Ed Carpenter


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Professor of Biology
Microbial Ecology
415) 338-3732


Research Interests
Our group has several major interests. One concerns nitrogen fixation in the sea. We work in tropical and subtropical waters on the biology and ecology of nitrogen fixation in marine planktonic cyanobacteria. We are attempting to determine factors that limit phytoplankton growth, as well as to understand the role of a species as a primary producer. This research requires a field program to collect phytoplankton and environmental data, and laboratory studies on species in culture. Other local research concerns studying the food web of a threatened fish in the San Francisco Bay Delta and understanding of nutrient cycling in Bay Area wetlands as it affects restoration efforts.Lastly, we have been investigating causes of blooms of harmful marine phytoplankton in coastal and estuarine waters. Proposed research involves:
1) a gene expression study of how ocean acidification would affect a calcifying marine phytoplankton species,
2) microbial activity in the hyporheic zone of Antarctic Dry Valley glacial melt water streams,
3) Saharan aeolian dust and its effect on plankton processes in the equatorial Atlantic and
4) influence of the Amazon River outflow on plankton productivity of the equatorial Atlantic Ocean.
Selected Publications
Benner, I., R.E. Diner, S. Lefebvre, D. Li, T. Komada, E.J. Carpenter, & J.H. Stillman. 2013. Warm and acidified conditions cause increased calcification but not shifts in expression of known calcification genes under long term culture  of the coccolithophore Emiliania huxleyi. Phil. Trans. Royal. Soc. B. vol 368 doi: 10.1098/rstb.2013.0049
Yeung, L.Y., W.M. Berelson, E.D. Young, M.G. Prokopenko, V.J. Coles, J.M. Montoya, E.J. Carpenter & P.L. Yager. 2012. Impact of diatom-diazotroph associations on carbon export in the Amazon River plume. Geophysical Research Letters. 39: LI8609, doi:10.1029/2012GLO53356
Niederberger, T.D., J.A. Sohm, J. Tirindelli, T. Gunderson, D.G. Capone, E.J. Carpenter & S. Craig Cary. 2012. Diverse and highly active diazotrophic assemblages inhabit ephemerally wetted soils of the Antarctic Dry Valleys. FEMS Microbiology Ecology doi: 10.1111/j.1574-6941.2012.01390
Luo, Y.W., S.C. Downey, S. Bonnet, D. Bottjer, D.G. Capone, E.J. Carpenter, M.J. Church, L.I. Falcon, R.A. Foster, K. Furya, S. Kitajima, R.M. Letelier, P. H. Moisander, C.M. Moore, J.A. Needoba, K.M. Orcutt, A.J. Poulton, P. Raimbault, A.P. Rees, T. Shiozaki, A. Subramaniam, T. Tyrrell, K.A. Turk, A. E. White, J.P. Zehr. 2012. Database of diazotrophs in Global Ocean: Abundances, Biomass and nitrogen fixation rates. Earth System Science Data. 4:47-73 doi:10.5194 essd-4-47-2012
Bergman, B., G. Sandh, S. Lin, J. Larsson, & E.J. Carpenter. 2012. Trichodesmium, a widespread marine cyanobacterium with unusual nitrogen fixation characteristics. FEMS Micro Rev.  doi: 10.1111/j.1574-6976.2012.00352.x.
Kimmerer, W. J., A.E. Parker, U.E. Lidstrom, & E.J. Carpenter. 2012. Short-term and interannual variability in primary production in the low-salinity zone of the San Francisco Estuary. Estuaries and Coasts. 35:913-929.
Sohm, J.A.,, A. Subramaniam, T. Gunderson, E. J. Carpenter & D. G. Capone. 2011. Nitrogen fixation by Trichodesmium and unicellular diazotrophs in the north Pacific subtropical gyre. Journal of Geophysical Research 116: 1-12
S. Lefebvre, I. Benner, M. Drake, P. Rossignol, K. Okimura, T. Komada, J. Stillman & E.J. Carpenter. 2011. Nitrogen source and pCO2 synergistically affect carbon allocation, growth and morphology of the coccolithophore Emiliania huxleyi. Global Change Biology (published online) doi 10.1111/j. 1365-2486.
Drake, J., E.J. Carpenter, M. Cousins, K.L. Nelson, A. Guido-Zarate, & K. Loftin. 2010. Effects of light and nutrients on seasonal phytoplankton succession in a temperate eutrophic coastal lagoon. Hydrobiologia 654 #1177-192.
Lin, S., , G. Sandh, H. Zhang , J. Cheng, K. Perkins, E.J. Carpenter & B. Bergman. 2009. Two flavodoxin genes in Trichodesmium (Oscillatoriales, Cyanophyta): Remarkable sequence divergence and possible functional diversification.  Journal of Experimental Marine Biology & Ecology 371:93-101.
Cohen, R., K. Walker, & E.J. Carpenter. 2009. Polysaccharide addition effects on rhizosphere nitrogen fixation rates and growth of  the California Cordgrass Spartina foliosa. Wetlands 29 (3):1063-1069
Subramaniam, A., E.J. Carpenter, S. Cooley, R. Del Veccio, C. Mahaffey, S. Sañudo-Wilhelmey, R. Shipe, A. Tovar-Sanchez, P.L. Yaeger, & D.G. Capone. 2008. Amazon River amplifies C and N cycles in the tropical North Atlantic Ocean. Proceeding of the National Academy of Sciences 105:10460-10465.
Carpenter, E.J. & D.G. Capone. 2008. Nitrogen fixation in the marine environment. IN: Nitrogen in the Marine Environment. Edited by: M. Mulholland, D. Bronk, D. Capone & E.J. Carpenter. Elsevier Press.
Eberl, R. & E.J. Carpenter. 2007.  Macrosetella gracilis (Harpacticoida) uses the cyanobacterium Trichodesmium spp. as a floating substrate but not as a major food source. Marine Ecology Progress Series 333:205-212.
Shipe, R. F., E.J. Carpenter, S. Govil, and D.G. Capone. 2007. Limitation of phytoplankton production by Si and N in the western Atlantic Ocean. Marine Ecology Prog. Ser. 338:33-45
Eberl, R., S. Cohen, F. Cipriano & E.J. Carpenter. 2007. Genetic diversity of the pelagic copepod Macrosetella gracilis on colonies of the cyanobacterium Trichodesmium.  Aquatic Biology 1, 1: 33-43.
Foster, R.A., D.G. Capone, E.J. Carpenter, C. Mahaffey, A. Subramaniam, & J.P. Zehr. 2007. Influence of the Amazon River plume on free-living and symbiotic cyanobacteria in the Western Tropical North Atlantic Ocean.  Limnology & Oceanography 52:517-532.
Shipe, R.F., J. Curatz, A. Subramaniam, E.J. Carpenter, & D.G. Capone. 2006. Diatom biomass and productivity in oceanic and plume-influenced waters of the western tropical Atlantic Ocean. Deep-Sea Res. I.
Foster, R.A., E.J. Carpenter & B. Bergman. 2006. Unicellular cyanobionts in open ocean dinoflagellates, radiolarians and tintinnids: ultrastructural characterization and immuno-localization of nitrogenase and phycoerythrin. Journal of Phycology 42:453-463