Induction of multiple prophages from a marine bacterium: A genomic approach

Applied and Environmental Microbiology

Volumn 72, Issue 7, 2006, Pages 4995-5001

  Chene, Feng ^a   Wang, Kui ^a   Stewart, Jeneen ^b   Belas, Robert ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b Brogden Middle School   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLIFICATION; BACTERIA; BIOASSAY; DNA; ELECTROPHORESIS; GENES; MICROBIOLOGY; TRANSMISSION ELECTRON MICROSCOPY;

BACTERIAL GENOMES; MARINE BACTERIUM; MULTIPLE PROPHAGES; VIRAL PARTICLES;

MARINE BIOLOGY;

DNA; MITOMYCIN C;

BACTERIUM; GENETIC ANALYSIS; GENOME;

ARTICLE; BACTERIAL COUNT; BACTERIOPHAGE; BACTERIOPLANKTON; CELL LYSATE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE SEQUENCE; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROPHAGE; PULSED FIELD GEL ELECTROPHORESIS; SILICIBACTER; TRANSMISSION ELECTRON MICROSCOPY; VIRUS PARTICLE;

BACTERIOPHAGES; DNA, VIRAL; GENOME, BACTERIAL; GENOME, VIRAL; MICROSCOPY, ELECTRON, TRANSMISSION; MITOMYCIN; POLYMERASE CHAIN REACTION; PROPHAGES; RHODOBACTERACEAE; SEAWATER; SIPHOVIRIDAE; VIRION; VIRUS ACTIVATION;

BACTERIA (MICROORGANISMS); SILICIBACTER;

EID: 33746039308     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00056-06     Document Type: Article

References (41)

