Use of the polymerase chain reaction and denaturing gradient gel electrophoresis to study diversity in natural virus communities

Hydrobiologia

Volumn 401, Issue , 1999, Pages 19-33

  Short, S M ^a   Suttle, C A ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

DGGE; Diversity; PCR; Phytoplankton; Polymerase; Viruses

Indexed keywords

DENATURING GRADIENT GEL ELECTROPHORESIS; DNA POLYMERASE; MICROBIAL POPULATION DYNAMICS; POLYMERASE CHAIN REACTION; VIRUS DETECTION;

COMMUNITY STRUCTURE; ELECTROKINESIS; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY; VIRUS;

ALGAE;

EID: 0033133475     PISSN: 00188158     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1003711115967     Document Type: Article

References (76)

1. Argos, P., A. D. Tucker, L. Philipson (1986). Primary structural relationships may reflect similar DNA replication strategies. Virology 149: 208-216.
2. Argos, P. (1988). A sequence motif in many polymerases. Nucl. Acids Res. 16(21): 9909-9916.
3. Bej, A. K., R. J. Steffan, J. DiCesare, L. Haff, R. M. Atlas (1990). Detection of coliform bacteria in water by polymerase chain reaction and gene probes. Appl. envir. Microbiol. 56: 307-314.
4. Bergh, O., K. Y. Børsheim, G. Bratbak, M. Heldal (1989). High abundance of viruses found in aquatic environments. Nature 340: 467-468.
5. Børsheim, K. Y., G. Bratbak, M. Heldal (1990). Enumeration and biomass estimation of planktonic bacteria and viruses by transmission electron microscopy. Appl. envir. Microbiol. 56(2): 352-356.
6. Braithwaite, D. K., J. Ito (1993). Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucl. Acids Res. 21(4): 787-802.
7. Bratbak, G., F. Thingstad, M. Heldal (1994). Viruses and the microbial loop. Microb. Ecol. 28: 209-221.
8. Brown R. M., Jr. (1972). Algal viruses. Advances in Virus Res. 17: 243-277.
9. Calisher, C. H., M. C. Horzinek, M. A. Mayo, H. -W. Ackermann, J. Maniloff. (1995). Sequence analyses and a unifying system of viral taxonomy: consensus via consent. Arch. Virol. 140: 2093-2099.
10. Chen, F., C. A. Suttle (1995a). Nested PCR with three highly degenerate primers for amplification and identification of DNA from related organisms. BioTechniques 18: 609-612.
11. Chen, F., C. A. Suttle (1995b). Amplification of DNA polymerase gene fragments from viruses infecting microalgae. Appl. envir. Microbiol 61: 1274-1278.
12. Chen, F., 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.
13. Chen, F., C. A. Suttle, S. M. Short (1996). Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes. Appl. envir. Microbiol. 62(8): 2869-2874.
14. Chiura, H. X. (1997). Generalized gene transfer by virus-like particles from marine bacteria. Aquat. microb. Ecol. 13: 75-83.
15. Cottrell, M. T., C. A. Suttle (1991). Wide-spread occurrence and clonal variation in viruses which cause lysis of a cosmopolitan, eukaryotic marine phytoplankter, Micromonas pusilla. Mar. Ecol. Prog. Ser. 78: 1-9.
16. Cottrell, M. T., C. A. Suttle (1995a). Dynamics of a lytic virus infecting the marine picoflagellate Micromonas pusilla. Limnol. Oceanogr. 40(4): 730-739.
17. Cottrell, M. T., C. A. Suttle (1995b). Genetic diversity of algal viruses which lyse the photosynthetic picoflagellate Micromonas pusilla (Prasinophyceae). Appl. envir. Mirobiol. 61(8): 3088-3091.
18. Damagnez, V., J. Tillit, A-M. de Recondo, G. Baldacci (1991). The POLI gene from fission yeast, Schizosaccharomyces pombe, shows conserved amino acid blocks specific for eukaryotic DNA polymerases alpha. Mol. Gen. Genet. 226: 182-189.
