Comparative metagenomics: Natural populations of induced prophages demonstrate highly unique, lower diversity viral sequences

Environmental Microbiology

Volumn 16, Issue 2, 2014, Pages 570-585

  Mcdaniel, Lauren D ^a   Rosario, Karyna ^a   Breitbart, Mya ^a   Paul, John H ^a  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACILLARIOPHYTA; CHAETOCEROS; SSDNA VIRUSES;

SEA WATER; SINGLE STRANDED DNA; VIRUS DNA;

ARTICLE; BAY; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; DNA VIRUS; GENE LIBRARY; GENETICS; ISOLATION AND PURIFICATION; METAGENOME; METAGENOMICS; MICROBIOLOGY; PROPHAGE; UNITED STATES; VIROLOGY; VIRUS GENOME;

BAYS; DNA VIRUSES; DNA, SINGLE-STRANDED; DNA, VIRAL; FLORIDA; GENE LIBRARY; GENOME, VIRAL; METAGENOME; METAGENOMICS; PROPHAGES; SEAWATER; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

EID: 84892988070     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12184     Document Type: Article

References (68)

1. Ackermann, H.W., and DuBow, M.S. (1987) Viruses of Prokaryotes Volume I: General Properties of Bacteriophages. Boca Raton, FL, USA: CRC Press.
2. Anderson, R.E., Brazelton, W.J., and Baross, J.A. (2011) Is the genetic landscape of the deep subsurface biosphere affected by viruses? Front Microbiol 2: 219. doi: 10.3389/fmicb.2011.00219
3. Angly, F., Rodriguez-Brito, B., etal. (2005) PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 6. doi: 10.1186/1471-2105-6-41
4. Angly, F.E., Willner, D., etal. (2009) The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol 5: e1000593.
5. Bhavsar, J., Polson, S.W., etal. (2009) VIROME: a resource for analysis of viral metagenomes. Abstracts of the General Meeting of the American Society for Microbiology 109.
6. Breitbart, M. (2012) Marine viruses: truth or dare. In Annual Review of Marine Science, Vol. 4. Carlson, C.A., and Giovannoni, S.J. (eds). Palo Alto, CA, USA: Annual Reviews, 4, pp. 425-448.
7. Cassman, N., Prieto-Davo, A., etal. (2012) Oxygen minimum zones harbour novel viral communities with low diversity. Environ Microbiol 14: 3043-3065.
8. Cochran, P.K., Kellogg, C.A., etal. (1998) Prophage induction of indigenous marine lysogenic bacteria by environmental pollutants. Mar Ecol Prog Ser 164: 125-133.
9. Cottrell, M., and Kirchman, D. (2012) Virus genes in Arctic marine bacteria identified by metagenomic analysis. Aquat Microb Ecol 66: 107-116.
10. De Corte, D., Sintes, E., etal. (2012) Links between viruses and prokaryotes throughout the water column along a North Atlantic latitudinal transect. ISME J 6: 1566-1577.
11. Desnues, C., Rodriguez-Brito, B., etal. (2008) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452: 340-345.
12. Diemer, G.S., and Stedman, K.M. (2012) A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biol Direct 7. doi:10.1186/1745-6150-7-13
13. Dinsdale, E.A., Edwards, R.A., etal. (2008) Functional metagenomic profiling of nine biomes. Nature 455. doi: 10.1038/nature06810
14. Emerson, J.B., Thomas, B.C., etal. (2012) Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol 78: 6309-6320.
15. Fane, B.A., Brentlinger, K.L., etal. (2006) The microviridae. In The Bacteriophages. Calendar, R. (ed.). New York, USA: Oxford University Press, pp. 129-145.
16. Ghai, R., Martin-Cuadrado, A.B., etal. (2010) Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME J 4: 1154-1166.
17. Haible, D., Kober, S., etal. (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135: 9-16.
18. Huson, D.H., and Mitra, S. (2012) Introduction to the analysis of environmental sequences: metagenomics with MEGAN. In Evolutionary Genomics: Statistical and Computational Methods. Vol. 2. Anisimova, M. (ed.). Totowa, NJ, USA: Humana Press Inc., 856, pp. 415-429.
