2003. Temperature and the chemical composition of poikilothermic organisms. Functional Ecology 17:237-245.
  68. Chen, C., R. Ji, D.J. Schwab, D. Beletsky, G.L. Fahnenstiel, M. Jiang, T.H. Johengen, H. Vanderploeg, B. Eadie, J.W. Budd, M.H. Bundy, W. Gardner, J. Cotner, and P.J. Lavrentyev. 2002. A model study of the coupled biological and physical dynamics in Lake Michigan. Ecol. Modeling. 152:145-168.
  69. Ji, R., C. Chen, J.W. Budd, D.J. Schwab, D. Beletsky, G.L. Fahnenstiel, T.H. Johengen, H. Vanderploeg, B. Eadie, J. Cotner, W. Gardner, and M.H. Bundy. 2002. Influences of suspended sediments on the ecosystem in Lake Michigan: a 3-D coupled bio-physical modeling experiment. Ecol. Modeling. 152: 169-190.
  70. Biddanda, B.A., and J.B. Cotner. 2002. Love handles in aquatic ecosystems: Role of dissolved organic carbon drawdown, resuspended sediments and terrigenous inputs in the carbon balance of a Great Lake (Michigan). Ecosystems 5: 431-445.
  71. Suplee, M.W. and J.B. Cotner. 2002. An evaluation of the importance of sulfate reduction and temperature to P fluxes from aerobic, lacustrine sediments. Biogeochemistry 61: 199-228.
  72. Cotner, J.B., and B.A. Biddanda. 2002. Small players, large role: Microbial influence on auto- heterotrophic coupling and biogeochemical processes in aquatic ecosystems. Ecosystems 5, 105-121.
  73. Cotner, J.B., M.L. Ogdahl, and B.A. Biddanda. 2001. dsDNA measurement in lakes with the fluorescent stain, PicoGreen, and application to bacterial bioassays. Aquatic Microbial Ecology 25: 65-74.
  74. Gardner, W.S., L. Yang, J.B. Cotner, T.H. Johengen, and P.J. Lavrentyev. 2001. Nitrogen dynamics in sandy freshwater sediments (Saginaw Bay, Lake Huron). Journal of Great Lakes Research. 27: 84-97.
  75. Biddanda, B., M. Ogdahl and J.B. Cotner. 2001. Dominance of bacterial metabolism in oligotrophic relative to eutrophic waters. Limnology and Oceanography 46: 730-739.
  76. Elser, J.J., R.W. Sterner, E. Gorokhova, W. Fagan, T. Markow, J. Cotner, J. Harrison, S. Hobbie, G. Odell, and L. Weider. 2000. Biological stoichiometry from genes to ecosystems. Ecology Letters 3: 540-550.
  77. Cotner, J.B., H. Bootsma, R. H. Sada, T. Johengen, J. F. Cavaletto, and W. S. Gardner. 2000. Nutrient limitation of heterotrophic bacteria in Florida Bay. Estuaries 23: 611-620.
  78. Cotner, J.B., T.H. Johengen, and B.A. Biddanda. 2000. Intense winter heterotrophic production stimulated by benthic resuspension. Limnology and Oceanography 45: 1672-1676.
  79. Winemiller, K.O., S. Tarim, D. Shormann, and J.B. Cotner. 2000. Spatial variation in fish assemblages of Brazos River oxbow lakes. Transactions of the American Fisheries Society 129:451-468.
  80. Cotner, JB. 2000. Heterotrophic bacterial growth and nutrient limitation in large, oligotrophic lakes and oceans. Verh. Internat. Verein. Limnol. 27: 1831-1835.
  81. Gardner, W.S., Lavrentyev, P.J, Bootsma, H.A., Cavaletto, J.F., Troncone, F., and Cotner, J.B. 2000. Effects of natural light on nitrogen dynamics in diverse aquatic environments. Verh. Internat. Verein. Limnol. 27: 64-73.
  82. Moore, C.K., and J.B. Cotner. 1998. Zooplankton community structure of Lake Livingston, Texas, as related to paddlefish food resources. Journal of Freshwater Ecology. 13: 115-128.
  83. 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.
  84. Shormann, D.E. and J.B. Cotner. 1997. The effects of benthivorous smallmouth buffalo (Ictiobus bubalus) on water quality and nutrient cycling in a shallow floodplain lake. Lake and Reservoir Management 13: 270-278.
