Award Abstract # 1153588
Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph

NSF Org: OCE
Division Of Ocean Sciences
Recipient: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
Initial Amendment Date: December 23, 2011
Latest Amendment Date: December 23, 2011
Award Number: 1153588
Award Instrument: Standard Grant
Program Manager: Michael Sieracki
OCE
 Division Of Ocean Sciences
GEO
 Directorate for Geosciences
Start Date: February 1, 2012
End Date: January 31, 2018 (Estimated)
Total Intended Award Amount: $803,201.00
Total Awarded Amount to Date: $803,201.00
Funds Obligated to Date: FY 2012 = $803,201.00
History of Investigator:
  • Sallie Chisholm (Principal Investigator)
    chisholm@mit.edu
Recipient Sponsored Research Office: Massachusetts Institute of Technology
77 MASSACHUSETTS AVE
CAMBRIDGE
MA  US  02139-4301
(617)253-1000
Sponsor Congressional District: 07
Primary Place of Performance: Massachusetts Institute of Technology
15 Vassar St
Cambridge
MA  US  02139-4308
Primary Place of Performance
Congressional District:
07
Unique Entity Identifier (UEI): E2NYLCDML6V1
Parent UEI: E2NYLCDML6V1
NSF Program(s): BIOLOGICAL OCEANOGRAPHY
Primary Program Source: 01001213DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 0000, 9117
Program Element Code(s): 165000
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.050

ABSTRACT

First discovered in 1988, Prochlorococcus is now recognized as the most abundant photosynthetic cell in the oceans and is responsible for a significant fraction of global primary productivity. Arguably one of the best studied marine microorganisms to date, Prochlorococcus is well-developed as a model system for advancing our understanding of microbial ecology. It is comprised of a collection of genetically and physiologically distinct populations that co-exist and are differentially distributed along quantifiable gradients of light, temperature, and inorganic nutrients. Early physiological studies using cultured isolates indicated that this group of cyanobacteria was unable to assimilate nitrate, typically the most abundant inorganic nitrogen source in the open ocean. This observation was supported by the first 12 genome sequences of Prochlorococcus which all lacked the genes necessary for nitrate assimilation. The lack of these genes in Prochlorococcus was puzzling given that closely related, and co-occurring, Synechococcus cells have them, and that nitrogen availability can be a significant limiting factor for primary production in marine ecosystems. Our understanding changed in 2009 with the discovery of nitrate assimilation genes in wild Prochlorococcus genomes and the isolation of an axenic strain capable of growth on nitrate (unpublished data). This discovery has lead to the overarching questions that are the subject of this project:

- What subset of the Prochlorococcus meta-population in the wild contains nitrate assimilation genes and how do the dynamics of this sub-population vary in time and space?
- What features of the environment select for cells with this functional trait?
- Is the phylogeny of Prochlorococcus nitrate assimilation genes better correlated with the local environment or the overall 16S-23S ITS phylogeny of Prochlorococcus?
- Do the genomes of cells that contain nitrate assimilation genes share specific features? What do they tell us
about what other environmental variables influence the fitness of nitrate-assimilating cells?
- What are the physiological tradeoffs underlying the loss or gain of assimilation genes in particular strains?

These questions will be addressed using an integrative cross-scale approach to characterize nitrate assimilation by Prochlorococcus at the population, cellular, and genomic levels. Specifically, the distribution and abundance of nitrate assimilating Prochlorococcus will be measured at two contrasting open ocean time-series stations (HOT and BATS), and along a longitudinal gradient in the Atlantic (AMT). The PI will examine the regulation of nitrate assimilation, the kinetics of growth on nitrate, and the ability of Prochlorococcus to compete with Synechococcus under nitrogen limiting conditions. Further, they will use a culture independent single cell genomics approach to assess the phylogenetic diversity of nitrate assimilation genes within the genomic context of several ribotypes. These studies will advance our understanding the biogeography of functional traits in microbes, how it is shaped by selection, and the role of intra-species functional diversity in the overall population dynamics of Prochlorococcus.

Broader Impacts:
The PIs will take advantage of several avenues available at MIT to work with under-represented groups. These include: the MIT Summer Research Program, CONVERGE (a preview weekend); SEED (a Saturday education program); KEYs (a program for girls), and the MIT Edgerton Center which facilitates visits from local K-12 classes. The PI is committed to communicating science to broad audiences. Chisholm, for example, has published a children's book on photosynthesis (Living Sunlight, Scholastic), and is currently working on the sequel about ocean food webs. Her work has been featured on NPR, MITWorld, and MicrobeWorld. Berube has participated with the SEA-IT-LIVE Project in the filming of a documentary series aimed at educating the general public about shipboard oceanographic research. Berube will participate in a COMPASS science communication workshop in Fall 2011. The proposal for this project was designed and written primarily by the post-doc involved, and the work will play a central role in his professional development. Data resulting from the project will be posted on a public web site: Prochlorococcus Portal (http://proportal.mit.edu/).