19. Hutchison, C.A., Smith, H.O., etal. (2005) Cell-free cloning using phi 29 DNA polymerase. Proc Natl Acad Sci USA 102: 17332-17336.
20. Jiang, S.C., Kellogg, C.A., etal. (1998) Characterization of marine temperate phage-host systems isolated from Mamala Bay, Oahu, Hawaii. Appl Environ Microbiol 64: 535-542.
21. Jiang, S.C., and Paul, J.H. (1996) Occurance of lysogenic bacteria in marine microbial communities as determined by prophage induction. Mar Ecol Prog Ser 142: 27-38.
22. Jiang, S.C., and Paul, J.H. (1998) Gene transfer by transduction in the marine environment. Appl Environ Microbiol 64: 2780-2787.
23. Keegan, K.P., Trimble, W.L., etal. (2012) A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE. PLoS Comput Biol 8: e1002541.
24. Kim, K.-H., Chang, H.-W., etal. (2008) Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl Environ Microbiol 74: 5975-5985.
25. Krupovic, M., and Forterre, P. (2011) Microviridae goes temperate: microvirus-related proviruses reside in the genomes of bacteroidetes. PLoS ONE 6: e19893.
26. Lang, A.S., Zhaxybayeva, O., etal. (2012) Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 10: 472-482.
27. Laybourn-Parry, J., Marshall, W.A., etal. (2007) Viral dynamics and patterns of lysogeny in saline Antartic lakes. Polar Biol 30: 351-358.
28. Li, L., Kapoor, A., etal. (2010) Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84: 1674-1682.
29. Long, A., McDaniel, L.D., etal. (2008) Comparison of lysogeny (prophage induction) in heterotrophic bacterial and Synechococcus populations in the Gulf of Mexico and Mississippi river plume. ISME J 2: 132-144.
30. Lopez-Bueno, A., Tamames, J., etal. (2009) High diversity of the viral community from an Antarctic Lake. Science 326: 858-861.
31. McDaniel, L., Breitbart, M., etal. (2008) Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression. PLoS One 3: Article No.: e3263.
32. McDaniel, L., Houchin, L.A., etal. (2002) Lysogeny in marine Synechococcus. Nature 415: 496.
33. Margulies, M., Egholm, M., etal. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
34. Maurice, C.F., Mouillot, D., etal. (2011) Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons. ISME J 5: 831-842.
35. Meyer, F., Paarmann, D., etal. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9. doi: 10.1186/1471-2105-9-386
36. Ohki, K., and Fujita, Y. (1996) Occurrence of a temperate cyanophage lysogenizing the marine cyanophyte Phormidium persicinum. J Phycol 32: 365-370.
37. Padan, E., Shilo, M., etal. (1972) Lysogeny of the blue-green alga Plectonema boryanum by LPP2-SPI cyanophage. Virology 47: 525-526.
38. Patel, A., Noble, R.T., etal. (2007) Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat Protoc 2: 269-276.
39. Paul, J.H. (2008) Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J 2: 579-589.
40. Pride, D.T., Salzman, J., etal. (2012) Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J 6: 915-926.
41. Rodriguez-Brito, B., Li, L., etal. (2010) Viral and microbial community dynamics in four aquatic environments. ISME J 4: 739-751.
42. Rosario, K., Duffy, S., etal. (2009) Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol 90: 2418-2424.
43. Rosario, K., Duffy, S., etal. (2012) A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol 157: 1-21.
44. Roux, S., Enault, F., etal. (2012) Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS ONE 7: e33641.
45. Roux, S., Faubladier, M., etal. (2011) Metavir: a web server dedicated to virome analysis. Bioinformatics 27: 3074-3075.
