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Research Spending & Results

Award Detail

Awardee:MASSACHUSETTS INSTITUTE OF TECHNOLOGY
Doing Business As Name:Massachusetts Institute of Technology
PD/PI:
  • Sallie W Chisholm
  • (617) 253-1771
  • chisholm@mit.edu
Co-PD(s)/co-PI(s):
  • Daniele Veneziano
Award Date:07/09/2004
Estimated Total Award Amount: $ 1,200,000
Funds Obligated to Date: $ 1,200,000
  • FY 2004=$1,200,000
Start Date:09/01/2004
End Date:08/31/2010
Transaction Type:Grant
Agency:NSF
Awarding Agency Code:4900
Funding Agency Code:4900
CFDA Number:47.050
Primary Program Source:490100 NSF RESEARCH & RELATED ACTIVIT
Award Title or Description:The Ecology of Prochlorococcus: Toward a Model System for Microbial Oceanography
Federal Award ID Number:0425602
DUNS ID:001425594
Parent DUNS ID:001425594
Program:BIOLOGICAL OCEANOGRAPHY

Awardee Location

Street:77 MASSACHUSETTS AVE
City:Cambridge
State:MA
ZIP:02139-4301
County:Cambridge
Country:US
Awardee Cong. District:07

Primary Place of Performance

Organization Name:Massachusetts Institute of Technology
Street:77 MASSACHUSETTS AVE
City:Cambridge
State:MA
ZIP:02139-4301
County:Cambridge
Country:US
Cong. District:07

Abstract at Time of Award

The power of a model system for advancing our understanding of the natural world has been proven repeatedly in diverse sub-disciplines of science. This approach is equally valuable for the study of marine microbial ecology, either through the sustained study of a particular ecosystem, or through the study of a particular organism at all scales of organization from the genome to the ecosystem level. In this project the investigators will do the latter through a diverse set of laboratory and field studies designed to advance the understanding of Prochlorococcus, the numerically dominant phytoplankter in the world oceans. The objective is to understand what regulates the distribution and abundance of this important primary producer. Prochlorococcus has a number of features that make it a useful model organism for understanding the forces that shape marine microbial systems, and for generating hypotheses that will advance the field of Microbial Oceanography. It is the smallest and most abundant photosynthetic cell in the oceans, it can be isolated into culture, and it can be easily enumerated and studied in situ. Furthermore, it has the smallest genome of any known photosynthetic cell -- the minimal phototroph to date. Prochlorococcus is really a collection of "ecotypes", i.e., closely related but physiologically distinct populations that co-exist with different distributions along the light, temperature, nutrient, and predator (including viruses) gradients that shape their habitat. These distributions are determined by the relative fitness of the cells, i.e. the balance of growth rates and death rates along these gradients. The broad challenge is to understand the forces that have shaped this microdiversity over evolutionary time, and that guide the self-organization of these populations under different selective regimes. This is a multi-dimensional project designed to understand the "bottom up" (growth limitation by light, temperature, oxygen, and nutrients) and "top down" (mortality from viruses and grazing) influences on the population growth of different Prochlorococcus ecotypes through both laboratory and field studies. The project will involve high-throughput studies of the growth of ecotypes along gradients of environmental variables in the laboratory, as well as studies of the distribution of ecotypes along spatial and temporal gradients in the field (at the Hawaii and Bermuda Time Series Stations, along a longitudinal Atlantic transect, and in Oxygen Minimum Zones in the Arabian Sea and Peruvian Upwelling) using Q-PCR to assess their relative abundance. The investigators will also study the life cycle of viruses that infect Prochlorococcus and cross infect between ecotypes, and the growth and mortality rates of specific ecotypes in field samples due to grazing pressure. Another set of analyses will measure the full diversity of co-occurring Prochlorococcus in selected field samples, and work toward understanding at what level genetic diversity corresponds to ecologically meaningful diversity. Finally, the study will develop statistical methods for the characterization and analysis of Prochlorococcus ecotype "fitness spaces" established in the laboratory, and compare them with the distribution of ecotypes along environmental gradients in the field. This will allow a rigorously analysis of the degree to which different selective pressures shape the relative abundance of the different Prochlorococcus ecotypes in the oceans, and how they change over time and space. Broader Impacts. This project will support (in whole or in part) the research of 5 graduate students and post-docs, three of them women, as well as undergraduate researchers. Through a formal collaboration with the Museum of Science we will also develop exhibits that focus on marine microbiology. The investigators are also participating in MIT's Knowledge Update Program, which produces multi-media educational briefings designed for both professional and student audiences to provide a focused, quick immersion into emerging fields. Finally, the participants will be working with an anthropologist at MIT who is working on a book, tentatively entitled Mapping a Sea of Genes, that will offer an anthropological look at exploring the ocean in the age of genomics. The author has been interacting with the research group to get a documentary sense of work on ocean microbes and their genes. This book will transform the way scientists, policy makers and lay public understand the sea.

