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Research Article

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

  • Shannon J. Williamson mail,

    To whom correspondence should be addressed. E-mail: swilliamson@jcvi.org

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Douglas B. Rusch,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Shibu Yooseph,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Aaron L. Halpern,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Karla B. Heidelberg,

    Affiliations: J. Craig Venter Institute, Rockville, Maryland, United States of America, University of Southern California, Los Angeles, California, United States of America

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  • John I. Glass,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Cynthia Andrews-Pfannkoch,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Douglas Fadrosh,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Christopher S. Miller,

    Affiliation: Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California, United States of America

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  • Granger Sutton,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Marvin Frazier,

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • J. Craig Venter

    Affiliation: J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Published: January 23, 2008
  • DOI: 10.1371/journal.pone.0001456
  • Published in PLOS ONE

Reader Comments (11)

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Journal club: How similar are viral communities, really?

Posted by HeleneMorlon on 19 Feb 2008 at 17:54 GMT

It has long been assumed that microbial populations are ubiquitous, but it is now understood that this idea is misleading, partly as a consequence of sampling only the most abundant 'species' or taxa in the communities.

You write “viral community composition is a function of geographic location”, but “different environments support similar viral communities”. Are the viral communities across sites actually dissimilar in your data set, as suggested by the first assertion, or similar, as suggested by the second assertion? Did you measure values of community similarity between sites (based on presence/absence and abundance using something like the Sorensen index or Chao's estimators)? One would expect in communities as diverse as viruses, for communities to show low similarity values. It is surprising that viral communities appear similar in this study: can you explain this?


RE: Journal club: How similar are viral communities, really?

shanca replied to HeleneMorlon on 26 Feb 2008 at 17:57 GMT

The two statements that you point to regard observations made by Angly and coworkers (2006). They were not intended to be taken independent of one-another. Rather, the authors found that there is an underlying "sameness" to the composition of viral assemblages across very different marine environments and that the main difference between oceanic regions was what viral "species" appeared to dominant. The similarities that we observed in our study was primarity at the viral family level (e.g. ubiquitous distribution of Myoviridae sequences). There is undoubtably a large degree of genotypic diversity within all of the viral families observed. Establishing diversity estimates based on the assembly or pair-wise overlap of shotgun reads was difficult in this study due to the mixed nature of the dataset (i.e. primarily prokaryote and viral sequences).