The marine viromes of four oceanic regions

被引:693
作者
Angly, Florent E.
Felts, Ben
Breitbart, Mya
Salamon, Peter
Edwards, Robert A.
Carlson, Craig
Chan, Amy M.
Haynes, Matthew
Kelley, Scott
Liu, Hong
Mahaffy, Joseph M.
Mueller, Jennifer E.
Nulton, Jim
Olson, Robert
Parsons, Rachel
Rayhawk, Steve
Suttle, Curtis A.
Rohwer, Forest [1 ]
机构
[1] San Diego State Univ, Dept Biol, San Diego, CA 92182 USA
[2] San Diego State Univ, Computat Sci Res Ctr, San Diego, CA 92182 USA
[3] San Diego State Univ, Dept Math, San Diego, CA 92182 USA
[4] San Diego State Univ, Ctr Microbial Sci, San Diego, CA 92182 USA
[5] Fellowship Interpretat Genomes, Burr Ridge, IL USA
[6] Univ Calif Santa Barbara, Santa Barbara, CA 93106 USA
[7] Univ British Columbia, Dept Earth & Ocean Sci, Vancouver, BC V5Z 1M9, Canada
[8] Argonne Natl Lab, Argonne, IL 60439 USA
[9] Bermuda Biol Stn Res, St Georges, Bermuda
[10] Univ British Columbia, Dept Microbiol & Immunol, Vancouver, BC V5Z 1M9, Canada
[11] Univ British Columbia, Dept Bot, Vancouver, BC V5Z 1M9, Canada
关键词
D O I
10.1371/journal.pbio.0040368
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct "marine-ness'' quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.
引用
收藏
页码:2121 / 2131
页数:11
相关论文
共 56 条
[1]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[2]   PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information [J].
Angly, F ;
Rodriguez-Brito, B ;
Bangor, D ;
McNairnie, P ;
Breitbart, M ;
Salamon, P ;
Felts, B ;
Nulton, J ;
Mahaffy, J ;
Rohwer, F .
BMC BIOINFORMATICS, 2005, 6 (1)
[3]  
Begon M., 1990, ECOLOGY INDIVIDUALS
[4]   Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing [J].
Breitbart, M ;
Rohwer, F .
BIOTECHNIQUES, 2005, 39 (05) :729-736
[5]   Global distribution of nearly identical phage-encoded DNA sequences [J].
Breitbart, M ;
Miyake, JH ;
Rohwer, F .
FEMS MICROBIOLOGY LETTERS, 2004, 236 (02) :249-256
[6]   Diversity and population structure of a near-shore marine-sediment viral community [J].
Breitbart, M ;
Felts, B ;
Kelley, S ;
Mahaffy, JM ;
Nulton, J ;
Salamon, P ;
Rohwer, F .
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2004, 271 (1539) :565-574
[7]   Metagenomic analyses of an uncultured viral community from human feces [J].
Breitbart, M ;
Hewson, I ;
Felts, B ;
Mahaffy, JM ;
Nulton, J ;
Salamon, P ;
Rohwer, F .
JOURNAL OF BACTERIOLOGY, 2003, 185 (20) :6220-6223
[8]   Genomic analysis of uncultured marine viral communities [J].
Breitbart, M ;
Salamon, P ;
Andresen, B ;
Mahaffy, JM ;
Segall, AM ;
Mead, D ;
Azam, F ;
Rohwer, F .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (22) :14250-14255
[9]   Phage as agents of lateral gene transfer [J].
Canchaya, C ;
Fournous, G ;
Chibani-Chennoufi, S ;
Dillmann, ML ;
Brüssow, H .
CURRENT OPINION IN MICROBIOLOGY, 2003, 6 (04) :417-424
[10]   Genomic islands and the ecology and evolution of Prochlorococcus [J].
Coleman, ML ;
Sullivan, MB ;
Martiny, AC ;
Steglich, C ;
Barry, K ;
DeLong, EF ;
Chisholm, SW .
SCIENCE, 2006, 311 (5768) :1768-1770