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PMID: 23985748 Published · ppublish 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.

Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton.

The ISME journal ·Vol. 8 ·No. 1 ·2014-01-00 ·Pages 103-14

Schmidt HF, Sakowski EG, Williamson SJ, Polson SW, Wommack KE

Abstract

Virioplankton have a significant role in marine ecosystems, yet we know little of the predominant biological characteristics of aquatic viruses that influence the flow of nutrients and energy through microbial communities. Family A DNA polymerases, critical to DNA replication and repair in prokaryotes, are found in many tailed bacteriophages. The essential role of DNA polymerase in viral replication makes it a useful target for connecting viral diversity with an important biological feature of viruses. Capturing the full diversity of this polymorphic gene by targeted approaches has been difficult; thus, full-length DNA polymerase genes were assembled out of virioplankton shotgun metagenomic sequence libraries (viromes). Within the viromes novel DNA polymerases were common and found in both double-stranded (ds) DNA and single-stranded (ss) DNA libraries. Finding DNA polymerase genes in ssDNA viral libraries was unexpected, as no such genes have been previously reported from ssDNA phage. Surprisingly, the most common virioplankton DNA polymerases were related to a siphovirus infecting an α-proteobacterial symbiont of a marine sponge and not the podoviral T7-like polymerases seen in many other studies. Amino acids predictive of catalytic efficiency and fidelity linked perfectly to the environmental clades, indicating that most DNA polymerase-carrying virioplankton utilize a lower efficiency, higher fidelity enzyme. Comparisons with previously reported, PCR-amplified DNA polymerase sequences indicated that the most common virioplankton metagenomic DNA polymerases formed a new group that included siphoviruses. These data indicate that slower-replicating, lytic or lysogenic phage populations rather than fast-replicating, highly lytic phages may predominate within the virioplankton.

MeSH Terms
Aquatic Organisms/enzymology,genetics DNA-Directed DNA Polymerase/genetics Genome, Viral/genetics Metagenomics Molecular Sequence Data Phylogeny Seawater/virology Viruses/classification,enzymology,genetics Water Microbiology
Chemicals
DNA-Directed DNA Polymerase
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Schmidt Helen F
Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
Sakowski Eric G
Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
Williamson Shannon J
Lake Pend Oreille Waterkeeper, Sandpoint, ID, USA.
Polson Shawn W ORCID
Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
Wommack K Eric
Department of Plant & Soil Science, College of Marine Studies, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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Article Info
Journal
The ISME journal
Abbr.
ISME J
ISSN
1751-7370
DOI
10.1038/ismej.2013.124
Published
2014-01-00
Epub
2013-00-29
Pages
103-14
Language
English
Region
England
NLM ID
101301086
PMCID
PMC3869006
Subset
IM
Grants
NIGMS NIH HHS · P20 GM103446 · United States
NCRR NIH HHS · P20 RR016472 · United States
Howard Hughes Medical Institute · United States
NCRR NIH HHS · 2 P20 RR016472-09 · United States
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External Links
PubMed source DOI: 10.1038/ismej.2013.124 PMC Full Text View journal details
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