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PMID: 21651822 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning.

Virology journal ·Vol. 8 ·2011-06-09 ·Pages 287

Steward GF, Preston CM

Abstract

Viruses have a profound influence on both the ecology and evolution of marine plankton, but the genetic diversity of viral assemblages, particularly those in deeper ocean waters, remains poorly described. Here we report on the construction and analysis of a viral metagenome prepared from below the euphotic zone in a temperate, eutrophic bay of coastal California. We purified viruses from approximately one cubic meter of seawater collected from 200 m depth in Monterey Bay, CA. DNA was extracted from the virus fraction, sheared, and cloned with no prior amplification into a plasmid vector and propagated in E. coli to produce the MBv200m library. Random clones were sequenced by the Sanger method. Sequences were assembled then compared to sequences in GenBank and to other viral metagenomic libraries using BLAST analyses. Only 26% of the 881 sequences remaining after assembly had significant (E≤0.001) BLAST hits to sequences in the GenBank nr database, with most being matches to bacteria (15%) and viruses (8%). When BLAST analysis included environmental sequences, 74% of sequences in the MBv200m library had a significant match. Most of these hits (70%) were to microbial metagenome sequences and only 0.7% were to sequences from viral metagenomes. Of the 121 sequences with a significant hit to a known virus, 94% matched bacteriophages (Families Podo-, Sipho-, and Myoviridae) and 6% matched viruses of eukaryotes in the Family Phycodnaviridae (5 sequences) or the Mimivirus (2 sequences). The largest percentages of hits to viral genes of known function were to those involved in DNA modification (25%) or structural genes (17%). Based on reciprocal BLAST analyses, the MBv200m library appeared to be most similar to viral metagenomes from two other bays and least similar to a viral metagenome from the Arctic Ocean. Direct cloning of DNA from diverse marine viruses was feasible and resulted in a distribution of virus types and functional genes at depth that differed in detail, but were broadly similar to those found in surface marine waters. Targeted viral analyses are useful for identifying those components of the greater marine metagenome that circulate in the subcellular size fraction.

MeSH Terms
Biodiversity California Cloning, Molecular/methods Cluster Analysis DNA Viruses/classification,genetics DNA, Viral/chemistry,genetics Metagenome Molecular Sequence Data Phylogeny Seawater/virology Sequence Analysis, DNA
Chemicals
DNA, Viral
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Steward Grieg F
Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, HI 96822, Hawaii. [email protected]
Preston Christina M
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Article Info
Journal
Virology journal
Abbr.
Virol J
ISSN
1743-422X
DOI
10.1186/1743-422X-8-287
Email
[email protected]
Published
2011-06-09
Epub
2011-00-09
Pages
287
Language
English
Region
England
NLM ID
101231645
PMCID
PMC3128862
Subset
IM
Grants
NCRR NIH HHS · P20RR016467 · United States
NCRR NIH HHS · P20RR018727 · United States
NCRR NIH HHS · U54RR026136 · United States
Databases
GENBANK
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PubMed source DOI: 10.1186/1743-422X-8-287 PMC Full Text View journal details
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