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Paul M. Berube, Allison Coe, Sara E. Roggensack, Sallie W. Chisholm "Temporal dynamics of Prochlorococcus cells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans" Limnology and Oceanography , 2015 10.1002/lno.10226
Paul M. Berube, Allison Coe, Sara E. Roggensack, Sallie W. Chisholm "Temporal dynamics of Prochlorococcus cells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans" Limnology and Oceanography , 2016 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 "Physiology and evolution of nitrate acquisition in Prochlorococcus" The ISME Journal , 2014 doi:10.1038/ismej.2014.211
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 "Physiology and evolution of nitrate acquisition in Prochlorococcus" The ISME Journal , 2015 10.1038/ismej.2014.211
Robert W Read, Paul M Berube, Steven J Biller, Iva 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" The ISME Journal , 2017
Steven J. Biller, Paul M. Berube, Debbie Lindell, Sallie W. Chisholm "Prochlorococcus: the structure and function of collective diversity" Nature Reviews Microbiology , v.13 , 2015 , p.13-27 doi:10.1038/nrmicro3378
Steven J. Biller, Paul M. Berube, Debbie Lindell, Sallie W. Chisholm "Prochlorococcus: the structure and function of collective diversity" Nature Reviews Microbiology , 2015 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 "Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus" Scientific Data , 2014 10.1038/sdata.2014.34
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 "Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus" Scientific Data , 2014 doi:10.1038/sdata.2014.34

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

Ocean element cycles (e.g. carbon, nitrogen, and phosphorus) are largely driven by microorganisms and the metabolisms encoded by their genes. These properties are distributed across a diverse community of microbial cells which act in concert to move energy and matter through the ecosystem. But how are these systems assembled and what mechanisms are responsible for the ‘division of labor’ within and between different sub-species or ‘ecotypes’? Studies of Prochlorococcus, the smallest and most abundant oxygen evolving photosynthetic cell in the oceans, have shed light on this question. The 3 billion billion billion Prochlorococcus cells in the global ocean encompasses an immense level of diversity. Our ability to map this diversity onto environmental gradients provides a powerful lens into key selective pressures that shape the functional capacity of Prochlorococcus populations.

In our project, we explored a single ecologically important trait in Prochlorococcus: the ability of cells to use nitrate as a nitrogen source. Nitrogen is often an important limiting factor for the growth of phytoplankton which in turn consume carbon dioxide and supply fixed carbon to higher levels of the food web. Nitrate is an abundant inorganic nitrogen source in the oceans and can fuel the growth of photosynthetic organisms in the sunlit surface layer when nitrate is supplied from deeper nutrient rich water. After the first isolates of Prochlorococcus were obtained in the early 1990s, it was observed that no Prochlorococcus could use nitrate for growth. This suggested, surprisingly, that there was a large standing stock of photosynthetic organisms that were unresponsive to stimulation by nitrate. Later, we discovered that some fraction of Prochlorococcus could indeed use nitrate, isolated these cells, and through the support of this grant examined the first genome sequences of cultured Prochlorococcus capable of assimilating nitrate.

We designed protocols to enumerate Prochlorococcus harboring the trait for nitrate assimilation in the wild and followed seasonal changes in their abundance in the North Pacific and North Atlantic subtropical gyres. Up to 50% of high-light adapted Prochlorococcus, typically the most abundant Prochlorococcus subgroup in surface waters, had the genes required for nitrate assimilation. Highest abundances were observed when overall nitrogen concentrations were low and likely limiting production. Thus, Prochlorococcus with access to a wide pool of potential nitrogen sources are at a selective advantage when nitrogen is a limiting resource. When understanding the role that nitrate has in fueling marine photosynthesis, we must now recognize Prochlorococcus as an important player and take into account how populations are assembled and how nitrogen assimilation potential varies within those populations.

We have also uncovered distinct evolutionary processes that occur on different timescales that drive the observed diversity of nitrate assimilation in Prochlorococcus. Exploring the genomes of over 500 Prochlorococcus wild single cells and cultured isolates, it was observed that this trait was patchily distributed among a few of the recently evolved ecotypes and virtually absent from the others, likely reflecting the partitioning of ecotypes into different layers in the ocean water column. As new ecotypes appeared and expanded within the surface layers, others were pushed deeper into layers with elevated nitrogen concentrations. Random loss of the trait across ecotypes resulted in the relative retention of the trait in ecotypes in environments where nitrate assimilation can be advantageous. Near elimination of the trait is observed in other ecotypes when costs outweighed the benefits. These evolutionary trajectories have likely helped shape the biogeochemistry of the contemporary ocean by facilitating consumption of inorganic nitrogen at the surface. This work illustrates the power of combining genomic studies of a model organism with detailed knowledge of its ecology to better explore the evolutionary forces that shape marine ecosystems.

 

BROADER IMPACTS

The outcomes of our work have the potential to benefit society through a better understanding of marine microbial ecosystems. Prochlorococcus are expected to increase in abundance as the ocean warms over the coming century. Developing baseline information about the inherent diversity of these cells and how they respond to environmental perturbation will enhance our ability to predict the function of future marine ecosystems. This grant supported in part the development of a large genomic data set of Prochlorococcus, benefiting the extended research community. These data will facilitate studies on evolution, ecology, and the potential development of biofuels. Throughout the lifetime of the grant, the principle investigator has published a series of children’s books (The Sunlight Series) in order to instill an appreciation of photosynthesis in our younger generation. She has also presented this work to general audiences, most recently at TED2018, to promote a better understanding of the importance of marine ecosystems to human society. The project has further supported the training of 4 technicians who have used their experience on the project to move onto the next stages of their career; 3 are now in Ph.D. programs and one is in the biotechnology industry.

 


Last Modified: 04/30/2018
Modified by: Sallie W Chisholm

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