  85. Gardner, W.S., J.F. Cavaletto, J.B. Cotner, and J.R. Johnson. 1997. Effects of natural light on nitrogen cycling rates in the Mississippi River plume. Limnology and Oceanography 42: 273-281.
  86. Suplee, Michael W. and James B. Cotner. 1996. The influence of organic carbon on oxygen dynamics and bacterial sulfate reduction in inland shrimp ponds. Aquaculture 145: 141-158.
  87. Gardner, W.S., R. Benner, R. Amon, J.B. Cotner, Jr., J. Cavaletto and J. Johnson. 1996. Effects of high molecular weight dissolved organic matter on nitrogen dynamics in the Gulf of Mexico Mississippi River Plume. Marine Ecology Progress Series 133: 287-297.
  88. Cotner, James B., Wayne S. Gardner, Jeffrey R. Johnson, Rosa H. Sada, Joann 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.
  89. Cotner Jr. 1995. Effects of the zebra mussel, Dreissena polymorpha, on community nitrogen dynamics in Saginaw Bay, Lake Huron. Journal of Great Lakes Research 21: 529-544.
  90. Gardner, W.S., R. Benner, G. Chin-Leo, J.B. Cotner, Jr., B.J. Eadie, J.F. Cavaletto and M.B. Lansing. 1994. Mineralization of organic material and bacterial dynamics in Mississippi River Plume water. Estuaries 7: 816-828.
  91. Eadie, B.J., R. Amon, R. Benner, J. Cavaletto, J. B. Cotner, W. S. Gardner, M. Lansing and D. Pakulski. 1994. Organic matter decomposition, nitrogen recycling, and oxygen consumption in the Mississippi River Plume/Gulf Shelf region. NECOP Synthesis Workshop Proceedings Louisiana Sea Grant.
  92. 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.
  93. Gardner, W.S., J.B. Cotner, Jr. and L. R. Herche. 1993. Chromatographic measurement of nitrogen mineralization rates in marine coastal waters with 15N. Marine Ecology Progress Series 93: 65-73.
  94. Benner, R., G. Chin-Leo, W. Gardner, B. Eadie, and J. Cotner. 1992. The fates and effects of riverine and shelf-derived DOM on Mississippi River plume/Gulf Shelf processes. Proceedings of the Nutrient Enhanced Coastal Ocean Productivity Workshop. pp. 84-94.
  95. 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.
  96. Cotner, J. B. Jr. and R. G. Wetzel. 1991. 5'-Nucleotidase activity in a eutrophic and an oligotrophic lake. Applied and Environmental Microbiology 57: 1306-1312.
  97. Cotner, J. B. Jr. and R. G. Wetzel. 1991. Characterization of bacterial phosphatases from different habitats in a small, hardwater lake, pp. 187-205 In R. Chrost, ed., Microbial Enzymes in Aquatic Environments.
  98. Cotner, J. B. Jr. and R. T. Heath. 1990. Iron redox state effects on photosensitive phosphorus release from dissolved humic materials. Limnology and Oceanography 35: 1175-1181.
  99. Cotner, J. B. Jr., and R. T. Heath. 1988. Potential phosphate release from phosphomonoesters by acid phosphatase in a bog lake. Archiv für Hydrobiologie 111: 329-338.
  100. Kieser, M. S. and J. B. Cotner, Jr. 1981. An analysis of the physical and chemical parameters of the Rock Run-Miller Creek watershed, Clark County, Ohio, as related to land use practices. Baccalauresearch 3: 52-70.

Non-peer reviewed:

Biddanda, B. A., J. B. Cotner and T. H. Johengen (2009): Toast to a Lake Brew. American Society of Limnology and Oceanography Bulletin 18 (3): 76.

Theses:

Cotner, J. B. 1990. Utilization of dissolved phosphorus compounds by bacteria and algae in lakes. Ph.D. thesis, University of Michigan, Ann Arbor, 137 pp. (Major professor: Robert G. Wetzel-deceased).

Cotner, J. B. Jr. 1984. Significance of dissolved phosphorus compounds in an acid bog lake. M.Sc. thesis, Kent State University, Kent, OH. 116 pp. (Major professor: Robert T. Heath).