46. Roux, S., Krupovic, M., etal. (2012) Evolution and diversity of the microviridae viral family through a collection of 81 new complete genomes assembled from virome reads. PLoS ONE 7: e40418.
47. Sawstrom, C., and Pollard, P. (2012) Environmental influences on virus-host interactions in an Australian subtropical reservoir. Environ Microbiol Rep 4: 72-81.
48. Sharon, I., Alperovitch, A., etal. (2009) Photosystem I gene cassettes are present in marine virus genomes. Nature 461: 258-262.
49. Sharon, I., Battchikova, N., etal. (2011) Comparative metagenomics of microbial traits within oceanic viral communities. ISME J 5: 1178-1190.
50. Sharon, I., Tzahor, S., etal. (2007) Viral photosynthetic reaction center genes and transcripts in the marine environment. ISME J 1: 492-501.
51. Sode, K., Oonari, R., etal. (1997) Induction of a temperate marine cyanophage by heavy metal. J Mar Biotechnol 5: 178-180.
52. Sode, K., Oozeki, M., etal. (1994) Isolation of a marine cyanophage infecting the marine unicellular cyanobacterium, Synechoccus sp. NKBG 042902. J Mar Biotechnol 1: 189-192.
53. Stopar, D., Cerne, A., etal. (2004) Viral abundance and a high proportion of lysogens suggest that viruses are important members of the microbial community in the Gulf of Trieste. Microb Ecol 47: 1-8.
54. Thomas, R., Berdjeb, L., etal. (2011) Viral abundance, production, decay rates and life strategies (lysogeny versus lysis) in Lake Bourget (France). Environ Microbiol 13: 616-630.
55. Thurber, R.L.V., Barott, K.L., etal. (2008) Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proc Natl Acad Sci USA 105: 18413-18418.
56. Thurber, R.V., Haynes, M., etal. (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4: 470-483.
57. Tomaru, Y., Shirai, Y., etal. (2008) Isolation and characterization of a new single-stranded DNA virus infecting the cosmopolitan marine diatom Chaetoceros dehilis. Aquat Microb Ecol 50: 103-112.
58. Tomaru, Y., Shirai, Y., etal. (2011) Isolation and characterisation of a single-stranded DNA virus infecting the marine planktonic diatom Chaetoceros tenuissimus. Aquat Microb Ecol 64: 175-184.
59. Tucker, K.P., Parsons, R., etal. (2011) Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean. ISME J 5: 822-830.
60. Wang, G.H., Murase, J., etal. (2009) Novel cyanophage photosynthetic gene psbA in the floodwater of a Japanese rice field. FEMS Microbiol Ecol 70: 79-86.
61. Wang, X.X., Kim, Y., etal. (2010) Cryptic prophages help bacteria cope with adverse environments. Nat Commun 1. doi: 10.1038/ncomms1146
62. Weinbauer, M.C., and Suttle, C.A. (1996) Potential significance of lysogeny to bacteriophage production and bacterial mortality in coastal waters of the Gulf of Mexico. Appl Environ Microbiol 62: 4374-4380.
63. Weinbauer, M.G., Brettar, I., etal. (2003) Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters. Limnol Oceanogr 48: 1457-1465.
64. Weinbauer, M.G., and Suttle, C.A. (1999) Lysogeny and prophage induction in coastal and offshore bacterial communities. Aquat Microb Ecol 18: 217-225.
65. Wilke, A., Harrison, T., etal. (2012) The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics 13. doi: 10.1186/1471-2105-13-141
66. Williamson, S.J., Cary, S.C., etal. (2008) Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents. ISME J 2: 1112-1121.
67. Williamson, S.J., Houchin, L.A., etal. (2002) Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida. Appl Environ Microbiol 68: 4307-4314.
68. Wommack, K.E., Bhavsar, J., etal. (2012) VIROME: a standard operating procedure for analysis of viral metagenome sequences. Stand Genomic Sci 6: 421-433.