All People

John Berges

  • Professor, Biological Sciences
  • Affiliate Faculty Member, School of Freshwater Sciences

Education

  • Lecturer, Queen's University of Belfast, 1996-2002
  • Postdoctoral Fellow Brookhaven National Laboratory 1994-6
  • PhD, University of British Columbia, 1994
  • MSc University of Guelph, 1989
  • BSc, University of Guelph, 1987

Courses Taught

BIOSCI-406 Marine Biology

BIOSCI-512 Limnology 1

BIOSCI-611 Recent Advances in Limnology and Oceanography

Teaching Interests

Marine and freshwater ecology

Biomathematics

Research Interests

My laboratory tackles questions in ecology and cell biology in aquatic organisms using a range of biophysical, physiological, biochemical and molecular tools. Although we tend to focus on planktonic systems, we are also interested in benthic and near-shore processes, and we work across the spectrum of living things, from bacteria to fishes. We move freely between the laboratory and the field. Our efforts have been informed by new genome sequence information becoming available, and we have been involved in several genome annotations of algal species.

We are especially interested in 1) developing indices of biological rates and processes in aquatic ecosystems using a variety of biochemical and molecular methods, especially those involving enzymes and 2) characterizing responses to stress and environmental change, using biophysical and biochemical approaches.

Invasive species offer a potentially useful way to examine ecosystem function, by looking at the the new organisms participate in the foodweb and local biogeochemical cycles.  The planktonic cladocerans Bythotrephes longimanus and Cercopagis pengoi have been of interest along with the more benthic mysid Hemimysis anomala. 

We have also become interested in the roles microplastics play in terms of their presence in the guts of crustaceans, and their interactions with organic contaminants.