1. Ackermann, H. W., and M. S. DuBow. 1987. Viruses of prokaryotes: general properties of bacteriophages. CRC Press, Inc., Boca Raton, Fla.
2. Arber, W., L. Enquist, B. Hohn, N. E. Murray, and K. Murray. 1983. Experimental methods for use with lambda, p. 433-466. In R. W. Hendrix, J. W. Roberts, F. W. Stahl, and R. A. Weisberg (ed.), Lambda II. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
3. Bergh, O., K. Y. Borsheim, G. Bratbak, and M. Heldal. 1989. High abundance of viruses found in aquatic environments. Nature 340:467-468.
4. Bordenstein, S. R., and W. S. Reznikoff. 2005. Mobile DNA in obligate intracellular bacteria. Nat. Rev. Microbiol. 3:688-698.
5. Brussow, H., C. Canchaya, and W. D. Hardt. 2004. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68:560-602.
6. Buchan, A., J. M. González, and M. A. Moran. 2005. An overview of the marine Roseobacter lineage. Appl. Environ. Microbiol. 71:5665-5677.
7. Canchaya, C., C. Proux, G. Fournous, A. Bruttin, and H. Brussow. 2003. Prophage genomics. Microbiol. Mol. Biol. Rev. 67:238-276.
8. Casjens, S. 2003. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49:277-300.
9. Chen, F., J. R. Lu, B. Binder, and R. E. Hodson. 2001. Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR gold. Appl. Environ. Microbiol. 67:539-545.
10. Chibani-Chennoufi, S., A. Bruttin, M. L. Dillmann, and H. Brussow. 2004. Phage-host interaction: an ecological perspective. J. Bacteriol 186:3677-3686.
11. Cochran, P. K., C. A. Kellog, and J. H. Paul. 1998. Prophage induction of indigenous marine lysogenic bacteria by environmental pollutants. Mar. Ecol. Prog. Ser. 164:125.
12. Cochran, P. K., and J. H. Paul. 1998. Seasonal abundance of lysogenic bacteria in a subtropical estuary. Appl. Environ. Microbiol. 64:2308-2312.
13. Frost, L. S., R. Leplae, A. O. Summers, and A. Toussaint. 2005. Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 3:722-732.
14. Giovannoni, S. J., and M. S. Rappé. 2000. Evolution, diversity and molecular ecology of marine prokaryotes, p. 47-84. In D. L. Kirchman (ed.), Microbial ecology of the oceans. Wiley and Sons, New York, N.Y.
15. González, J. M., and M. A. Moran. 1997. Numerical dominance of a group of marine bacteria in the α-subclass of proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63:4237-4242.
16. González, J. M., R. Simó, R. Massana, J. S. Covert, E. O. Casamayor, C. Pedrós-Alió, and M. A. Moran. 2000. Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl. Environ. Microbiol. 66:4237-4246.
17. Gottesman, M. E., and R. A. Weisberg. 1971. Prophage insertion and excision, p. 113-138. In A. D. Hershey (ed.), The bacteriophage lambda. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
18. Hershey, A. D., and W. Dove. 1983. Introduction to lambda, p. 3-20. In R. W. Hendrix, J. W. Roberts, F. W. Stahl, and R. A. Weisberg (ed.), Lambda II. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
19. Jiang, S. C., C. A. Kellogg, and J. H. Paul. 1998. Characterization of marine temperate phage-host systems isolated from Mamala Bay, Oahu, Hawaii. Appl. Environ. Microbiol. 64:535-542.
20. Jiang, S. C., and J. H. Paul. 1996. Occurrence of lysogenic bacteria in marine microbial communities as determined by prophage induction. Mar. Ecol. Prog. Ser. 142:27-38.
21. Jiang, S. C., and J. H. Paul. 1994. Seasonal and diel abundance of viruses and occurrence of lysogeny/bacteriocinogeny in the marine environment. Mar. Ecol. Prog. Ser. 104:163-172.
22. Jiang, S. C., and J. H. Paul. 1998. Significance of lysogeny in the marine environment: studies with isolates and a model of lysogenic phage production. Microb. Ecol. 35:235-243.
23. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
24. McDaniel, L., L. A. Houchin, S. J. Williamson, and J. H. Paul. 2002. Lysogeny in marine Synechococcus. Nature 415:496.
25. McDaniel, L., and J. H. Paul. 2005. Effect of nutrient addition and environmental factors on prophage induction in natural populations of marine Synechococcus species. Appl. Environ. Microbiol. 71:842-850.
26. Miller, T. R., and R. Belas. 2004. Dimethylsulfoniopropionate metabolism by Pfiesteria-associated Roseobacter spp. Appl. Environ. Microbiol. 70:3383-3391.
27. Moebus, K. 1983. Lytic and inhibition responses to bacteriophages among marine bacteria, with special reference to the origin of phage-host systems. Helgoländer Meeresuntersuch. 36:375-391.
28. Moran, M. A., A. Buchan, J. M. González, J. F. Heidelberg, W. B. Whitman, R. P. Kiene, J. R. Henriksen, G. M. King, R. Belas, C. Fuqua, L. Brinkac, M. Lewis, S. Johri, B. Weaver, G. Pai, J. A. Eisen, E. Rahe, W. M. Sheldon, W. Ye, T. R. Miller, J. Carlton, D. A. Rasko, I. T. Paulsen, Q. Ren, S. C. Daugherty, R. T. Deboy, R. J. Dodson, A. S. Durkin, R. Madupu, W. C. Nelson, S. A. Sullivan, M. J. Rosovitz, D. H. Haft, J. Selengut, and N. Ward. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.
29. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
30. Ohnishi, M., K. Kurokawa, and T. Hayashi. 2001. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9:481-485.
31. Paul, J. H. 1982. Use of Hoechst dyes 33258 and 33342 for enumeration of attached and planktonic bacteria. Appl. Environ. Microbiol. 43:939-944.
32. Prigent, M., M. Leroy, F. Confalonieri, M. Dutertre, and M. S. DuBow. 2005. A diversity of bacteriophage forms and genomes can be isolated from the surface sands of the Sahara desert. Extremophiles 9:289-296.
33. Proctor, L. M., and J. A. Fuhrman. 1990. Viral mortality of marine bacteria and cyanobacteria. Nature 343:60-62.
34. Roberts, J. W., and R. Devoret. 1983. Lysogenic induction, p. 123-144. In R. W. Hendrix, J. W. Roberts, F. W. Stahl, and R. A. Weisberg (ed.), Lambda II. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
35. Suttle, C. A. 2005. Viruses in the sea. Nature 437:356-361.
36. Suttle, C. A., and F. Chen. 1992. Mechanisms and rates of decay of marine viruses in seawater. Appl. Environ. Microbiol. 58:3721-3729.
37. Suzuki, M. T., C. M. Preston, F. P. Chavez, and E. F. DeLong. 2001. Quantitative mapping of bacterioplankton populations in seawater: field tests across an upwelling plume in the Monterey Bay. Aquat. Microb. Ecol. 24:117-127.
38. Weinbauer, M. G., and F. Rassoulzadegan. 2004. Are viruses driving microbial diversification and diversity? Environ. Microbiol. 6:1-11.
39. Williamson, S. J., L. A. Houchin, L. McDaniel, and J. H. Paul. 2002. Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida. Appl. Environ. Microbiol. 68:4307-4314.
40. Wommack, K. E., and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69-114.
41. Wommack, K. E., J. Ravel, R. T. Hill, and R. R. Colwell. 1999. Population dynamics of Chesapeake Bay virioplankton: total community analysis using pulsed-field gel electrophoresis. Appl. Environ. Microbiol. 65:231-240.