Expanding the Marine Virosphere Using Metagenomics

PLoS Genetics

Volumn 9, Issue 12, 2013, Pages

  Mizuno, Carolina Megumi ^a   Rodriguez Valera, Francisco ^a   Kimes, Nikole E ^a   Ghai, Rohit ^a  

^a MIGUEL HERNÁNDEZ UNIVERSITY   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPHYLL; CONTIG; VIRUS DNA;

ARTICLE; BACTERIOPHAGE; CLADISTICS; CONTROLLED STUDY; FOSMID; GENETIC VARIABILITY; HOST SELECTION; MARINE SPECIES; METAGENOMICS; NONHUMAN; PREDICTION; SEQUENCE ANALYSIS; SPECIES DIVERSITY; VIRUS GENOME; VIRUS ISOLATION;

ACTINOBACTERIA; BACTERIOPHAGES; CYANOBACTERIA; DNA, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; MOLECULAR SEQUENCE DATA; PROKARYOTIC CELLS; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 84892736640     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003987     Document Type: Article

References (86)

1. Rohwer F, Prangishvili D, Lindell D, (2009) Roles of viruses in the environment. Environmental Microbiology 11: 2771-2774.
2. Suttle CA, (2007) Marine viruses-major players in the global ecosystem. Nature Reviews Microbiology 5: 801-812.
3. Weinbauer MG, (2004) Ecology of prokaryotic viruses. Fems Microbiol Rev 28: 127-181.
4. Breitbart M, (2012) Marine viruses: truth or dare. Marine Science 4: 425-448.
5. Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pasic L, Thingstad TF, et al. (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7: 828-836.
6. Amann RI, Ludwig W, Schleifer K-H, (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological reviews 59: 143-169.
7. Hugenholtz P, Goebel BM, Pace NR, (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology 180: 4765-4774.
8. Staley JT, Konopka A, (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annual Reviews in Microbiology 39: 321-346.
9. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
10. Ghai R, Martin-Cuadrado A-B, Molto AG, Heredia IG, Cabrera R, et al. (2010) Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. The ISME Journal 4: 1154-1166.
11. 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.
12. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
13. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, et al. (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
14. Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, et al. (2013) Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences 110: 11463-11468.
15. Duhaime MB, Deng L, Poulos BT, Sullivan MB, (2012) Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environmental Microbiology 14: 2526-2537.
16. Duhaime MB, Sullivan MB, (2012) Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology 434: 181-186.
17. John SG, Mendez CB, Deng L, Poulos B, Kauffman AKM, et al. (2011) A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental Microbiology Reports 3: 195-202.
18. Mizuno CM, Rodriguez-Valera F, Garcia-Heredia I, Martin-Cuadrado A-B, Ghai R, (2013) Reconstruction of Novel Cyanobacterial Siphovirus Genomes from Mediterranean Metagenomic Fosmids. Applied and Environmental Microbiology 79: 688-695.
19. Haible D, Kober S, Jeske H, (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. Journal of virological methods 135: 9-16.
20. McDaniel LD, Rosario K, Breitbart M, Paul JH, (2013) Comparative metagenomics: Natural populations of induced prophages demonstrate highly unique, lower diversity viral sequences. Environmental Microbiology doi: 10.1111/1462-2920.12184. In press.
21. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. (2006) The marine viromes of four oceanic regions. PLoS Biology 4: e368.
22. Hurwitz BL, Sullivan MB, (2013) The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 8: e57355.
23. Sharon I, Battchikova N, Aro E-M, Giglione C, Meinnel T, et al. (2011) Comparative metagenomics of microbial traits within oceanic viral communities. The ISME Journal 5: 1178-1190.
24. Williamson SJ, Allen LZ, Lorenzi HA, Fadrosh DW, Brami D, et al. (2012) Metagenomic exploration of viruses throughout the Indian Ocean. PLoS One 7: e42047.
25. Williamson SJ, Rusch DB, Yooseph S, Halpern AL, Heidelberg KB, et al. (2008) The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS One 3: e1456.
26. Labonté JM, Suttle CA, (2013) Previously unknown and highly divergent ssDNA viruses populate the oceans. The ISME Journal 7: 2169-2177.
