Paul Berube

pmberube

Research Scientist
Civil and Environmental Engineering

MIT 48-106
15 Vassar Street
Cambridge, MA 02139

617.253.8686 (lab)
617.258.7009 (fax)
Email: pmberube at mit.edu

 

 

 

 

Education:

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:

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. Utilizing computational approaches (e.g. comparative genomics and metagenomics) combined with microbial physiology and ecology studies, I have identified new interactions between Prochlorococcus and the nitrogen cycle and assessed the evolutionary mechanisms behind the emergence of nitrate assimilation in these globally important cyanobacteria.

 

Publications:

  • Maria G. Pachiadaki, Julia M. Brown, Joseph Brown, Oliver Bezuidt, Paul M. Berube, Steven J. Biller, Nicole J. Poulton, Michael D. Burkart, James J. La Clair, Sallie W. Chisholm, Ramunas Stepanauskas. 2019. Charting the Complexity of the Marine Microbiome through Single-Cell Genomics. Cell 179:1623-1635.
  • Paul M. Berube, Anna Rasmussen, Rogier Braakman, Ramunas Stepanauskas, Sallie W. Chisholm. 2019. Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus. eLife 8:e41043.
  • Steven J. Biller, Paul M. Berube, Keven Dooley, Madeline Williams, Brandon M. Satinsky, Thomas Hackl, Shane L. Hogle, Allison Coe, Kristin Bergauer, Heather A. Bouman, Thomas J. Browning, Daniele De Corte, Christel Hassler, Debbie Hulston, Jeremy E. Jacquot, Elizabeth W. Maas, Thomas Reinthaler, Eva Sintes, Taichi Yokokawa, Sallie W. Chisholm. 2018. Marine microbial metagenomes sampled across space and time. Scientific Data 5:180176. doi:10.1038/sdata.2018.176
  • Paul M. Berube, Steven J. Biller, Thomas Hackl, Shane L. Hogle, Brandon M. Satinsky, Jamie W. Becker, Rogier Braakman, Sara B. Collins, Libusha Kelly, Jessie Berta-Thompson, Allison Coe, Kristin Bergauer, Heather A. Bouman, Thomas J. Browning, Daniele De Corte, Christel Hassler, Yotam Hulata, Jeremy E. Jacquot, Elizabeth W. Maas, Thomas Reinthaler, Eva Sintes, Taichi Yokokawa, Debbie Lindell, Ramunas Stepanauskas, Sallie W. Chisholm. 2018. Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments. Scientific Data 5:180154. doi:10.1038/sdata.2018.154 
  • Wei Qin, Shady A. Amin, Rachel A. Lundeen, Katherine R. Heal, Willm Martens-Habbena, Serdar Turkarslan, Hidetoshi Urakawa, Kyle C. Costa, Erik L. Hendrickson, Tony Wang, David A.C. Beck, Sonia M. Tiquia-Arashiro, Fred Taub, Andrew D. Holmes, Neeraja Vajrala, Paul M. Berube, Todd M. Lowe, James W. Moffett, Allan H. Devol, Nitin S. Baliga, Daniel J. Arp, Luis A. Sayavedra-Soto, Murray Hackett, E. Virginia Armbrust, Anitra E. Ingalls, David A. Stahl. 2018. Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. The ISME Journal 12(2):508-519. doi:10.1038/ismej.2017.186
  • Robert W. Read, Paul M. Berube, Steven J. Biller, Iva P. Neveux, Andres Cubillos-Ruiz, Sallie W. Chisholm, Joseph J. Grzymski. 2017. Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells. The ISME Journal 11:2267-2278.
  • 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, 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.

 

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:

Scientific Steering Committee, Ocean nucleic acids ‘omics intercalibration and standardization workshop, Chapel Hill, NC, January 9-11, 2020. https://www.us-ocb.org/ocean-nucleic-acids-omics-workshop/

Editorial Board, Journal of Plankton Research, 2017-present.

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, Journal of Phycology, and The ISME Journal.

 

 https://orcid.org/0000-0001-5598-6602