Metagenomic Contrasts of Viruses in Soil and Aquatic Environments
K. Eric Wommack
Delaware Biotechnology Institute, Newark, Delaware, USA
Search for more papers by this authorSharath Srinivasiah
Delaware Biotechnology Institute, Newark, Delaware, USA
Search for more papers by this authorJaysheel Bhavsar
University of Maryland School of Medicine, Baltimore, Maryland, USA
Search for more papers by this authorShellie Bench
Ocean Sciences Department, University of California, Santa Cruz, California, USA
Search for more papers by this authorKurt E. Williamson
The College of William and Mary, Williamsburg, Virginia, USA
Search for more papers by this authorShawn W. Polson
Delaware Biotechnology Institute, Newark, Delaware, USA
Search for more papers by this authorK. Eric Wommack
Delaware Biotechnology Institute, Newark, Delaware, USA
Search for more papers by this authorSharath Srinivasiah
Delaware Biotechnology Institute, Newark, Delaware, USA
Search for more papers by this authorJaysheel Bhavsar
University of Maryland School of Medicine, Baltimore, Maryland, USA
Search for more papers by this authorShellie Bench
Ocean Sciences Department, University of California, Santa Cruz, California, USA
Search for more papers by this authorKurt E. Williamson
The College of William and Mary, Williamsburg, Virginia, USA
Search for more papers by this authorShawn W. Polson
Delaware Biotechnology Institute, Newark, Delaware, USA
Search for more papers by this authorFrans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorSummary
This chapter contains sections titled:
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Introduction
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Materials and Methods
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Results and Discussion
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Internet Resources
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References
INTERNET RESOURCES
- Viral Informatics Resource for Metagenome Exploration-Beta release (http://virome.dbi.udel.edu)
- REFERENCES
- Angly F, Rodriguez-Brito B, Bangor D, McNairnie P, Breitbart M, et al. 2005. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 6: 41.
- Angly FE, Felts B, Breitbart M, Salamon P., Edwards RA, et al. 2006. The marine viromes of four oceanic regions. PLoS Biol 4.
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25: 25–29.
- Azam F. 1998. Microbial control of oceanic carbon flux: The plot thickens. Science 280: 694–696.
- Azam F, Malfatti F. 2007. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5: 782–791.
- Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, et al. 2007. Metagenomic characterization of chesapeake bay virio-plankton. Appl. Environ. Microbiol. 73: 7629–7641.
- Bidle. D, Haramaty L, Barcelos E, Ramos J, Falkowski, P. 2007. Viral activation and recruitment of metacaspases in the unicellular coccolithophore, Emiliania huxleyi. Proc. Natl. Acad. Sci. USA 104: 6049–6054.
- Breitbart M, Salamon P, Andresen B, Mahaffy JM., Segall AM, et al. 2002. Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. USA 99: 14250–14255.
- Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, et al. 2009. The Carbohydrate-Active EnZymes database (CAZy): An expert resource for glycogenomics. N.A.R. 37: D233–D238.
- Chen F, Lu J. 2002. Genomic sequence and evolution of marine cyanophage P60: A new insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68: 2589–2594.
- Danovaro R, Dell'Anno A, Corinaldesi C, Magagnini M., Noble R, et al. 2008. Major viral impact on the functioning of benthic deep-sea ecosystems. Nature 454: 1084–1087.
- Dinsdale EA, Edwards RA, Hall D, Angly FE, Breitbart M, et al. 2008. Functional metagenomic profiling of nine biomes. Nature 452: 629–632.
- Fierer N., Breitbart M, Nulton J, Salamon P, Lozupone C, et al. 2007. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl. Environ. Microbiol. 73: 7059–7066.
- Hambly E, Tetart F, Desplats C, Wilson WH, Krisch HM, et al. 2001. A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc. Natl. Acad. Sci. USA 98: 11411–11416.
- Hatfull G., Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, et al. 2006. Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform. PLoS Genet. 2: e92.
- Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF. 1999. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc. Natl. Acad. Sci. USA 96: 2192–2197.
- Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. 2008. KEGG for linking genomes to life and the environment. N.A.R. 36: D480–D484.
- Karl DM, 1999. A sea of change: Biogeochemical variability in the North Pacific Subtropical Gyre. Ecosystems 2: 181–214.
- Lairson LL, Henrissat B, Davies GF, Withers SG, 2008. Glycosyltransferases: structures, functions, and mechanisms. Annu. Rev. Biochem 77: 521–555.
- Leplae R, Hebrant A, Wodak SJ, Toussaint A. 2004. ACLAME: A classification of mobile genetic elements. Nucleic Acids Res. 32: D45–D49.
- Lowe TM, Eddy, SR 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955–964.
- Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, et al. 2001. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 65: 44–79.
- Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa, et al. 2003. Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67: 86–156, table of contents.
- Noguchi H, Taniguchi T., Itoh, T. 2008. MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 15: 387–396.
- Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33: 5691–5702.
- Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M. 2009. Metagenomic analysis of viruses in reclaimed water. Environ. Micro-biol. 11: 2806–2820.
- Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. 2007. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5: e77.
- Sambrook J, Russell DW. 2001. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
- Schoenfeld T, Patterson M, Richardson PM, Wommack KE, Young M, et al. 2008. Assembly of viral metagenomes from yellowstone hot springs. Appl. Environ. Microbiol 74: 4164–4174.
- Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. 2007. CAMERA: A community resource for metagenomics. PLoS Biol 5: e75.
- Srinivasiah S, Bhavsar J, Thapar K, Liles M, Schoenfeld T, et al. 2008. Phages across the biosphere: contrasts of viruses in soil and aquatic environments. Res. Microbiol. 159: 349–357.
- Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. 2005. Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations. PLoS Biol 3: e144.
- Suttle CA, 2005. Viruses in the sea. Nature 437: 356–361.
- Suzek BE., Huang H, McGarvey P, Mazumder R, Wu CH. 2007. UniRef: Comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23: 1282–1288.
- Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR., Kiryutin B, et al. 2003. The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4: 41.
- Torsvik V, Ovreas L, Thingstad TF. 2002. Prokaryotic diversity— Magnitude, dynamics, and controlling factors. Science 296: 1064–1066.
- Vardi A, Van Mooy BAS, Fredricks HF, Popendorf KJ, Ossolinski JE, et al. 2009. Viral glycosphingolipids induce lytic infection and cell death in marine phytoplankton. Science 326: 861–865.
- Weigele PR, Pope WH, Pedulla ML, Houtz JM., Smith AL, et al. 2007. Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. Environ. Microbiol. 9: 1675–1695.
- White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, et al. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286: 1571–1577.
- Williamson KE, Wommack KE, Radosevich M. 2003. Sampling natural viral communities from soil for culture-independent analyses. Appl. Environ. Microbiol. 69: 6628–6633.
- Williamson KE, Radosevich M, Wommack KE. 2005. Abundance and diversity of viruses in six Delaware soils. Appl. Environ. Micro-biol. 71: 3119–3125.
- Williamson E, Radosevich M, Smith DW, Wommack KE. 2007. Incidence of lysogeny within temperate and extreme soil environments. Environ. Microbiol. 9: 2563–2574.
- Wilson WH, Schroeder DC, Allen MJ, Holden MT, Parkhill J, et al. 2005. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science 309: 1090–1092.
- Winget DM, Wommack, KE. 2009. Diel and daily fluctuations in virioplankton production in coastal ecosystems. Environ. Microbiol. 11: 2904–2914.
- Wommack KE, Colwell RR. 2000. Virioplankton: Viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64: 69–114.
- Wommack KE, Bhavsar J., Ravel, J. 2008. Metagenomics: read length matters. Appl. Environ. Microbiol. 74: 1453–1463.
- Yin Y, Fischer D. 2008. Identification and investigation of ORFans in the viral world. BMC Genomics 9: 24.