27. Angly F, Youle M, Nosrat B, Srinagesh S, Rodriguez-Brito B, et al. (2009) Genomic analysis of multiple Roseophage SIO1 strains. Environmental Microbiology 11: 2863-2873.
28. Huang S, Wang K, Jiao N, Chen F, (2012) Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges. Environmental Microbiology 14: 540-558.
29. Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, et al. (2013) Genomes of marine cyanopodoviruses reveal multiple origins of diversity. Environmental Microbiology 15: 1356-1376.
30. Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW, (2005) Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations. PLoS Biology 3: e144.
31. Rappé MS, Connon SA, Vergin KL, Giovannoni SJ, (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
32. Zhao Y, Temperton B, Thrash JC, Schwalbach MS, Vergin KL, et al. (2013) Abundant SAR11 viruses in the ocean. Nature 494: 357-360.
33. Dean FB, Nelson JR, Giesler TL, Lasken RS, (2001) Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome research 11: 1095-1099.
34. Christaki U, Van Wambeke F, Lefevre D, Lagaria A, Prieur L, et al. (2011) Microbial food webs and metabolic state across oligotrophic waters of the Mediterranean Sea during summer. Biogeosciences 8: 1839-1852.
35. Siokou-Frangou I, Christaki U, Mazzocchi MG, Montresor M, Ribera d'Alcalá M, et al. (2010) Plankton in the open Mediterranean Sea: a review. Biogeosciences 7: 1543-1586.
36. Gonzaga A, Martin-Cuadrado A-B, López-Pérez M, Mizuno CM, García-Heredia I, et al. (2012) Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome biology and evolution 4: 1360-1374.
37. Kristensen DM, Cai X, Mushegian A, (2011) Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts. Journal of Bacteriology 193: 1806-1814.
38. Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, et al. (2011) Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proceedings of the National Academy of Sciences 108: E757-E764.
39. Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, et al. (2007) Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 449: 83-86.
40. Casjens SR, Gilcrease EB, Winn-Stapley DA, Schicklmaier P, Schmieger H, et al. (2005) The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. Journal of Bacteriology 187: 1091-1104.
41. Ackermann HW, Manilof J, (1998) Taxonomy of bacterial viruses: establishment of tailed virus genera and the order Caudovirales. Arch Virol 143: 2051-2063.
42. Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, et al. (2009) Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiology 9: 224.
43. Lavigne R, Seto D, Mahadevan P, Ackermann H-W, Kropinski AM, (2008) Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Research in Microbiology 159: 406-414.
44. Rohwer F, Edwards R, (2002) The Phage Proteomic Tree: a genome-based taxonomy for phage. Journal of Bacteriology 184: 4529-4535.
45. Holmfeldt K, Solonenko N, Shah M, Corrier K, Riemann L, et al. (2013) Twelve previously unknown phage genera are ubiquitous in global oceans. Proceedings of the National Academy of Sciences 110: 12798-12803.
46. Kang I, Jang H, Cho J-C, (2012) Complete Genome Sequences of Two Persicivirga Bacteriophages, P12024S and P12024L. Journal of virology 86: 8907-8908.
47. Alperovitch-Lavy A, Sharon I, Rohwer F, Aro EM, Glaser F, et al. (2011) Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets. Environmental Microbiology 13: 24-32.
48. Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, et al. (2004) Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proceedings of the National Academy of Sciences of the United States of America 101: 11013-11018.
49. Mann NH, Cook A, Millard A, Bailey S, Clokie M, (2003) Marine ecosystems: bacterial photosynthesis genes in a virus. Nature 424: 741-741.
50. Millard A, Clokie MR, Shub DA, Mann NH, (2004) Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proceedings of the National Academy of Sciences of the United States of America 101: 11007-11012.
51. Chenard C, Suttle C, (2008) Phylogenetic diversity of sequences of cyanophage photosynthetic gene psbA in marine and freshwaters. Applied and Environmental Microbiology 74: 5317-5324.
52. Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, et al. (2006) Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biology 4: e234.
53. Garcia-Heredia I, Martin-Cuadrado A-B, Mojica FJ, Santos F, Mira A, et al. (2012) Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS One 7: e33802.