19. Field, K. G., D. Gordon, T. Wright, m Rappé, E. Urbach, K. Vergin, S. J. Giovannoni (1997). Diversity and Depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl. envir. Microbiol. 63(1): 63-70.
20. Ferris, M. J., G. Muyzer, D. M. Ward (1996). Denaturing gradient gel electrophoresis profiles of 15S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. envir. Microbiol. 62: 340-346.
21. Fuhrman, J. A., K. McCallum, A. A. Davis (1992). Novel major archaebacterial group from marine plankton. Nature 356: 148-149.
22. Fuhrman, J. A., C. A. Suttle (1993). Viruses in marine planktonic systems. Oceanography 6(2): 51-63.
23. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, K. G. Field (1990). Genetic diversity in Sargasso Sea bacterioplankton. Nature 345: 60-63.
24. Giovannoni, S., S. C. Cary (1993). Probing marine systems with ribosomal RNAs. Oceanography 6(3): 95-104.
25. Grabherr, R., P. Strasser, J. L. Van Etten (1992). The DNA polymerase gene from Chlorella viruses PBCV-1 and NY-2A contains and intron with nuclear splicing sequences. Virology 188: 721-731.
26. Heuer, H., M. Krsek, P. Baker, K. Smalla, E. M. H. Wellington (1997). Analysis of Actinomycete communities by specific amplification of genes encoding 16s rRNA and gel-electrophoretic separation in denaturing gradients. Appl. envir. Microbiol. 63(8): 3233-3241.
27. Illana, B., L. Blanco, M. Salas (1996). Functional characterization of the genes coding for the terminal protein and DNA polymerase from bacteriophage GA-1. Evidence for a sliding-back mechanism during protein-primed GA-1 DNA replication. J. mol. Biol. 264: 453-464.
28. Innis, M. A., D. H. Gefland, J. J. Sninsky, T. J. White (1990). PCR protocols: A Guide to Methods and Applications. Academic Press, Inc., San Diego. 482 pp.
29. Ito, J., D. K. Braithwaite (1990). Yeast mitochondrial DNA polymerase is related to the family A DNA polymerases. Nucl. Acids Res. 18(22): 6716.
30. Ito, J., D. K. Braithwaite (1991). Compilation and alignment of DNA polymerase sequences. Nucl. Acids. Res. 19(15): 4045-4057.
31. Iwasaki, H., Y. Ishino, H. Toh, A. Nakata, H. Shinagawa (1991). Escherichia coli DNA polymerase II is homologous to a-like DNA polymerases. Mol. Gen. Genet. 226: 24-33.
32. Jacobsen, A., G. Bratbak, M. Heldal (1996). Isolation and characterization of a virus infecting Phaeocystis pouchetii (Prymnesiophyceae). J. Phycol. 23: 923-927.
33. Jiang, S. C., J. H. Paul (1994). Seasonal and diel abundance of viruses and the occurrence of lysogeny/bacteriocinogy in the marine environment. Mar. Ecol. Prog. Ser. 104: 163-172.
34. Joyce C. M., Steitz, T. A. (1994). Function and Structure Relationships in DNA Polymerases. Annu. Rev. Biochem. 63: 777-822.
35. Jung, G., M. C. Leavitt, J.-C., Hsieh, J. Ito (1987). Bacteriophage PRD1 DNA polymerase: Evolution of DNA polymerases. Proc. natl. Acad. Sci. 84: 8287-8291.
36. Kamer, G., Argos P. (1984). Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucl. Acids Res. 12(18): 7269-7282.
37. Kopecka, H. S., S. Dubrou, J. Prevut, J. Marechal, J. M. Lopez-Pila (1993). Detection of naturally occurring enteroviruses in waters by reverse transcription, polymerase chain reaction, and hybridization. Appl. envir. Microbiol. 59: 1213-1219.
38. Liesack, W., H. Weyland, E. Stackebrandt (1991). Potential risks of gene amplification by PCR as determined by 16s rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21: 191-198.