Selected Publications

Flynn, K.J., Atkinson, A., Beardall, J., Berges, J.A., Boersma, M., Brunet, C., Calbet, A., Caron, D.A., Dam, H.G., Glibert, P.M., Hansen, P.J., Jin, P., Lønborg, C., Mayor, D.J., Menden-Deuer, S., Mock, T., Mulholland, M.R., Needham, D.M., Polimene, L., Poulton, A.J., Robinson, C., Rokitta, S.D., Rost, B., Saiz, E., Scanlan, D.J., Schmidt, K., Sherr, E., Stoecker, D.K., Svensen, C., Thiele, S., Thingstad, T.F., Våge, S., 2025. More realistic plankton simulation models will improve projections of ocean ecosystem responses to global change. Nature Ecology & Evolution 9: 1562–1570. doi.org/10.1038/s41559-025-02788-3     
Wachala, S.N., Janssen, J., Young, E.B., Berges, J.A., 2025. Seasonal population characteristics and gut contents of the invasive mysid, Hemimysis anomala, in Milwaukee Harbor, Lake Michigan. Journal of Great Lakes Research 51: 102462.  doi.org/10.1016/j.jglr.2024.102462.
Trevathan-Tackett, S.M., Kepfer-Rojas, S., Malerba, M., Macreadie, P.I., Djukic, I., Zhao, J., Young, E.B., York, P.H., Yeh, S.-C., Xiong, Y., Winters, G., Whitlock, D., Weaver, C.A., Watson, A., Visby, I., Tylkowski, J., Trethowan, A., Tiegs, S., Taylor, B., Szpikowski, J., Szpikowska, G., Strickland, V.L., Stivrins, N., Sousa, A.I., Sinutok, S., Scheffel, W.A., Santos, R., Sanderman, J., Sánchez-Carrillo, S., Sanchez-Cabeza, J.-A., Rymer, K.G., Ruiz-Fernandez, A.C., Robroek, B.J.M., Roberts, T., Ricart, A.M., Reynolds, L.K., Rachlewicz, G., Prathep, A., Pinsonneault, A.J., Pendall, E., Payne, R., Ozola, I., Onufrock, C., Ola, A., Oberbauer, S.F., Numbere, A.O., Novak, A.B., Norkko, J., Norkko, A., Mozdzer, T.J., Morgan, P., Montemayor, D.I., Martin, C.W., Malone, S.L., Major, M., Majewski, M., Lundquist, C.J., Lovelock, C.E., Liu, S., Lin, H.-J., Lillebo, A., Li, J., Kominoski, J.S., Khuroo, A.A., Kelleway, J.J., Jinks, K.I., Jerónimo, D., Janousek, C., Jackson, E.L., Iribarne, O., Hanley, T., Hamid, M., Gupta, A., Guariento, R.D., Grudzinska, I., da Rocha Gripp, A., González Sagrario, M.A., Garrison, L.M., Gagnon, K., Gacia, E., Fusi, M., Farrington, L., Farmer, J., de Assis Esteves, F., Escapa, M., Domańska, M., Dias, A.T.C., de los Santos, C.B., Daffonchio, D., Czyryca, P.M., Connolly, R.M., Cobb, A., Chudzińska, M., Christiaen, B., Chifflard, P., Castelar, S., Carneiro, L.S., Cardoso-Mohedano, J.G., Camden, M., Caliman, A., Bulmer, R.H., Bowen, J., Boström, C., Bernal, S., Berges, J.A., Benavides, J.C., Barry, S.C., Alatalo, J.M., Al-Haj, A.N., Adame, M.F., 2024. Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands. Environmental Science & Technology 58, 21589-21603. doi.org/10.1021/acs.est.4c02116.
Berges, John A., Young, Erica B., Thamatrakoln, Kimberlee, and Taylor, Alison R. “Chapter 14: From genes to ecosystems: using molecular information from diatoms to understand ecological processes” Advances in Phytoplankton Ecology: Applications of Emerging Technologies (2022).
Strzepek, Robert, Nunn, Brook, Bach, Lennart, Berges, John A., Young, Erica B., and Boyd, Philip. “The ongoing need for rates: can physiology and omics come together to co-design the measurements needed to understand complex ocean biogeochemistry?” Journal of Plankton Research fbac026. (2022).
Young, Erica B., Reed, Lindsay A., and Berges, John A. “Growth parameters and responses of green algae across a gradient of phototrophic, mixotrophic and heterotrophic conditions” PEER J (2022).
Gareis, J A., Larson , E I., Ardón , M, Berges, John A., Brandt , J E., Busch, K M., Chraibi, V L., Gallagher, E N., Hondula , K L., Kincaid , D W., Levine , T D., Little , C J., Nodine , E R., Rock, A M., Shogren , A J., and Vanni , M J. “Using Wikipedia Assignments to Teach Critical Thinking and Scientific Writing in STEM Courses” Frontiers in Education 7. (2022): 905777.
Berges, John A., Driskill, Allison M., Guinn, Emily J., Pokrzywinski, Kaytee, Quinlan, Jessica, von Korff, Benjamin, and Young, Erica B. “Role of nearshore benthic algae in the Lake Michigan silica cycle” PLOS one 16.8 (2021): e0256838.
Minina, Elena A., Staal, Jens, Alvarez, Vanina E., Berges, John A., Berman-Frank, Ilana, Beyaert, Rudi, Bidle, Kay D., Bornancin, Frederic, Casanova, Magali, Cazzulo, Juan J., Choi, Chang J., Coll, Nuria S., Dixit, Vishva M., Dolinar, Marko, Fasel, Nicolas, Funk, Christiane, Gallois, Patrick, Gevaert, Kris, Gutierrez-Beltran, Emilio, Hailfinger, Stephan, Klemencic, Marina, Koonin, Eugene V., Krappmann, Daniel, Linusson, Anna, Machado, Mauricio F. M., , Madeo, Frank, Megeney, Lynn A., Moschou, Panagiotis N., Mottram, Jeremy C., Nystrom, Thomas, Osiewacz, Heinz D., Overall, Christopher M., Pandey, Kailash C., Ruland, Juergen, Salvesen, Guy S., Shi, Yigong, Smertenko, Andrei, Stael, Simon, Stahlberg, Jerry, Fernanda Suarez, Maria, , Thome, Margot, Tuominen, Hannele, Van Breusegem, Frank, , van der Hoorn, Renier A. L., , Vardi, Assaf, Zhivotovsky, Boris, Lam, Eric, and Bozhkov, Peter V. “Classification and Nomenclature of Metacaspases and Paracaspases: No More Confusion with Caspases” MOLECULAR CELL 77.5 (2020): 927-929.
Berges, John A., Gronquist, David J., Engevold, Paul G., Thorngate-Rein, Nathaniel, Sandgren, Craig D., Bowen, Kelly L., and Currie, Warren J. S., . “Immunochemical methods for identification of prey in freshwater zooplankton” LIMNOLOGY AND OCEANOGRAPHY-METHODS 18.6 (2020): 221-234.
Kozik, Christine, Young, Erica B., Sandgren, Craig D., and Berges, John A. “Cell death in individual freshwater phytoplankton species: relationships with population dynamics and environmental factors” European Journal of Phycology 54.3 (2019): 369-379.
Hanson, Alicia M., Berges, John A., and Young, Erica B. “Virus diversity and relationship to bacteria and chlorophyll across a freshwater trophic gradient in the Lake Michigan watershed” Hydrobiologia 741.1 (2017): 93-108.
Luo, Shuai, Berges, John A., He, Zhen, and Young, Erica B. “Algal-Microbial Community Collaboration for Energy Recovery and Nutrient Remediation from Wastewater in Integrated Photo-Bioelectrochemical Systems” Algal Research (2017).
Young, Erica B., and Berges, John A. “Nitrate reductase: a nexus of disciplines, organisms and metabolism” Aquatic Nutrient Biogeochemistry and Microbial Ecology: A Dual Perspective Ed. Glibert, Patricia. (2016).
Young, Erica B., and Berges, John A. “Nitrogen stress in the marine environment: from scarcity to surfeit” Stressors in the Marine Environment: physiological responses and ecological implications Ed. Solan, Martin. (2016).
Engevold, Paul, Young, Erica B., Sandgren, Craig D., and Berges, John A. “Pressure from top and bottom: lower food web responses to nutrient cycling changes and invasive species in western Lake Michigan” Journal of Great Lakes Research 41. (2015).
Berges, John A., Choi, Chang Jae, and . “Cell death in algae: physiological processes and relationships with stress” Perspectives in Phycology (2014).
Berges, John A., Jiang, Y, Sterner, R W., Bullerjahn, G S., Ivanikova, N A., and McKay, R M. “Identification of factors constraining nitrate assimilation in Lake Superior, Laurentian Great Lakes” Hydrobiologia 731. (2014): 81-94.
Schaefer, Wayne, Schmitz, Mark, Blazer, Vicki, Ehlinger, Timothy J., and Berges, John A. “Seasonal variation in the abundance of sandercyanin, a novel blue pigment in the mucus of walley (Sander vitreus) in northwestern Ontario, Canada” Can. J. Fish. Aquat. Sci 72. (2014): 1-9.
Hellweger, F L., Frederick, N D., and Berges, John A. “Age-correlated stress resistance improves fitness of yeast: support from agent-based simulations” BMC Systems Biology 8. (2014): 18.