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Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology

The ISME Journalvolume 12pages21032113 (2018) | Download Citation

Abstract

Copepods harbor diverse bacterial communities, which collectively carry out key biogeochemical transformations in the ocean. However, bulk copepod sampling averages over the variability in their associated bacterial communities, thereby limiting our understanding of the nature and specificity of copepod–bacteria associations. Here, we characterize the bacterial communities associated with nearly 200 individual Calanus finmarchicus copepods transitioning from active growth to diapause. We find that all individual copepods sampled share a small set of “core” operational taxonomic units (OTUs), a subset of which have also been found associated with other marine copepod species in different geographic locations. However, most OTUs are patchily distributed across individual copepods, thereby driving community differences across individuals. Among patchily distributed OTUs, we identified groups of OTUs correlated with common ecological drivers. For instance, a group of OTUs positively correlated with recent copepod feeding served to differentiate largely active growing copepods from those entering diapause. Together, our results underscore the power of individual-level sampling for understanding host–microbiome relationships.

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Acknowledgements

This work was supported in part by National Science Foundation grants OCE-1132567 to MFB and AMT and OCE-1435993 to MFP. MSD was supported by the Department of Defense through the National Defense Science and Engineering Graduate (NDSEG) Fellowship program. AAA was supported by an EPA STAR Fellowship, NSF GRFP, and the WHOI Ocean Venture Fund. We thank Sarah Preheim for help with performing the distribution-based clustering, Michael Cutler for providing advice regarding 16S rRNA library preparation, Nadine Lysiak for assistance in the field, Morgan Rubanow for assistance with the morphometric analysis, Krista Longnecker for her advice regarding the bacterial abundance counts, Bjørn Henrik Hansen, Dag Altin, Trond Nordtug, and Anders Olsen for significant logistical support in Trondheim, Norway, and the captain and crew of the R/V Gunnerus.

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Author notes

  1. These authors contributed equally: Manoshi S. Datta, Amalia A. Almada

Affiliations

  1. Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

    • Manoshi S. Datta
  2. Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA, 02543, USA

    • Amalia A. Almada
    • , Mark F. Baumgartner
    • , Tracy J. Mincer
    •  & Ann M. Tarrant
  3. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

    • Martin F. Polz

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The authors declare that they have no conflict of interest.

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Correspondence to Martin F. Polz.

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DOI

https://doi.org/10.1038/s41396-018-0182-1