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Sallie (Penny) Chisholm, Ph.D.

Professor of Civil and Environmental Engineering, and Biology
Lee and Geraldine Martin Professor of Environmental Studies

Room 48-419
617-253-1771 (phone)


Ph.D. Biology 1974
State University New York, Albany

Research Summary

The research goal of the Chisholm lab is to understand the ecology of phytoplankton in the oceans and the biogeochemical cycles that they mediate. Currently, we are focused on the cyanobacterium Prochlorococcus as a model system. It is the most abundant photosynthetic microbe in the sea and can account for up to half of the photosynthetic biomass over vast oceanic regions. Prochlorococcus is a “minimal phototroph,” which means that it converts CO2, solar energy and inorganic nutrients into a living cell with approximately 1,700 genes. It is a useful model for understanding the autotrophic mode of life, for studies of comparative genomics and metabolic reconstruction, and for investigating the role of microdiversity in shaping the structure and evolution of microbial communities.

The global abundance of Prochlorococcus arises in part from the existence of physiologically and genetically distinct “ecotypes” that have different light and temperature optima for growth and have adapted to life under different nutrient conditions in the oceans. The genomes of 13 Prochlorococcus strains have been sequenced, allowing us to compare differences in genomic architecture within and between ecotypes, the core genes shared by all, and the genes that are unique in each strain. Some of these unique genes have obvious roles in determining relative fitness in different environments; many have unknown functions, and likely hold clues to unknown agents of natural selection in the oceans.

Other aspects of our research include:

  • Studies of different strains of lytic phage that infect Prochlorococcus, including phage/host specificity, infection dynamics, genome comparisons, whole genome expression analyses, and phage-host genetic exchange.
  • Whole genome expression profiles of two model Prochlorococcus ecotypes, helping us understand their adaptations to particular conditions that they experience in the oceans.
  • Comparisons of the distribution and abundance of Prochlorococcus ecotypes in the global oceans, to provide a framework for interpreting the evolution of their metabolic differences.
  • Sequencing the genomes of individual wild Prochlorococcus cells, to help us understand co-existing genomic diversity among wild populations.

Ultimately, we wish to understand how genomic and metabolic differences among Prochlorococcus ecotypes determine their global distributions in the oceans. The challenge will be to link our understanding of their biology at fundamentally different scales, and to work toward a unified understanding of this one small representative of the diversity of life on earth.


Selected Publications

  • 2003 Rocap G, Larimer F, Lamerdin J, Malfatti S, Chain P, Ahlgren N, Arellano A, Coleman M, Hauser L, Hess W, Johnson Z, Land M, Lindell D, Post A, Regala W, Shah M, Shaw S, Steglich C, Sullivan M, Ting C, Tolonen A, Webb E, Zinser E, Chisholm S . Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047.
  • 2005 Lindell, D, J. D. Jaffe, Z. I. Johnson, G. M. Church, S. W. Chisholm. 2005. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438:86-89.
  • 2006 Martiny, A.C., Coleman, M.L and S. W, Chisholm. Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation. Proc. Nat. Acad. Sci. 103 (33): 12552–12557
  • 2006 Coleman, M.L., M.B. Sullivan, C. Steglich, E.F. DeLong and S.W. Chisholm. Genomic Islands and the ecology and evolution of Prochlorococcus. Science311:1768-1770
  • 2006 Johnson Z, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311:1737-1740.
  • 2007 Lindell, D. J.D. Jaffe, M.l. Coleman, I.M. Axmann, T. Rector, G. Kettler, M.B. Sullivan, R. Steen, W.R. Hess, G.M. Church, and S. W. Chisholm. Genome-wide expression dynamics of a marine virus and host reveal features of coevolution. Nature 449: 83-86
  • 2009 Rodrigue, S. R. R. Malmstrom, A.M. Berlin, B.W. Birren, M.R. Henn, and S.W. Chisholm. Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 4(9): e6864. doi:10.1371/journal.pone.0006864
  • 2010 Coleman, M. L. and S. W. Chisholm. Ecosystem-specific selection pressures revealed by comparative population genomics.  PNAS 107 (43): 18634–18639.

Last Updated: March 22, 2011