39. Mayer, J. A., F. J. R. Taylor (1979). A virus which lyses the marine nanoflagellate Micromonas pusilla. Nature 281: 299-301.
40. Meyer, G., C. Vlcek, V. Paces, M. K. O'Hara, P.-P. Pastoret, E. Thiry, M. Schwyzer (1997). Sequence analysis of the bovine herpesvirus type 1 genes homologous to the DNA polymerase (UL30), the major DNA-binding protein (UL29) and ICP18.5 assembly protein (UL28) genes of herpes simplex virus. Arch Virol 142: 89-102.
41. Milligan, K. L., E. M. Cosper (1994). Isolation of virus capable of lysing the brown tide microalga, Aureococcus anaphagefferens. Science 266: 805-807.
42. Mullis, K. B., Faloona, F. A. (1987). Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 155: 335-351.
43. Muyzer, G., E. C. De Waal, 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. envir. Microbiol. 59: 695-700.
44. Myers, R. M., T. Maniatis, L. S. Lerman (1987). Detection and localization of single base changes by denaturing gradient gel electrophoresis. Meth. Enzymol. 155: 501-527.
45. Nagasaki, K., M. Yamaguchi (1997). Isolation of a virus infectious to the harmful bloom forming alga Heterosigma akashiwo (Raphidophyceae). Aquat. microb. Ecol. 13: 135-140.
46. Nübel, U., F. Garcia-Pichel, G. Muyzer (1997). PCR primers to amplify 16s rRNA genes from cyanobacteria. Appl. envir. Microbiol. 63(8): 3327-3332.
47. Ohki, K., Y. Fujita (1996). Occurrence of a temperate cyanophage lysogenizing the marine cyanophyte Phormidium persicinium. J. Phycol. 32: 365-370.
48. Paul, J. H., S. C. Jiang, J. B. Rose (1991). Concentration of viruses and dissolved DNA from aquatic environments by vortex flow filtration. Appl. envir. Microb. 57: 2197-2204.
49. Pizzagalli, A., P. Valsasnini, P. Plevani, G. Lucchini (1988). DNA polymerase I gene of Saccharomyces cerevisiae: Nucleotide sequence, mapping of a temperature-sensitive mutation, and protein homology with other DNA polymerases. Proc. natl. Acad. Sci. 85: 3772-3776.
50. Proctor, L. M., J. A. Fuhrman (1990). Viral mortality of marine bacteria and cyanobacteria. Nature 343: 60-62.
51. Reysenbach, A.-L., L. J. Giver, G. S. Wickham, N. R. Pace (1992). Differential amplification of rRNA genes by polymerase chain reaction. Appl. envir. Microbiol. 58(10): 3417-3418.
52. Ridley, R. G., J. H. White, S. M. McAleese, M. Goman, P. Alano, E. de Vries, B. J. Kilbey (1991). DNA polymerase δ: gene sequences from Plasmodium falciparum indicate that this enzyme is more highly conserved that DNA polymerase α. Nucl. Acids Res. 19(24): 6731-6736.
53. Rohozinski, J., J. L. Van Etten (1989). Characterization of DNA polymerases in an uninfected and viras PBCV-1 infected green algae - Chlorella strain NC64A. Intervirology 30: 156-162.
54. Rölleke, S., G. Muyzer, C. Wawer, G. Wanner, W. Lubitz (1996). Identification of bacteria in abiodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16s rRNA. Appl. envir. Microbiol. 62(6): 2059-2065.
55. Sambrook, J., E. F. Fritsch, T. Maniatis (1989). Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbour Laboratory Press, Cold Spring Harbour, N. Y.
56. Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. G. Higuchi, T. T. Horn, K. B. Mullis, H. A. Erlich (1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.
57. Santegoeds, C. M., S. C. Nold, D. M. Ward (1996). Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat. Appl. envir. Microbiol. 62: 3922-3928.