Publications Produced as a Result of this Research

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Ahlgren, NA; Rocap, G; Chisholm, SW "Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies" ENVIRONMENTAL MICROBIOLOGY, v.8, 2006, p.441. doi:10.1111/j.1462-2920.2005.00910.  View record at Web of Science

Rodrigue S., R.R. Malmstrom, A. Berlin, B. Birren, M. Henn and S.W. Chisholm "Whole Genome Amplification and De novo Assembly of Single Bacterial Cells" PLoS ONE, v.4 (9), 2009, p.e6864.

Osburne, Marcia, Holmbeck, Brianne, Frias-Lopez, Jorge, Steen, Robert, Huang, Katherine, Waraska, Kristin, Gagne, Andrew, Chisholm, Sallie "UV hyper-resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase" Enviromental Microbiol., v.12, 2010, p.1978.

Coleman, ML; Chisholm, SW "Code and context: Prochlorococcus as a model for cross-scale biology" TRENDS IN MICROBIOLOGY, v.15, 2007, p.398. doi:10.1016/j.tim.2007.07.00  View record at Web of Science

Johnson, ZI; Zinser, ER; Coe, A; McNulty, NP; Woodward, EMS; Chisholm, SW "Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients" SCIENCE, v.311, 2006, p.1737. doi:10.1126/science.111805  View record at Web of Science

Zhang, K; Martiny, AC; Reppas, NB; Barry, KW; Malek, J; Chisholm, SW; Church, GM "Sequencing genomes from single cells by polymerase cloning" NATURE BIOTECHNOLOGY, v.24, 2006, p.680. doi:10.1038/nbt121  View record at Web of Science

Sullivan, M., B. Krastins, J. Hughes, L. Kelly, M. Chase, D. Sarracino, S.W. Chisholm "The genome and structural proteome of an ocean cyanobacterial siphovirus" Env. Microbiol., v.11 (11), 2009, p.2935.

Lindell, D; Jaffe, JD; Coleman, ML; Futschik, ME; Axmann, IM; Rector, T; Kettler, G; Sullivan, MB; Steen, R; Hess, WR; Church, GM; Chisholm, SW "Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution" NATURE, v.449, 2007, p.83. doi:10.1038/nature0613  View record at Web of Science

Lindell, D; Jaffe, JD; Johnson, ZI; Church, GM; Chisholm, SW "Photosynthesis genes in marine viruses yield proteins during host infection" NATURE, v.438, 2005, p.86. doi:10.1038/nature0411  View record at Web of Science

Frias-Lopez, J; Thompson, A; Waldbauer, J; Chisholm, SW "Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters" ENVIRONMENTAL MICROBIOLOGY, v.11, 2009, p.512. doi:10.1111/j.1462-2920.2008.01793.  View record at Web of Science

Strong, A., C, Miller, S. W. Chisholm and J. Cullen, "Ocean Fertilization: Time to move on" Nature, v.361, 2009, p.347.

Steglich, C. ME Futschik, D. Lindell, B. Boss, SW Chisholm and WR Hess "The challenge of regulation in a minimal phototroph: Non-coding RNA's in Prochlorococcus" Genome Biology, v.4, 2008, p.e100017.

Martiny, AC; Coleman, ML; Chisholm, SW "Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation" PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v.103, 2006, p.12552. doi:10.1073/pnas.060130110  View record at Web of Science

Martiny AC, Kathuria S, Berube PM. "Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes" PNAS, v.106 (26, 2009, p.10787.

Strong, A. J.J. Cullen, and S. W. Chisholm "Ocean fertilization: Science, policy, and commerce" Oceanography Magazine, v.22 (3), 2009, p.236.

Marsh, MP; Cruciano, AC; Thompson, LR; Chisholm, SW; Chiu, W "Electron cryo-tomography of Prochlorococcus shows cytoplasmic and periplasmic structural features" BIOPHYSICAL JOURNAL, v., 2007, p.504A. View record at Web of Science

Lindell, D., J.D. Jaffe, Z.I. Johnson, G.M. Church, S.W. Chisholm "Photosynthesis genes in marine viruses yield proteins during host infection." Nature, v.--, 2005, p..

Sullivan, MB; Coleman, ML; Weigele, P; Rohwer, F; Chisholm, SW "Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations" PLOS BIOLOGY, v.3, 2005, p.790. doi:10.1371/journal.pbio.003014  View record at Web of Science

Martiny, AC; Tai, APK; Veneziano, D; Primeau, F; Chisholm, SW "Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus" ENVIRONMENTAL MICROBIOLOGY, v.11, 2009, p.823. doi:10.1111/j.1462-2920.2008.01803.  View record at Web of Science

Paul, J.H., and M.B. Sullivan "Marine phage genomics: what have we learned?" Curr Opin Biotechnol, v.16, 2005, p.299.

