Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

ISME Journal

Volumn 5, Issue 5, 2011, Pages 822-830

  Tucker, Kimberly P ^a,c   Parsons, Rachel ^b   Symonds, Erin M ^a   Breitbart, Mya ^a  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b BERMUDA INSTITUTE OF OCEAN SCIENCES   (Bermuda)

^c School of Business and Public Management   (United States)

Author keywords

Marine; Microviridae; phage; single stranded DNA; virus

Indexed keywords

HELICASE; REPLICATION INITIATOR PROTEIN; SEA WATER; SINGLE STRANDED DNA; TRANSACTIVATOR PROTEIN; VIRUS DNA;

GENOME; HOST RANGE; MARINE ECOSYSTEM; MITOCHONDRIAL DNA; POLYMERASE CHAIN REACTION; PROTEIN; VIRUS;

ARTICLE; ATLANTIC OCEAN; BIODIVERSITY; CLASSIFICATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; GEOGRAPHY; METAGENOME; MICROBIOLOGY; MICROVIRIDAE; TIME; VIROLOGY; VIRUS GENE; VIRUS GENOME;

ATLANTIC OCEAN; BASE COMPOSITION; BIODIVERSITY; DNA HELICASES; DNA, SINGLE-STRANDED; DNA, VIRAL; GENES, VIRAL; GENOME, VIRAL; GEOGRAPHY; METAGENOME; MICROVIRIDAE; SEAWATER; SEQUENCE ANALYSIS, DNA; TIME FACTORS; TRANS-ACTIVATORS; WATER MICROBIOLOGY;

ATLANTIC OCEAN; ATLANTIC OCEAN (NORTH); SARGASSO SEA;

MICROVIRIDAE;

EID: 79955068424     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.188     Document Type: Article

References (68)

