Paul Berube

MIT 48-106
15 Vassar Street
Cambridge, MA 02139

617.253.8686 (lab)
617.258.7009 (fax)
Email: pmberube at


2008 Ph.D. Microbiology. University of Washington, Seattle, WA
2000 B.A. Biology. Colby College, Waterville, ME


Academic Appointments:

2013-present. Research Scientist. Massachusetts Institute of Technology, Cambridge, MA
2008-2013. Postdoctoral Associate. Massachusetts Institute of Technology, Cambridge, MA


Research Interests:

The overarching goal of my research is to elucidate the role of microorganisms and microbial communities in driving major biogeochemical cycles. The microbial biosphere harbors an incredible diversity of traits that impact marine ecosystem function. Unraveling microbial interdependencies and interactions that modulate marine elemental cycling will be necessary to more precisely evaluate the response of ecosystems to natural and anthropogenic perturbations. My research pairs computational genomics approaches with model systems of microbial ecology and evolution. By combining pattern identification and physiological experimentation, key questions can be constrained and then rigorously tested in the laboratory and the field. In this way, my work has extended our knowledge of the diverse roles of microorganisms in elemental cycling and how microbial interactions might regulate ocean biogeochemistry.

At MIT, I study the marine cyanobacterium, Prochlorococcus, a well developed model system for studying microbial ecology. This organism has proven to be an ideal tool for exploring my questions on how microbial diversity and function can impact ocean biogeochemistry. When Prochlorococcus was first isolated and the first Prochlorococcus genomes were sequenced, an unusual lack of the nitrate assimilation pathway was observed. The absence of this pathway in such a large standing stock of phytoplankton was surprising, especially given that nitrate is often the most abundant nitrogen source and nitrogen typically limits phytoplankton growth in vast regions of the ocean. Utilizing computational approaches (e.g. comparative genomics and metagenomics) combined with microbial physiology and ecology studies, I have found that a significant fraction of Prochlorococcus in the wild are capable of nitrate assimilation and that overall nitrogen limitation is an important factor in selecting for these cells.



  • Paul M. Berube, Allison Coe, Sara E. Roggensack, Sallie W. Chisholm. 2016. Temporal dynamics of Prochlorococcus cells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans. Limnology and Oceanography 61(2):482-495. doi:10.1002/lno.10226
  • Paul M. Berube, Steven J. Biller, Alyssa G. Kent, Jessie W. Berta-Thompson, Sara E. Roggensack, Kathryn H. Roache-Johnson, Marcia Ackerman, Lisa R. Moore, Joshua D. Meisel, Daniel Sher, Luke R. Thompson, Lisa Campbell, Adam C. Martiny, Sallie W. Chisholm. 2015. Physiology and evolution of nitrate acquisition in Prochlorococcus. The ISME Journal 9(5):1195-1207. doi:10.1038/ismej.2014.211
  • Steven J. Biller, Paul M. Berube, Debbie Lindell, Sallie W. Chisholm. 2015. Prochlorococcus: the structure and function of collective diversity. Nature Reviews Microbiology 13:13-27. doi:10.1038/nrmicro3378
  • Steven J. Biller, Paul M. Berube, Jessie W. Berta-Thompson, Libusha Kelly, Sara E. Roggensack, Lana Awad, Kathryn H. Roache-Johnson, Huiming Ding, Stephen J. Giovannoni, Gabrielle Rocap, Lisa R. Moore, Sallie W. Chisholm. 2014. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. Scientific Data doi:10.1038/sdata.2014.34
  • Jamie W. Becker, Paul M. Berube, Christopher L. Follett, John B. Waterbury, Sallie W. Chisholm, Edward F. DeLong, and Daniel J. Repeta. 2014. Closely related phytoplankton species produce similar suites of dissolved organic matter. Frontiers in Microbiology 5:1-14.
  • Rex R. Malmstrom, Sébastien Rodrigue, Katherine H. Huang, Libusha Kelly, Suzanne E. Kern, Anne Thompson, Sara Roggensack, Paul M. Berube, Matthew R. Henn, Sallie W. Chisholm. 2013. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. The ISME Journal 7:184-198.
  • Paul M. Berube, David A. Stahl. 2012. The divergent AmoC3 subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea. Journal of Bacteriology 194(13):3448-3456.
  • Willm Martens-Habbena, Paul M. Berube, Hidetoshi Urakawa, José R. de la Torre, David A. Stahl. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976-979.
  • Adam C. Martiny, Satish Kathuria, Paul M. Berube. 2009. Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes. Proceedings of the National Academy of Sciences of the United States of America 106:10787–10792.
  • Paul M. Berube, Ram Samudrala, David A. Stahl. 2007. Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. Journal of Bacteriology 189:3935-3944.
  • Lisa Y. Stein, Daniel J. Arp, Paul M. Berube, Patrick S. G. Chain, Loren Hauser, Mike S. M. Jetten, Martin G. Klotz, Frank W. Larimer, Jeanette M. Norton, Huub J. M. Op den Camp, Maria Shin, Xueming Wei. 2007. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environmental Microbiology 9:2993-3007.

Unpublished Preprints:

  • Robert W .Read, Paul M. Berube, Steven J. Biller, Iva P. Neveux, Andres Cubillos-Ruiz, Sallie W. Chisholm, Joseph J. Grzymski. Nitrogen cost minimization is promoted by structural changes in the transcriptome of N deprived Prochlorococcus cells. bioRxiv 087643; doi:


Research Cruises:

Junior Chief Scientist. C-MORE HOE-DYLAN VII Cruise. Prochlorococcus population dynamics in response to transient nitrate upwelling. Station ALOHA. R/V Kilo Moana. Chief Scientist Sonya Dyhrman. August 4-14, 2012.

Participant. C-MORE BiG-RAPA Cruise. Ecology of Prochlorococcus along nutrient and light gradients. Eastern Subtropical South Pacific. R/V Melville. Chief Scientist Daniel Repeta. November 18 – December 14, 2010.

Participant. HOT 212 Cruise. Culturing novel Prochlorococcus capable of nitrate assimilation. Station ALOHA. R/V Kilo Moana. Chief Scientist Susan Curless. July 2-6, 2009.


Selected Service Activities:

Editorial Board, Journal of Plankton Research, tenure term: 2017-2019.

MIT representative for the BioGEOTRACES component of the international GEOTRACES study. The Chisholm Lab is one of three inaugural BioGEOTRACES labs with a focus on examining relationships between microbial ecology and trace metal distributions.

Ad hoc reviewer for the National Science Foundation’s Ocean Sciences, Environmental Biology, and Integrative Organismal Systems Divisions.

Ad hoc reviewer for Limnology and Oceanography, mBio, Environmental Microbiology, FEMS Microbiology Letters, Frontiers in Microbiology, and Journal of Phycology.