Kettler, GC; Martiny, AC; Huang, K; Zucker, J; Coleman, ML; Rodrigue, S; Chen, F; Lapidus, A; Ferriera, S; Johnson, J; Steglich, C; Church, GM; Richardson, P; Chisholm, SW "Patterns and implications of gene gain and loss in the evolution of Prochlorococcus" PLOS GENETICS, v.3, 2007, p.2515. doi:10.1371/journal.pgen.003023  View record at Web of Science

Sullivan, MB; Coleman, ML; Quinlivan, V; Rosenkrantz, JE; DeFrancesco, AS; Tan, G; Fu, R; Lee, JA; Waterbury, JB; Bielawski, JP; Chisholm, SW "Portal protein diversity and phage ecology" ENVIRONMENTAL MICROBIOLOGY, v.10, 2008, p.2810. doi:10.1111/j.1462-2920.2008.01702.  View record at Web of Science

Sullivan, MB, ML Coleman, V Auinlivan, JE Roesnkrantz, AS DeFrancesco, G. Tan, R Fu, JA Lee, JB Waterbury, JP. Bielawski, and SW Chisholm "Portal Protein Diversity and Phage Ecology" Env. Microbiology, v.10, 2008, p.2810.

Sullivan, MB, ML Coleman, V Auinlivan, JE Roesnkrantz, AS DeFrancesco, G. Tan, R Fu, JA Lee, JB Waterbury, JP. Bielawski, and SW Chisholm "Portal Protein Diversity and Phage Ecology" Env. Microbiology, v.10, 2008, p.2810.

Zinser, ER, D. Lindell, Z.I. Johnson, M.E. Futschik, C. Steglich, M.L. Coleman, M.A. Wright, T. Rector, R. Steen, N. McNulty, L.R. Thompson, and S.W. Chisholm "Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus" PLoS ONE, v.4, 2009, p.5135.

Zinser, ER; Coe, A; Johnson, ZI; Martiny, AC; Fuller, NJ; Scanlan, DJ; Chisholm, SW "Prochlorococcus ecotype abundances in the North Atlantic Ocean as revealed by an improved quantitative PCR method" APPLIED AND ENVIRONMENTAL MICROBIOLOGY, v.72, 2006, p.723. doi:10.1128/AEM.72.1.723-732.200  View record at Web of Science

Liu, X. Q. Zhang, K. Murata, M.L. Baker, M.B. Sullivan, C. Fu, M.F. Schmid, M. S. Osburne, S. W. Chisholm & W. Chiu "Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus" Nature Structure and Mol Biol, v.17, 2010, p.830.

Steglich, C; Futschik, ME; Lindell, D; Voss, B; Chisholm, SW; Hess, WR "The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus" PLOS GENETICS, v.4, 2008, p.. doi:10.1371/journal.pgen.100017  View record at Web of Science

Martiny, A.C., S. Kathuria, and P.M. Berube "Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus" PNAS, v.106, 2009, p.10787.

Martiny, A.C., S. Kathuria, and P.M. Berube "Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus" PNAS, v.106, 2009, p.10787.

Tolonen, AC; Liszt, GB; Hess, WR "Genetic manipulation of Prochlorococcus strain MIT9313: green fluorescent protein expression from an RSF1010 plasmid and Tn5 transposition" APPLIED AND ENVIRONMENTAL MICROBIOLOGY, v.72, 2006, p.7607. doi:10.1128/AEM.02034-0  View record at Web of Science

M. R. Henn, M. B. Sullivan, N. Stange-Thomann, M. S. Osburne, A. M. Berlin, L. Kelly, C. Yandava, C. Kodira, Q. Zeng, M. Weiand, T. Sparrow, S. Saif, G. Giannoukos, S. K. Young, C. Nusbaum, B. W. Birren, S. W. Chisholm. "Analysis of high-throughput sequencing and annotation strategies for phage genomes." PLoS ONE, v.5 (2), 2010, p.e9083.

Brag, JG and SW Chisholm "Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene" PLoS One, v.3, 2008, p.e3550.

Frias-Lopez, J; Shi, Y; Tyson, GW; Coleman, ML; Schuster, SC; Chisholm, SW; DeLong, EF "Microbial community gene expression in ocean surface waters" PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v.105, 2008, p.3805. doi:10.1073/pnas.070889710  View record at Web of Science

Coleman, ML; Sullivan, MB; Martiny, AC; Steglich, C; Barry, K; DeLong, EF; Chisholm, SW "Genomic islands and the ecology and evolution of Prochlorococcus" SCIENCE, v.311, 2006, p.1768. doi:10.1126/science.112205  View record at Web of Science

Brag, JG and SW Chisholm "Modeling the fitness consequences of a cyanophage-encoded photosynthesis gene" PLoS One, v.3, 2008, p.e3550.

