John A. Berges
John A. Berges
Associate Professor
Ecophysiology and Biochemistry
Phytoplankton and Zooplankton

BSc University of Guelph 1987
MSc University of Guelph 1989
PhD University of British Columbia 1994
Postdoctoral Fellow Brookhaven National Laboratory 1994-6
Lecturer Queen's University of Belfast 1996-2002
Affiliate Faculty Member, School of Freshwater Sciences, UWM, 2011-present

Office: Lapham 587
Phone: 414-229-3258
FAX: 414-229-3926
Personal Homepage:

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.

  1. Developing indices of biological rates and processes in aquatic ecosystems
    We work with a variety of biochemical and molecular methods to examine ecological processes and estimate rates in both marine and freshwaters.
    1. a) We have used measurements of the enzyme nitrate reductase (NR) to examine rates of nitrogen uptake and metabolism in marine and freshwater phytoplankton and macroalgae, both in the laboratory and in the field. There are several interesting questions that could be addressed in Lake Michigan, including origins of deep-water nitrite maxima, and the relative importance of new versus recycled nitrogen sources in the lake ecosystem.
    2. b) The significance of ‘natural’ mortality and pathogenesis in aquatic ecosystems is poorly understood. Biochemical and molecular methods are being used to understand how phytoplankton cells die under different stresses, and how such death related to processes like apoptosis. We are also working with bacterial and algal viruses found in local freshwaters, and examining how they vary seasonally.
    3. c) The biogeochemical processes affecting silicate and sulfur are not well understood in many aquatic systems. We are examining blooms of the macroalga, Cladophora,in Lake Michigan to understand the factors driving them, and how they affect silica cycling. We are also measuring sulfur content of marine and freshwater algae to see how it varies under different environmental conditions, and determine the location of the major pools of S.
    4. d) We are using antibodies raised against putative prey species to examine the diets of the invasive zooplankton predators Bythotrephes longimanus and Cercopagis pengoi and make predictions about their effects on in Lake Michigan food webs.
  2. Characterizing responses to stress and environmental change
    Our interests in stress responses and acclimation to different environmental conditions span a wide range of organisms including phytoplankton, zooplankton, corals and fishes, and include work in the laboratory and in the field.
    1. a) Measurements of fluorescence emissions (Fv:Fm) in phytoplankton and macroalgae have helped us to assess photosynthetic efficiency and how it changes under different conditions.
    2. b) Stress response proteins (some of which are proteases) have been of considerable interest in examing responses to freezing in phytoplankton species, and in characterizing stress responses in fish under typical aquarium conditions (vibration, crowding, lighting).
    3. c) We have also been interested in acclimation of seaweeds to high concentrations of heavy metals, measured using ICPMS methods. Some species show remarkable tolerances and may be useful in biomonitoring and/or bioremediation of metals wastes.
  3. Selected Publications

    Choi, C.J. and J.A. Berges. 2013. New types of metacaspases in phytoplankton reveal diverse origins of cell death proteases. Cell Death and Disease 4: e490; doi:10.1038/cddis.2013.21.

  4. Gronquist, D. and J.A. Berges. 2013. Effects of aquarium-related stressors on the Zebrafish: A comparison of behavioral, physiological, and biochemical indicators. Journal of Aquatic Animal Health 25: 53-65

  5. Choi, C.J., Berges, J.A. and E.B. Young. 2012. Rapid effects of diverse toxic water pollutants on chlorophyll a fluorescence: Variable responses among freshwater microalgae. Water Resources 46:2 2615-26

  6. Franklin, D.J., Airs, R.L., Fernades, M., Bell, T.G., Bongaerts, R.J., Berges, J.A. and G. Malin. 2012. Identification of senescence and death in Emiliania huxleyi and Thalassiosira pseudonana: Cell staining, chlorophyll alterations, and dimethylsulfoniopropionate (DMSP) metabolism. Limnology & Oceanography 57: 305-17.

  7. Xiao, L., Young, E.B., Berges, J.A. and Z. He. 2012. Integrated photo-bioelectrochemical system for contaminants removal and bioenergy production. Environmental Science & Technology 46: 11459-66.

  8. Fuhrman, K.M., Pinter, G.A. and J.A. Berges. 2011. Dynamics of a virus-host model with an intrinsic quota. Mathematical and Computer Modeling 53:716-30

  9. Franklin, D.J., Choi, C.J., Hughes, C., Malin, G. and J.A. Berges. 2009. Effect of dead phytoplankton cells on the apparent efficiency of Photosystem II. Marine Ecology Progress Series. 382: 35-40.

  10. Young, E.B., Berges, J.A., and M.J. Dring. 2009. Physiological responses of intertidal marine brown algae to nitrogen deprivation and resupply of nitrate and ammonium. Physiologia Plantarum 135: 200-11

  11. Bowler, C., allen, A.E., Badger, J.H., Grimwood, J., Jabbari, K., Kuo, A., Maheswari, U., Martens, C., Maumus, F., Otillar, R.P., Rayko, E., Salamov, A., Vandepoele, K., Beszteri, B., Gruber, A., Heijde, M., Katinka, M., Mock, T., Valentin, K., Verret, F., Berges, J.A., et al. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456: 239-44.

  12. Berges, J. A. and M. Mulholland. 2008. Chapter 32: Enzymes and N Cycling. pp. 1361-1420. In D. G. Capone et al. Nitrogen in the Marine Environment. Elsevier.

    Ribalet F., Berges J. A., Ianora A., and Cassotti R. 2007. Growth inhibition of cultured marine phytoplankton by toxic algal-derived polyunsaturated aldehydes. Aquatic Toxicology. 85: 219-227.

    Young E. B., Dring M. J., Savidge G., Birkett D. A., Berges J. A. 2007. Seasonal variations in nitrate reductase activity and internal N pools in intertidal brown algae are correlated with ambient nitrate concentrations. Plant Cell & Environment. 30: 764-774.

    Kirkpatrick, A.J., Gerhardt, A., Dick, J.T.A., Laming, P. & Berges, J.A. 2006. Suitability of Crangonyx pseudogracilis (Crustacea: Amphipoda) as an early warning indicator in the Multispecies Freshwater Biomonitor. Env. Sci. Pollut. Res. 13: 242-250.

    Franklin, D.J., Brussaard, C.P.D. & Berges, J.A. 2006. What is the role and nature of programmed cell death in phytoplankton ecology? Eur. J. Phycol. 41: 1-14.

    Armbrust, E.V., Berges, J.A., Bowler, C. et al. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution and metabolism. Science 306: 79-86.

    Franklin, D. J., O. Hoegh-Guldberg, R. J. Jones & J. A. Berges, 2004, 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. 272:117-130.

    Berges, J. A., C. E. Gibson & B. M. Stewart, 2004, Physiological responses of phytoplankton communities in the Irish Sea to simulated upwelling. Hydrobiologia 517: 121-132.

    Segovia, M., L. Haramaty, J. A. Berges, and P. G. Falkowski. 2003. Caspases and cell death in a unicellular chlorophyte alga: the evolution of apoptosis. Plant Physiol. 132: 95-105.