Genomic analysis of uncultured marine viral communities.
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Journal: 2002/December - Proceedings of the National Academy of Sciences of the United States of America
ISSN: 0027-8424
Abstract:
Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.
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Proc Natl Acad Sci U S A 99(22): 14250-14255
PMID: 12384570

Genomic analysis of uncultured marine viral communities

Department of Biology, San Diego State University, San Diego, CA 92182-4614; Department of Mathematical Sciences, San Diego State University, San Diego, CA 92182-7720; Ørsted Laboratory, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark; Lucigen, Middleton, WI 53562; and Marine Biology Division, Scripps Institution of Oceanography, La Jolla, CA 92093
To whom correspondence should be addressed. E-mail: ude.usds.ekortsnus@tserof.
Communicated by Allan Campbell, Stanford University, Stanford, CA
Communicated by Allan Campbell, Stanford University, Stanford, CA
Received 2002 Feb 22; Accepted 2002 Aug 14.
Copyright © 2002, The National Academy of Sciences

Abstract

Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2–3% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.

Abstract

Marine viruses, the majority of which are phages, have enormous influences on global biogeochemical cycles (1), microbial diversity (2, 3), and genetic exchange (4). Despite their importance, virtually nothing is known about marine viral biodiversity or the evolutionary relationships of marine and nonmarine viruses (5–7). Addressing these issues is difficult because viruses must be cultured on hosts, the majority of which cannot be cultivated by using standard techniques (8). In addition, viruses do not have ubiquitously conserved genetic elements such as rDNA that can be used as diversity and evolutionary distance markers (9). To circumvent these limitations, we developed a method to shotgun clone and sequence uncultured aquatic viral communities.

The models are listed in order of preference, which was determined from the minimum weighted error found for the model and the number of parameters used. n/a, Not applicable.

Acknowledgments

We thank Steven Rayhawk, Colleen Kelly, Ben Felts, James Nulton, Sherwood Casjens, and Richard Long for helpful conversations and suggestions related to this work. B.A. thanks San Diego State University for its hospitality. This work was sponsored by National Science Foundation Small Grant for Exploratory Research OCE01-16900.

Acknowledgments

Abbreviations

  • SP, Scripps Pier

  • MB, Mission Bay

  • LASL, linker-amplified shotgun library

  • MM%, minimal mismatch percentage

Abbreviations

Notes

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY079522–AY080585 and BH898061–BH898933).

Notes
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY079522–AY080585 and BH898061–BH898933).

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