Tolonen, AC; Aach, J; Lindell, D; Johnson, ZI; Rector, T; Steen, R; Church, GM; Chisholm, SW "Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability" MOLECULAR SYSTEMS BIOLOGY, v.2, 2006, p.. doi:10.1038/msb410008  View record at Web of Science

Moore, LR; Coe, A; Zinser, ER; Saito, MA; Sullivan, MB; Lindell, D; Frois-Moniz, K; Waterbury, J; Chisholm, SW "Culturing the marine cyanobacterium Prochlorococcus" LIMNOLOGY AND OCEANOGRAPHY-METHODS, v.5, 2007, p.353. View record at Web of Science

Steglich, C. M. Futschik, D. Lindell, T. Rector, R. Steen, and S. W. Chisholm. "Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus" Genome Biology, v.11, 2010, p.R54.

Li, B. D. Sher, L. Kelly, K. Huang, I. Joewono, D. Rusch, S.W. Chisholm and W. A. van der Donk "Natural combinatorial biosynthesis of secondary metabolites in planktonic marine cyanobacteria." PNAS, v.107, 2010, p.10430.

Klein, M.G., P. Zward, S.C. Bagby, F. Cai, S.W. Chisholm, S. Heinhorst, G.C. Cannon, and C. A Kerfeld "Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport" J. Mol. Biol., v.392, 2009, p.319.

Follows, MJ; Dutkiewicz, S; Grant, S; Chisholm, SW "Emergent biogeography of microbial communities in a model ocean" SCIENCE, v.315, 2007, p.1843. doi:10.1126/science.113854  View record at Web of Science

Zinser, ER; Johnson, ZI; Coe, A; Karaca, E; Veneziano, D; Chisholm, SW "Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean" LIMNOLOGY AND OCEANOGRAPHY, v.52, 2007, p.2205. View record at Web of Science

Dutkiewicz, S., M.J. Follows. and J.G. Bragg "Modeling the coupling of ocean ecology and biogeochemistry" Global Biogeochem. Cycles, v.23, 2009, p.GB4017.

Dammeyer, T; Bagby, SC; Sullivan, MB; Chisholm, SW; Frankenberg-Dinkel, N "Efficient phage-mediated pigment biosynthesis in oceanic cyanabacteria" CURRENT BIOLOGY, v.18, 2008, p.442. doi:10.1016/j.cub.2008.02.06  View record at Web of Science

Rodrigue, S. A. C. Materna, S. C. Timberlake, M. C. Blacburn, R.R. Malmstrom, E. J. Alm, and S. W. Chisholm "Unlocking Short Read Sequencing for Metagenomics" PLoSONE, v.5 (7), 2010, p.e11840.

DeLong, EF; Preston, CM; Mincer, T; Rich, V; Hallam, SJ; Frigaard, NU; Martinez, A; Sullivan, MB; Edwards, R; Brito, BR; Chisholm, SW; Karl, DM "Community genomics among stratified microbial assemblages in the ocean's interior" SCIENCE, v.311, 2006, p.496. doi:10.1126/science.112025  View record at Web of Science

Bragg, J. G., S. Dutkiewicz, O. Jahn, M. Follows. and S.W. Chisholm "Modeling selective pressures on phytoplankton in the global ocean" PLoS One, v.5 (3), 2010, p.e9569i.

Steglich, C; Futschik, M; Rector, T; Steen, R; Chisholm, SW "Genome-wide analysis of light sensing in Prochlorococcus" JOURNAL OF BACTERIOLOGY, v.188, 2006, p.7796. doi:10.1128/JB.01097-0  View record at Web of Science

McCarren, J., J.W. Becker, D.J. Repeta, Y. Shia, C.R. Young, R.R. Malmstrom, S.W. Chisholm, and E. F. DeLong "Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea." PNAS, v.107, 2010, p.16420.

Sullivan, MB; Lindell, D; Lee, JA; Thompson, LR; Bielawski, JP; Chisholm, SW "Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts" PLOS BIOLOGY, v.4, 2006, p.1344. doi:10.1371/journal.pbio.004023  View record at Web of Science

Bertilsson, S; Berglund, O; Pullin, MJ; Chisholm, SW "Release of dissolved organic matter by Prochlorococcus" VIE ET MILIEU-LIFE AND ENVIRONMENT, v.55, 2005, p.225. View record at Web of Science

Sullivan, M.B., M. Coleman, P. Weigele, and S.W. Chisholm "Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations." PLoS Biology, v.3 (5), 2005, p.e144:0001.

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