John Berges

Biological Sciences

Education and Experience

  • Affiliate Faculty Member, School of Freshwater Sciences, UW-Milwaukee, 2011-present
  • 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


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.

Selected Publications

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.
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).
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).
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.
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.
Ribalet, F, Bastianini, M, Vidoudez, C, Berges, John A., Ianoura, A, Miralto, A, Pohnert, G, Romano, G, Wichard, T, and Casotti, R. “Phytoplankton cell lysis associated with polyunsaturated aldehyde release in the northern Adriatic Sea.” PloS One 9.1 (2014): e85947.
Bechette, Audrey, Stojsavljevic, Thomas, Tessmer, Maxx, Berges, John A., Pinter, Gabriella A., and Young, Erica B. “Mathematical Modeling of Bacteria-Virus Interactions in Lake Michigan Incorporating Phosphorus Content.” Journal of Great Lakes Research, Elsevier 39.4 (2013).
Gronquist, David, and Berges, John A. “Effects of aquarium-related stresses on the zebrafish, Danio rerio:a comparison of behavioral, physiological and biochemical indicators.” Journal of Aquatic Animal Health 25. (2013): 53-65.
Choi, Chang Jae, and Berges, John A. “New types of metacaspases in phytoplankton reveal diverse origins of cell death proteases.” Cell Death and Disease 4. (2013): e490.
Xiao, Li, Young, Erica B., Berges, John A., and He, Zhen. “Integrated Photo-Bioelectrochemical System for Contaminant Removal and Bioenergy Production.” Environmental Science and Technology 46. (2012): 11459-11466.
Franklin, Daniel J., Airs, Ruth L., Fernandes, Michelle, Bell, Thomas G., Bongaerts, Roy G., Berges, John A., and Malin, Gill. “Identification of senescence and death using live/dead stains and chlorophyll alterations in Emiliania huxleyi and Thalassiosira pseudonana.” Limnology and Oceanography 57. (2012): 305-317.
Franklin, Daniel J., Choi, Chang J., Hughes, Claire J., Malin, Gillian, and Berges, John A. “Effect of dead phytoplankton cells on the apparent efficiency of Photosystem II.” Mar. Ecol. Prog. Ser. 382. (2009): 35-40.
Young, Erica B., Berges, John A., and Dring, Matthew J. “Physiological responses of intertidal marine brown algae to nitrogen deprivation and resupply of nitrate and ammonium.” Physiol. Plant. 135. (2009): 400-11.
Berges, John A., and Mulholland, Margaret. “Chapter 32: Enzymes and N Cycling.” Nitrogen in the Marine Environment. Ed. Capone, D. G. Elsevier, (2008): 1361-1420.
Kirkpatrick, A. J., Gerhardt, A., Dick, J. T., Laming, P., and Berges, John A. “Suitability of Crangonyx pseudogracilis (Crustacea: Amphipoda) as an early warning indicator in the Multispecies Freshwater Biomonitor.” Env. Sci. Pollut. Res. 13. (2006): 242-250.
Franklin, D. J., Brussaard, C. P., and . “What is the role and nature of programmed cell death in phytoplankton ecology?.” Eur. J. Phycol. 41. Ed. Berges, John A. (2006): 1-14.
Franklin, D. J., Hoegh-Guldberg, O., Jones, R. J., and Berges, John A. “Cell death and degeneration in the symbiotic dinoflagellates of the Stylophora pistillata (Esper) in response to the combined effects of elevated temperature and light.” Mar. Ecol. Prog. Ser. 272. (2004): 117-130.
Berges, John A., Gibson, C. E., and Stewart, B. M. “Physiological responses of phytoplankton communities in the Irish Sea to simulated upwelling.” Hydrobiologia 517. (2004): 121-132.
Armbrust, E. V., Berges, John A., Bowler, C., Green, B. R., Martinez, D., Putnam, N. H., Zhou, S., Allen, A. E., Apt, K. E., Bechner, M., Brzezinski, M. A., Chaal, B. K., Chiovitti, A., Davis, A. K., Demarest, M. S., Detter, J. C., Glavina, T., Goodstein, D., Hadi, M. Z., Hellsten, U., Hildebrand, M., Jenkins, B. D., Jurka, J., Kapitonov, V. V., Kröger, N., Lau, W. W., Lane, T. W., Larimer, F. W., Lippmeier, J. C., Lucas, S., Medina, M., Montsant, A., Obornik, M., Parker, M. S., Palenik, B., Pazour, G. J., Richardson, P. M., Rynearson, T. A., Saito, M. A., Schwartz, D. C., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F. P., and Rokhsar, D. S. “The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.” Science 306.5693 (2004): 79-86.