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Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments

Authors

  • Yingfei Ma,

    1. Marine Biology Research Division, University of California, San Diego, La Jolla, CA 92093-0202, USA.
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    • Present address: New York University School of Medicine, 423 East 23rd Street, 6030w, New York, NY 10010-6481, USA.

  • Ian T. Paulsen,

    1. Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia.
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  • Brian Palenik

    Corresponding author
    1. Marine Biology Research Division, University of California, San Diego, La Jolla, CA 92093-0202, USA.
      E-mail bpalenik@ucsd.edu; Tel. (+1) 858 534 7505; Fax (+1) 858 534 7313.
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E-mail bpalenik@ucsd.edu; Tel. (+1) 858 534 7505; Fax (+1) 858 534 7313.

Summary

Plasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry-sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.

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