Original Article | Published:

Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus

The ISME Journal volume 11, pages 19972011 (2017) | Download Citation

Abstract

The Atlantic and Pacific Oceans represent different biogeochemical regimes in which the abundant marine cyanobacterium Prochlorococcus thrives. We have shown that Prochlorococcus populations in the Atlantic are composed of hundreds of genomically, and likely ecologically, distinct coexisting subpopulations with distinct genomic backbones. Here we ask if differences in the ecology and selection pressures between the Atlantic and Pacific are reflected in the diversity and genomic composition of their indigenous Prochlorococcus populations. We applied large-scale single-cell genomics and compared the cell-by-cell genomic composition of wild populations of co-occurring cells from samples from Station ALOHA off Hawaii, and from Bermuda Atlantic Time Series Station off Bermuda. We reveal fundamental differences in diversity and genomic structure of populations between the sites. The Pacific populations are more diverse than those in the Atlantic, composed of significantly more coexisting subpopulations and lacking dominant subpopulations. Prochlorococcus from the two sites seem to be composed of mostly non-overlapping distinct sets of subpopulations with different genomic backbones—likely reflecting different sets of ocean-specific micro-niches. Furthermore, phylogenetically closely related strains carry ocean-associated nutrient acquisition genes likely reflecting differences in major selection pressures between the oceans. This differential selection, along with geographic separation, clearly has a significant role in shaping these populations.

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Acknowledgements

We thank Paul M Berube for helpful comments on the manuscript. We thank the Bermuda Atlantic time-series Study and the Hawaii Ocean Time-Series (HOT) for sample collection and the BioMicroCenter facility at MIT for their contributions to the generation of genomic data. We thank Huiming Ding for his contribution to the generation of Clusters of Orthologous Genes database. NK acknowledges the Rothschild Foundation (Yad Hanadiv) and the NOAA ‘Climate and Global Change’ Postdoctoral Research Fellowships. This work was supported in part by grants to SWC from the National Science Foundation (NSF) Evolutionary Biology Section and Biological Oceanography Section, the NSF Center for Microbial Oceanography Research and Education (C-MORE), the Gordon and Betty Moore Foundation Marine Microbiology Initiative, the Simons Foundation (SCOPE award ID 329108, and LIFE Award ID: 337262) and to RS from the NSF Biological Oceanography Section.

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Affiliations

  1. Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel

    • Nadav Kashtan
    •  & Maor Grinberg
  2. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    • Nadav Kashtan
    • , Sara E Roggensack
    • , Jessie W Berta-Thompson
    •  & Sallie W Chisholm
  3. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA

    • Ramunas Stepanauskas
  4. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA

    • Sallie W Chisholm

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The authors declare no conflict of interest.

Corresponding authors

Correspondence to Nadav Kashtan or Sallie W Chisholm.

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https://doi.org/10.1038/ismej.2017.64

Supplementary Information accompanies this paper on The ISME Journal website (http://www.nature.com/ismej)