1. Abascal F, Zardoya R, Posada D. (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105. (Pubitemid 40668057)
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402. (Pubitemid 27359211)
3. Angly F, Felts B, Breitbart M, Salamon P, Edwards R, Carlson C et al. (2006). The marine viromes of four oceanic regions. PLoS Biol 4: e368.
4. Anisimova M, Gascuel O. (2006). Approximate likelihoodratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 55:539-552. (Pubitemid 43922340)
5. Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, Salamon P et al. (2004). Diversity and population structure of a near-shore marine-sediment viral community. Proc R Soc Lond B Biol Sci 271:565-574. (Pubitemid 38365844)
6. Breitbart M, Rohwer F. (2004). Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol Lett 236:245-252.
7. Breitbart M, Rohwer F. (2005). Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13:278-284. (Pubitemid 40779816)
8. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D et al. (2002). Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 99:14250-14255. (Pubitemid 35257658)
9. Brentlinger K, Hafenstein S, Novak C, Fane B, Borgon R, McKenna R et al. (2002). Microviridae, a family divided: isolation, characterization, and genome sequence of φMH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus. J Bacteriol 184:1089-1094. (Pubitemid 34113377)
10. Carlson C, Morris R, Parsons R, Treusch A, Giovannoni S, Vergin K. (2009). Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea. ISME J 3:283-295.
11. Cuevas J, Duffy S, Sanjuan R. (2009). Point mutation rate of bacteriophage φX174. Genetics 183:747-749.
12. Culley A, Steward G. (2007). New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences. Appl Environ Microbiol 73:5937-5944. (Pubitemid 47463007)
13. Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, Haynes M et al. (2008). Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452:340-343. (Pubitemid 351430793)
14. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM et al. (2008). Functional metagenomic profiling of nine biomes. Nature 452:629-632. (Pubitemid 351483360)
15. Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Heled J et al. (2010). Geneious v5.0.4 http://www.geneious.com.
16. Drummond A, Strimmer K. (2001). PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17:662-663. (Pubitemid 32707592)
17. Duffy S, Holmes E. (2009). Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol 90:1539-1547.
18. Duffy S, Shackelton L, Holmes E. (2008). Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 9:267-276. (Pubitemid 351399833)
19. Edgar R. (2004a). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. (Pubitemid 38832724)
20. Edgar R. (2004b). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform 5:113.
21. Fane B (2005). Family microviridae. In: Fauquet C, Mayo M, Maniloff J, Desselberger U, Ball L (eds). Virus Taxonomy: Classification and Nomenclature of Viruses. Elsevier Academic Press: San Diego, pp 289-299.
22. Faruque SM, Rahman MM, Asadulghani, Islam KMN, Mekalanos JJ. (1999). Lysogenic conversion of environmental Vibrio mimicus strains by CTXφ. Infect Immun 67:5723-5729. (Pubitemid 29508091)
23. Fauquet C, Mayo M, Maniloff J, Desselberger U, Ball L (eds) (2005). Virus Taxonomy: Classification and Nomenclature of Viruses. Elsevier Academic Press: San Diego.
24. Fuhrman J, Schwalbach M. (2003). Viral influence of aquatic bacterial communities. Biol Bull 204:192-195. (Pubitemid 36516707)
25. Garner S, Everson J, Lambden P, Fane B, Clarke I. (2004). Isolation, molecular characterisation and genome sequence of a bacteriophage (Chp3) from Chlamydophila percorum. Virus Genes 28:207-214. (Pubitemid 38393429)
26. Guindon S, Daufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O. (2010). New algorithms and methods to estimate maximum likelihood phylogenies: assessing the performance of PhyML3.0. Syst Biol 59:307-321.
27. Guindon S, Gascuel O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704. (Pubitemid 37365050)
28. Haible D, Kober S, Jeske H. (2006). Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135:9-16. (Pubitemid 43728848)
29. Hall T. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
30. Huang SJ, Wilhelm SW, Jiao NAZ, Chen F. (2010). Ubiquitous cyanobacterial podoviruses in the global oceans unveiled through viral DNA polymerase gene sequences. ISME J 4:1243-1251.
31. Jiang SC, Paul JH. (1998). Gene transfer by transduction in the marine environment. Appl Environ Microbiol 64:2780-2787. (Pubitemid 28363141)
32. Kellogg CA, Rose JB, Jiang SC, Turmond JM, Paul JH. (1995). Genetic diversity of related vibriophages isolated from marine environments around Florida and Hawaii, USA. Mar. Ecol Prog Ser 120:89-98.
33. Kim K, Chang H, Nam Y, Roh S, Kim M, Sung y et al. (2008). Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl Environ Microbiol 74:5975-5985.
34. Labonte JM, Reid KE, Suttle CA. (2009). Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences. Appl Environ Microbiol 75:3634-3640.
35. LeClerc J. (2002). Single-stranded DNA phages. In: Streips U, Yasbin R (eds). Modern Microbial Genetics 2nd edn. Wiley-Liss, Inc.: New York, pp 145-176.
