Genomic analysis of uncultured marine viral communities

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.

[1]  C. E. SHANNON,et al.  A mathematical theory of communication , 1948, MOCO.

[2]  Claude E. Shannon,et al.  The mathematical theory of communication , 1950 .

[3]  Feller William,et al.  An Introduction To Probability Theory And Its Applications , 1950 .

[4]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[5]  H. Sambrook.  Molecular cloning : a laboratory manual. Cold Spring Harbor, NY , 1989 .

[6]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[7]  G. Bratbak,et al.  Dynamics of virus abundance in coastal seawater , 1996 .

[8]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[9]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[10]  I. Joint,et al.  Occurrence of a Sequence in Marine Cyanophages Similar to That of T4 g20 and Its Application to PCR-Based Detection and Quantification Techniques , 1998, Applied and Environmental Microbiology.

[11]  J. Fuhrman,et al.  Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria , 1998 .

[12]  J. Fuhrman.  Marine viruses and their biogeochemical and ecological effects , 1999, Nature.

[13]  J. Paul.  Microbial gene transfer: an ecological perspective. , 1999, Journal of molecular microbiology and biotechnology.

[14]  K. Wommack,et al.  Virioplankton: Viruses in Aquatic Ecosystems , 2000, Microbiology and Molecular Biology Reviews.

[15]  F. Azam,et al.  Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments , 2000 .

[16]  W. Ulrich.  Models of relative abundance distributions I: Model fitting by stochastic models , 2001 .

[17]  H. Krisch,et al.  A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2 , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  A. Segall,et al.  Production of shotgun libraries using random amplification. , 2001, BioTechniques.

[19]  J. Hughes,et al.  Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity , 2001, Applied and Environmental Microbiology.

[20]  Feng Chen,et al.  Genomic Sequence and Evolution of Marine Cyanophage P60: a New Insight on Lytic and Lysogenic Phages , 2002, Applied and Environmental Microbiology.

[21]  R. Edwards,et al.  The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage , 2002, Journal of bacteriology.