Phylogenetic analysis indicates evolutionary diversity and environmental segregation of marine podovirus DNA polymerase gene sequences

Applied and Environmental Microbiology

Volumn 75, Issue 11, 2009, Pages 3634-3640

  Labonté, Jessica M ^a   Reid, Karen E ^a   Suttle, Curtis A ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BRITISH COLUMBIA , CANADA; COASTAL SEDIMENTS; CYANOPHAGE; DNA POLYMERASE; DNA POLYMERASE GENES; EVOLUTIONARY DIVERSITY; EVOLUTIONARY RELATIONSHIPS; GENE FRAGMENTS; GENETIC DIVERSITY; GEOGRAPHIC REGIONS; GEORGIA; MARINE SAMPLES; METAGENOMICS; NORTHEASTERN GULF OF MEXICO; OPERATIONAL TAXONOMIC UNITS; PCR PRIMERS; PCR PRODUCTS; PHYLOGENETIC ANALYSIS; POLYMERASE GENES; RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS; WATER SAMPLES;

AGRICULTURAL PRODUCTS; BIODIVERSITY; DNA; GENES; NUCLEIC ACIDS; OCEAN ENGINEERING; OCEANOGRAPHY; POLYMERS;

DNA SEQUENCES;

DNA FRAGMENT; DNA POLYMERASE; PRIMER DNA;

ENZYME ACTIVITY; EVOLUTION; GENETIC VARIATION; PHYLOGENETICS; POLYMERASE CHAIN REACTION; RELATEDNESS; SPATIAL DISTRIBUTION; SPECIES DIVERSITY; VIRUS;

ARTICLE; BACTERIOPHAGE; CANADA; CONTROLLED STUDY; CYANOPHAGE; GENE AMPLIFICATION; GENE SEGREGATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; MARINE PODOVIRUS; METAGENOMICS; MEXICO; MOLECULAR CLONING; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERATIONAL TAXONOMIC UNIT; PHYLOGENY; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; ROSEOPHAGE; SEDIMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURAL GENE; TAXONOMY; TECHNIQUE; WATER SAMPLING;

BRITISH COLUMBIA; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA PRIMERS; DNA, VIRAL; DNA-DIRECTED DNA POLYMERASE; EVOLUTION, MOLECULAR; GEOLOGIC SEDIMENTS; GEORGIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PODOVIRIDAE; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEAWATER; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; VIRAL PROTEINS;

ATLANTIC OCEAN; BRITISH COLUMBIA; CANADA; GULF OF MEXICO; NORTH AMERICA; STRAIT OF GEORGIA;

OTUS; T7-LIKE VIRUSES;

EID: 66249128247     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02317-08     Document Type: Article

References (51)

1. Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-415. (Pubitemid 38262773)
2. Angly, F. E., B. Felts, M. Breitbart, P. Salamon, R. A. Edwards, C. Carlson, A. M. Chan, M. Haynes, S. Kelley, H. Liu, J. M. Mahaffy, J. E. Mueller, J. Nulton, R. Olson, R. Parsons, S. Rayhawk, C. A. Suttle, and F. Rohwer. 2006. The marine viromes of four oceanic regions. PLoS Biol. 4:e368.
3. Borsheim, K. Y. 1993. Native marine bacteriophages. FEMS Microbiol. Lett. 102:141-159.
4. Breitbart, M., J. H. Miyake, and F. Rohwer. 2004. Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol. Lett. 236:249-256.
5. Breitbart, M., and F. Rohwer. 2005. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13:278-284.
6. Breitbart, M., P. Salamon, B. Andresen, J. M. Mahaffy, A. M. Segall, D. Mead, F. Azam, and F. Rohwer. 2002. Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. USA 99:14250-14255.
7. Chen, F., and J. Lu. 2002. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68:2589-2594.
8. Chen, F., and C. A. Suttle. 1996. Evolutionary relationships among large double-stranded DNA viruses that infect microalgae and other organisms as inferred from DNA polymerase genes. Virology 219:170-178. (Pubitemid 26180394)
9. Chen, F., C. A. Suttle, and S. M. Short. 1996. Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes. Appl. Environ. Microbiol. 62:2869-2874.
10. Cottrell, M. T., and C. A. Suttle. 1991. Wide-spread occurence and clonal variation in viruses which cause lysis of a cosmopolitain, eukaryotic marine phytoplankter, Micromonas pusilla. Mar. Ecol. Prog. Ser. 78:1-9.
11. DePaola, A., M. L. Motes, A. M. Chan, and C. A. Suttle. 1998. Phages infecting Vibrio vulnificus are abundant and diverse in oysters (Crassostrea virginica) collected from the Gulf of Mexico. Appl. Environ. Microbiol. 64:346-351.
12. Dorigo, U., S. Jacquet, and J. F. Humbert. 2004. Cyanophage diversity, inferred from g20 gene analyses, in the largest natural lake in France, Lake Bourget. Appl. Environ. Microbiol. 70:1017-1022.
13. Dunn, J. J., and F. W. Studier. 1983. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166:477-535.
14. Filee, J., F. Tetart, C. A. Suttle, and H. M. Krisch. 2005. Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Proc. Natl. Acad. Sci. USA 102:12471-12476.
15. Filippini, M., and M. Middelboe. 2007. Viral abundance and genome size distribution in the sediment and water column of marine and freshwater ecosystems. FEMS Microbiol. Ecol. 60:397-410.
16. Frank, H., and F. Moebus. 1987. An electron microscopic study of bacteriophages from marine waters. Helgolander Meeresunters. 41:385-414.
17. Frederickson, C. M., S. M. Short, and C. A. Suttle. 2003. The physical environment affects cyanophage communities in British Columbia inlets. Microb. Ecol. 46:348-357.
18. Fuller, N. J., W. H. Wilson, I. R. Joint, and N. H. Mann. 1998. Occurrence of a sequence in marine cyanophages similar to that of T4 g20 and its application to PCR-based detection and quantification techniques. Appl. Environ. Microbiol. 64:2051-2060.
19. Garcia, E., J. M. Elliott, E. Ramanculov, P. S. Chain, M. C. Chu, and I. J. Molineux. 2003. The genome sequence of Yersinia pestis bacteriophage φA1122 reveals an intimate history with the coliphage T3 and T7 genomes. J. Bacteriol. 185:5248-5262.
20. Hambly, E., F. Tetart, C. Desplats, W. H. Wilson, H. M. Krisch, and N. H. Mann. 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.
21. Hardies, S. C., A. M. Comeau, P. Serwer, and C. A. Suttle. 2003. The complete sequence of marine bacteriophage VpV262 infecting Vibrio parahaemolyticus indicates that an ancestral component of a T7 viral supergroup is widespread in the marine environment. Virology 310:359-371.
22. Hennes, K. P., C. A. Suttle, and A. M. Chan. 1995. Fluorescently labeled virus probes show that natural virus populations can control the structure of marine microbial communities. Appl. Environ. Microbiol. 61:3623-3627.
23. Kovalyova, I. V., and A. M. Kropinski. 2003. The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida-evidence for close relationship to the T7 group. Virology 311:305-315.
24. Larsen, A., T. Castberg, R. A. Sandaa, C. P. D. Brussaard, J. Egge, M. Heldal, A. Paulino, R. Thyrhaug, E. J. V. Hannen, and G. Bratbak. 2001. Population dynamics and diversity of phytoplankton, bacteria and viruses in seawater enclosure. Mar. Ecol. Prog. Ser. 221:47-57.