58. Sheffield, V. C., D. R. Cox, L. S. Lerman, R. M. Meyers (1989). Attachment of a 40-base-pair G +C rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. natl. Acad. Sci 86: 232-236.
59. Sheffield, V. C., J. S. Beck, E. M. Stone. (1992). A simple efficient method for attachment of a 40-base pair, GC-rich sequence to PCR-amplified DNA. BioTechmques 12(3): 386-387.
60. Scholin, C. A., D. M. Anderson (1994). Identification of group- and strain-specific genetic markers for globally distributed Alexandrium (Dinophyceae). I. RFLP analysis of SSU rRNA genes. J. Phycol. 30: 744-754.
61. Steffan, R. J., R. M. Atlas (1991). Polymerase chain reaction: applications in environmental microbiology. Annu. Rev. Microbiol. 45: 137-161.
62. Suttle, C. A., A. M. Chan, M. T. Cottrell (1990). Infection of phytoplankton by viruses and reduction of primary productivity. Nature 347: 467-469.
63. Suttle, C. A. (1992). Inhibition of photosynthesis in phytoplankton by the submicron size fraction concentrated from seawater. Mar. Ecol. Prog. Ser. 87: 105-112.
64. Suttle, C. A. (1994). The significance of viruses to mortality in aquatic microbial communities. Microb. Ecol. 28: 237-243.
65. Suttle, C. A., A. M. Chan (1995). Viruses infecting the marine Prymnesiophyte Chyrsochromulina spp.: isolation, preliminary characterization and natural abundance. Mar. Ecol. Prog. Ser. 118: 275-282.
66. Suzuki, M. T., M. S. Rappé, Z. W. Haimberger, H. Winfield, N. Adair, J. Ströbel, S. J. Giovannoni (1997). Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl. envir. Microbiol. 63(3): 983-989.
67. Thingstad, T.F., M. Heldal, G. Bratback, I. Dundas (1993). Are viruses important partners in pelagic food webs? Trends ecol. Evol. 8(6): 209-213.
68. Torella, F., R. Y. Morita (1979). Evidence by electron micrographs for a high incidence of bacteriophage particles in the waters of Yaquina Bay, Oregon: ecological and taxonomic implications. Appl. envir. Microbiol. 37: 774-778.
69. Van Etten, J. L., L. C. Lane, R. H. Meints (1991). Viruses and virus like particles of eukaryotic algae. Microbiol. Rev. 55: 586-620.
70. Wang, S.-F. (1991). Eukaryotic DNA Polymerases. Annu. Rev. Biochem. 60: 513-552.
71. Waterbury, J. B., F. W. Valois (1993). Resistance to co-occurring phages enables marine Synechococcus communities to coexist with cyanophages abundant in seawater. Appl. envir. Microbiol. 59(10): 3393-3399.
72. Weinbauer, M. G., D. Fuks, P. Peduzzi (1993). Distribution of viruses and dissolved DNA along a coastal trophic gradient in the northern Adriatic Sea. Appl. envir. Microbiol. 59: 4074-4082.
73. Wiggins, B. A., M. Alexander (1985). Minimum bacterial density for bacteriophage replication: implications for significance of bacteriophages in natural ecosystems. Appl. envir. Microbiol. 49(1): 19-23.
74. Wong, S. W., A. F. Wahl, P-M. Yuan, N. Arai, B. E. Pearson, K. Arai, D. Korn, M. W. Hunkapiller, T. S. F. Wang (1988). Human DNA polymerase a gene expression is cell proliferation dependent and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases. EMBO 7(1): 37-47.
75. Wright, T. D., K. L. Vergin, P. W. Boyd, S. J. Giovannoni (1997). A novel δ-subdivision proteobacterial lineage from the lower ocean surface layer. Appl. envir. Microbiol. 63(4): 1441-1448.
76. Zhang, Y. P., C. A. Suttle (1994). Design and use of PCR primers for B-family DNA polymerase genes to detect and identify viruses and microbes (abstract), p. a-85. ASLO/PSA Joint Meeting, Florida, June 12-16, 1994.