期刊
ISME JOURNAL
卷 8, 期 1, 页码 103-114出版社
SPRINGERNATURE
DOI: 10.1038/ismej.2013.124
关键词
viral ecology; metagenomics; phage diversity
资金
- NSF Microbial Genome Sequencing Program [EF 0626826]
- Gordon and Betty Moore Foundation
- Delaware EPSCoR program
- Howard Hughes Medical Institute
- Delaware Water Resources Center
- Delaware INBRE [NIH NCRR 2 P20 RR016472-09]
- Delaware EPSCoR [NSF EPS-0814251]
- Office Of The Director
- Office of Integrative Activities [1301765] Funding Source: National Science Foundation
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 alpha-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.
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