25. Lingohr, E. J., A. Villegas, Y. M. She, P. J. Ceyssens, and A. M. Kropinski. 2008. The genome and proteome of the Kluyvera bacteriophage Kvp1 - another member of the T7-like Autographivirinae. Virol. J. 5:122.
26. Loytynoja, A., and N. Goldman. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl. Acad. Sci. USA 102:10557-10562.
27. Maniloff, J., and H. W. Ackermann. 1998. Taxonomy of bacterial viruses: establishment of tailed virus genera and the order Caudovirales. Arch. Virol. 143:2051-2063. (Pubitemid 28537106)
28. Middelboe, M., A. Hagstrom, N. Blackburn, B. Sinn, U. Fischer, N. H. Borch, J. Pinhassi, K. Simu, and M. G. Lorenz. 2001. Effects of bacteriophages on the population dynamics of four strains of pelagic marine bacteria. Microb. Ecol. 42:395-406.
29. Pajunen, M. I., M. R. Elizondo, M. Skurnik, J. Kieleczawa, and I. J. Molineux. 2002. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. J. Mol. Biol. 319:1115-1132.
30. Pajunen, M. I., S. J. Kiljunen, M. E. Soderholm, and M. Skurnik. 2001. Complete genomic sequence of the lytic bacteriophage φYeO3-12 of Yersinia enterocolitica serotype O:3. J. Bacteriol. 183:1928-1937.
31. Pope, W. H., P. R. Weigele, J. Chang, M. L. Pedulla, M. E. Ford, J. M. Houtz, W. Jiang, W. Chiu, G. F. Hatfull, R. W. Hendrix, and J. King. 2007. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus. J. Mol. Biol. 368:966-981.
32. Rambaut, A., N. C. Grassly, S. Nee, and P. H. Harvey. 1996. Bi-De: an application for simulating phylogenetic processes. Comput. Appl. Biosci. 12:469-471.
33. Rohwer, F., A. M. Segall, G. Steward, V. Seguritan, M. Breitbart, F. Wolven, and F. Azam. 2000. The complete genomic sequence of the marine phage Roseophage SI01 shares homology with nonmarine phages. Limnol. Oceanogr. 45:408-418.
34. Scholl, D., and C. Merril. 2005. The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. J. Bacteriol. 187:8499-8503. (Pubitemid 41780515)
35. Seshadri, R., S. A. Kravitz, L. Smarr, P. Gilna, and M. Frazier. 2007. CAMERA: a community resource for metagenomics. PLoS Biol. 5:e75. (Pubitemid 46422964)
36. Shackelton, L. A., and E. C. Holmes. 2004. The evolution of large DNA viruses: combining genomic information of viruses and their hosts. Trends Microbiol. 12:458-465. (Pubitemid 39286124)
37. Short, C. M., and C. A. Suttle. 2005. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl. Environ. Microbiol. 71:480-486.
38. Short, S. M., and C. A. Suttle. 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.
39. Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
40. Sullivan, M. B., M. L. Coleman, P. Weigele, F. Rohwer, and S. W. Chisholm. 2005. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol. 3:e144.
41. Suttle, C. A. 2005. Viruses in the sea. Nature 437:356-361. (Pubitemid 41613491)
42. Suttle, C. A., A. M. Chan, and M. T. Cottrell. 1991. Use of ultrafiltration to isolate viruses from seawater which are pathogens of marine phytoplankton. Appl. Environ. Microbiol. 57:721-726.
43. Thingstad, T. F. 2000. Elements of a theory for the mechanism controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol. Oceanogr. 45:1320-1328.
44. Wang, K., and F. Chen. 2004. Genetic diversity and population dynamics of cyanophage communities in the Chesapeake Bay. Aquat. Microbiol. 34:105-116.
45. Waterbury, J. B., and F. W. Valois. 1993. Resistance to co-occurring phages enables marine Synechococcus communities to coexist with cyanophages abundant in seawater. Appl. Environ. Microbiol. 59:3393-3399.
46. Weinbauer, M. G. 2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28:127-181.
47. Weinbauer, M. G., and F. Rassoulzadegan. 2004. Are viruses driving microbial diversification and diversity? Environ. Microbiol. 6:1-11. (Pubitemid 38162022)
48. Williamson, S. J., D. B. Rusch, S. Yooseph, A. L. Halpern, K. B. Heidelberg, J. I. Glass, C. Andrews-Pfannkoch, D. Fadrosh, C. S. Miller, G. Sutton, M. Frazier, and J. C. Venter. 2008. The Sorcerer II Global Ocean Sampling expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS ONE 3:e1456.
49. Wilson, W. H., N. J. Fuller, I. R. Joint, and N. H. Mann. 1999. Analysis of cyanophage diversity and population structure in a south-north transect of the Atlantic Ocean. Bull. Inst. Oceanogr. 19:209-216.
50. Wommack, K. E., and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69-114.
51. Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier, and J. C. Venter. 2007. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 5:e16. (Pubitemid 46422965)