54. Barre F-X, Sherratt DJ, (2002) Xer site-specific recombination: promoting chromosome segregation. Mobile DNA II 1: 149-161.
55. Huber KE, Waldor MK, (2002) Filamentous phage integration requires the host recombinases XerC and XerD. Nature 417: 656-659.
56. Sullivan MB, Krastins B, Hughes JL, Kelly L, Chase M, et al. (2009) The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'. Environmental Microbiology 11: 2935-2951.
57. Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F, (2013) Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria. Scientific Reports 3: 2471.
58. Kang I, Oh H-M, Kang D, Cho J-C, (2013) Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans. Proceedings of the National Academy of Sciences 110: 12343-12348.
59. Oh H-M, Kwon KK, Kang I, Kang SG, Lee J-H, et al. (2010) Complete genome sequence of "Candidatus Puniceispirillum marinum" IMCC1322, a representative of the SAR116 clade in the Alphaproteobacteria. Journal of Bacteriology 192: 3240-3241.
60. Rybniker J, Nowag A, Van Gumpel E, Nissen N, Robinson N, et al. (2010) Insights into the function of the WhiB-like protein of mycobacteriophage TM4- a transcriptional inhibitor of WhiB2. Molecular Microbiology 77: 642-657.
61. Brum JR, Schenck RO, Sullivan MB, (2013) Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. The ISME Journal 7: 1738-1751.
62. Rodriguez-Valera F, Ussery DW, (2012) Is the pan-genome also a pan-selectome? F1000Research 1: 16.
63. Kwan T, Liu J, DuBow M, Gros P, Pelletier J, (2005) The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proceedings of the National Academy of Sciences of the United States of America 102: 5174-5179.
64. Juhala RJ, Ford ME, Duda RL, Youlton A, Hatfull GF, et al. (2000) Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. Journal of molecular biology 299: 27-51.
65. Breitbart M, Miyake JH, Rohwer F, (2004) Global distribution of nearly identical phage-encoded DNA sequences. FEMS microbiology letters 236: 249-256.
66. Short CM, Suttle CA, (2005) Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Applied and Environmental Microbiology 71: 480-486.
67. Monaco AP, Larin Z, (1994) YACs, BACs, PACs and MACs: artificial chromosomes as research tools. Trends in biotechnology 12: 280-286.
68. McCarthy A, (2010) Third generation DNA sequencing: pacific biosciences' single molecule real time technology. Chemistry & biology 17: 675-676.
69. Culley AI, Lang AS, Suttle CA, (2006) Metagenomic analysis of coastal RNA virus communities. Science 312: 1795-1798.
70. Kim K-H, Chang H-W, Nam Y-D, Roh SW, Kim M-S, et al. (2008) Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Applied and Environmental Microbiology 74: 5975-5985.
71. Cuadros-Orellana S, Martin-Cuadrado A-B, Legault B, D'Auria G, Zhaxybayeva O, et al. (2007) Genomic plasticity in prokaryotes: the case of the square haloarchaeon. The ISME Journal 1: 235-245.
72. Pašić L, Rodriguez-Mueller B, Martin-Cuadrado A-B, Mira A, Rohwer F, et al. (2009) Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. BMC Genomics 10: 570.
73. Coleman ML, Sullivan MB, Martiny AC, Steglich C, Barry K, et al. (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science 311: 1768-1770.
74. Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, et al. (2013) Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity. PLoS One 8: e68731.
75. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research 18: 821-829.
76. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
77. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, et al. (2004) The Pfam protein families database. Nucleic acids research 32: D138-D141.
78. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic acids research 29: 22-28.
79. Söding J, Biegert A, Lupas AN, (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic acids research 33: W244-W248.
80. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25: 3389-3402.
81. Quinlan AR, Hall IM, (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
82. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research 13: 2498-2504.
83. Felsenstein J (1993) PHYLIP: phylogenetic inference package, version 3.5 c.
84. Eddy SR, (2011) Accelerated profile HMM searches. PLoS computational biology 7: e1002195.
85. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32: 1792-1797.
86. Price MN, Dehal PS, Arkin AP, (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.