36. Lui B, Everson J, Fane B, Giannikopoulou P, Vertou E, Lambden P et al. (2000). Molecular characterization of a bacteriophage (Chp2) from Chlamydia psittaci. J Virol 74:3464-3469. (Pubitemid 30180287)
37. Marie D, Brussaard C, Thyrhaug R, Bratbak G, Vaulot D. (1999). Enumeration of marine viruses in culture and natural samples by flow cytometry. Appl Environ Microbiol 65:45-52. (Pubitemid 29029617)
38. McDaniel L, Paul J, de la Rosa M. (2006). Temperate and lytic cyanophages from the Gulf of Mexico. J Mar. Biol Assoc UK 86:517-527.
39. Morris RM, Vergin KL, Cho JC, Rappe MS, Carlson CA, Giovannoni SJ. (2005). Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time-series Study site. Limnol Oceanogr 50:1687-1696. (Pubitemid 41356448)
40. Nagasaki K, Tomaru Y, Takao Y, Nishida K, Shirai Y, Suzuki H et al. (2005). Previously unknown virus infects marine diatom. Appl Environ Microbiol 71:3528-3535. (Pubitemid 40980517)
41. Parks D, Porter M, Churcher S, Wang S, Blouin C, Whalley J et al. (2009). GenGIS: a geospatial information system for genomic data. Genome Res 19:1896-1904.
42. Paul JH. (2008). Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J 2:579-589. (Pubitemid 351793245)
43. Posada D. (2008). jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253-1256. (Pubitemid 351882013)
44. Read T, Brunham R, Shen C, Gill S, Heidelberg J, White O et al. (2000). Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res 28:1397-1406. (Pubitemid 30142683)
45. Renaudin J, Paracel M, Bove J. (1987). Spiroplasma virus 4: nucleotide sequence of the viral DNA, regulatory signals, and the proposed genome organization. J Bacteriol 169:4950-4961.
46. Rohwer F, Thurber RV. (2009). Viruses manipulate the marine environment. Nature 459:207-212.
47. Rokyta D, Burch C, Caudle S, Wichman H. (2006). Horizontal gene transfer and the evolution of microvirid coliphage genomes. J Bacteriol 188:1134-1142. (Pubitemid 43146429)
48. Rosario K, Duffy S, Breitbart M. (2009). Diverse circoviruslike genome architectures revealed by environmental metagenomics. J Gen Virol 90:2418-2424.
49. Rozen S, Skaletsky H. (2000). Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds). Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press: Totowa, NJ, pp 365-386.
50. Sambrook J, Fritsch E, Maniatis T. (1989). Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press: New York.
51. Sandaa R. (2008). Burden or benefit? Virus-host interactions in the marine environment. Res Microbiol 159:374-381.
52. Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA et al. (1977). Nucleotide sequence of bacteriophage φX174 DNA. Nature 265:687-695. (Pubitemid 8039446)
53. Short C, Suttle C. (2005). Nearly identical bacteriophage structural gene sequences are widely distributed in marine and freshwater environments. Appl Environ Microbiol 71:480-486. (Pubitemid 40116304)
54. Short SM, Suttle CA. (2002). Sequence analysis of marine virus communities reveals that groups of related algal viruses are widely distributed in nature. Appl Environ Microbiol 68:1290-1296. (Pubitemid 34205368)
55. Steward G. (2001). Fingerprinting viral assemblages by pulsed field gel electrophoresis. In: Paul J (ed). Methods in Microbiology. Academic Press: San Diego, pp 85-103. (Pubitemid 33805046)
56. Steward G, Montiel J, Azam F. (2000). Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments. Limnol Oceanogr 45:1697-1706. (Pubitemid 32040143)
57. Storey CC, Lusher M, Richmond SJ. (1989). Analysis of the complete nucleotide sequence of Chp1, a phage which infects avian Chlamydia psittaci. J Gen Virol 70:3381-3390. (Pubitemid 20044077)
58. Sullivan M, Coleman M, Quinlivan V, Rosenkrantz J, DeFrancesco A, Tan G et al. (2008). Portal protein diversity and phage ecology. Enviro Microbiol 10:2810-2823.
59. Thurber R, Haynes M, Breitbart M, Wegley L, Rohwer F. (2009). Laboratory procedures to generate viral metagenomes. Nat Protocols 4:470-483.
60. Tomaru Y, Nagasaki K. (2007). Flow cytometric detection and enumeration of DNA and RNA viruses infecting marine eukaryotic microalgae. J Oceanogr 63:215-221. (Pubitemid 46390099)
61. Tomaru Y, Shirai Y, Suzuki H, Nagumo T, Nagasaki K. (2008). Isolation and characterization of a new singlestranded DNAvirus infecting the cosmopolitan marine diatom Chaetoceros debilis. Aqua Microbial Ecol 50:103-112. (Pubitemid 351300189)
62. Treusch A, Vergin K, Finlay L, Donatz M, Burton R, Carlson C et al. (2009). Seasonality and vertical structure of microbial communities in an ocean gyre. ISME J 3:1148-1163.
63. Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F. (2007). Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9:2707-2719. (Pubitemid 47547539)
64. Weinbauer M. (2004). Ecology of prokaryotic viruses. FEMS Microbiol Rev 28:127-181. (Pubitemid 38510500)
65. Weinbauer M, Rassoulzadegan F. (2004). Are viruses driving microbial diversification and diversity? Environ Microbiol 6:1-11. (Pubitemid 38162022)
66. Wommack K, Colwell R. (2000). Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64:69-114. (Pubitemid 30143841)
67. Xia X, Xie Z. (2001). DAMBE: software package for data analysis in molecular biology and evolution. J Hered 92:371-373. (Pubitemid 32848767)
68. Yu Y, Breitbart M, McNairnie P, Rohwer F. (2006). FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinform 7:57.