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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
Award Date:01/10/2012
Estimated Total Award Amount: $ 300,000
Funds Obligated to Date: $ 300,000
  • FY 2012=$300,000
Start Date:01/15/2012
End Date:12/31/2014
Transaction Type:Grant
Agency:NSF
Awarding Agency Code:4900
Funding Agency Code:4900
CFDA Number:47.074
Primary Program Source:040100 NSF RESEARCH & RELATED ACTIVIT
Award Title or Description:Microevolution and population dynamics of Prochlorococcus cells in the ocean: Insights through single-cell genomics
Federal Award ID Number:1145734
DUNS ID:001425594
Parent DUNS ID:001425594
Program:EVOLUTIONARY ECOLOGY
Program Officer:
  • Samuel Scheiner
  • (703) 292-7175
  • sscheine@nsf.gov

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:15 Vassar St
City:Cambridge
State:MA
ZIP:02139-4308
County:Cambridge
Country:US
Cong. District:07

Abstract at Time of Award

Prochlorococcus is a bacterium that is widespread and abundant in the world oceans. As a photosynthetic cell, it uses sunlight to fix carbon dioxide into organic carbon, similar to plants on land. The global Prochlorococcus population in the oceans is made up of a diversity of "ecotypes," each of which has slightly different conditions for optimal growth. It is hypothesized that the diversity of this group of microbes allows it to thrive over broadly varying ocean habitats, but the genetic underpinnings of this diversity is very poorly understood. This research aims at advancing our understanding of the ecology and evolution of Prochlorococcus, by studying the genetic composition of single wild Prochlorococcus cells isolated from the Atlantic and Pacific oceans at different times of year. The study is motivated by two fundamental questions: (i) what is the relationship between the genetic composition of the cells and their ecological dynamics? (ii) how do populations adapt to their environment over ecological and evolutionary time scales? The broader significance of this work lies in the central role that Prochlorococcus plays in ocean ecology and the global carbon cycle. As the most abundant photosynthetic group in the oceans, Prochlorococcus is a critical component of the base of the food web. Because it conducts a sizable fraction of ocean photosynthesis, it plays an important role in the global carbon cycle and global climate processes. Understanding what regulates Prochlorococcus' diversity and dynamics is critical for developing predictive models of these important Earth system features.

Publications Produced as a Result of this Research

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Kashtan, N. SE Roggensack, S. Rodrigue, JW Thompson, SJ Biller, A Coe, H Ding, P Marttinen, R Stocker, M. Follows, R. Stephanauskas, and SW Chisholm. "Single cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus" Science, v.344, 2014, p.416.

Biller, SJ, P Berube, D Lindell, and SW Chisholm. "Prochlorococcus The structure and function of collective diversity." Nature Rev. Microbiol., v.Online, 2014, p.. doi:doi:10.1038/nrmicro3378 


Project Outcomes Report

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Intellectual Merit

The smallest, most abundant marine microbe, Prochlorococcus, is a photosynthetic bacterial species essential to the marine ecosystem. An estimated billion billion billion of the single-cell creatures live in the oceans, forming the base of the marine food chain and occupying a range of ecological niches based on temperature, light and chemical preferences, and interactions with other species. But the full extent and characteristics of diversity within this single species remains a puzzle. 

This project set out to probe this question, using cell-by-cell genomic analysis on a wild population of Prochlorococcus living in a milliliter — less than a quarter teaspoon — of ocean water.  This was an enormous challenge because these cells are extremely tiny (100 lined up are the width of a hair) and very dilute in the oceans.  We first had to separate them into single wells, then amplify their DNA, and then sequence them.  We learned that each subpopulation of cells in those few drops of water is characterized by a set of core gene alleles linked to a few flexible genes — a “genomic backbone” — that endows the subpopulation with a finely tuned suitability for a particular ecological niche. Diversity also exists within the backbone subpopulations; most individual cells in the samples studied carried at least one set of flexible genes not found in any other cell in its subpopulation.  We estimate that the subpopulations diverged at least a few million years ago. The backbone is an older, more slowly evolving component of the genome, while the flexible genes reside in areas of the genome where gene exchange is relatively frequent, facilitating more rapid evolution.

The study also revealed that the relative abundance of the backbone subpopulations changes with the seasons at the study site, near Bermuda, adding strength to the argument that each subpopulation is finely tuned for optimal growth under different conditions.

The sheer enormity of diversity that must be in the octillion Prochlorococcus cells living in the seas is daunting to consider, and it creates a robust and stable population in the face of environmental instability.

Ocean turbulence also plays a role in the evolution and diversity of Prochlorococcus: A fluid mechanics model predicts that in typical ocean flow, just-divided daughter cells drift rapidly, placing them centimeters apart from one another in minutes, tens of meters apart in an hour, and kilometers apart in a week’s time.

The interesting question is ‘Why does such a diverse set of subpopulations exist?’ The huge population size of Prochlorococcus suggests that this remarkable diversity and the way it is organized is not random, but is a masterpiece of Darwinian natural selection.

We conclude that evolutionary and ecological distinctions among the subpopulations is probably common in other wild, free-living (not attached to particles or other organisms) bacteria species with large populations and highly mixed habitats.

Broader Impacts

The results of this project were published in Science Magazine, which receives very broad news coverage.  There was a press release about the paper, as well as a perspectives piece in the Journal.

This project supported the work of a post-doctoral researcher as well as helped train a female graduate student in bioinformatics, a field in which women are under-represented.  The PI published a book for children:  Bang and Chisholm:  Buried Sunlight:  How fossil fuels have changed the Earth (Scholastic 2014) which draws on the role of phytoplankton and plants in shaping our world.  

 

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