Chapter 36 : Viral Community Structure

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Viral Community Structure, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815882/9781555813796_Chap36-1.gif /docserver/preview/fulltext/10.1128/9781555815882/9781555813796_Chap36-2.gif


This chapter brings together methods that can be used to count and examine the genetic diversity of communities and populations of aquatic viral communities, although many of the methods can be adapted for other environments. The first studies on viral abundance in aquatic systems used transmission electron microscopy (TEM) to count virus-like particles (VLPs). Interestingly, although TEM images of natural communities suggest that viruses with small noncontractile tails are most abundant, the most frequently isolated viruses are tailed sipho-and myoviruses. This discrepancy may be due to the method of sample preparation used in many TEM studies of natural virus communities or due to the fact that viral isolates are not representative of native viral communities. Breitbart et al. constructed a metagenomic library of two coastal DNA phage communities, using the linkeramplified shotgun library (LASL) method. In this study, 200 liters of seawater was prefiltered and concentrated by tangential flow filtration. Community approaches are useful for studies of the total abundance of viral particles or for documentation of the dominant morphotypes in viral communities. Viruses are an abundant, dynamic, and ecologically important component of aquatic ecosystems, and there is now strong evidence that they are the most genetically diverse biological entities on the planet. Targeting the viral DNA polymerase, this research revealed a vast amount of genetic variation that was not represented in cultures and showed that very similar sequences were distributed on a global scale.

Citation: Culley A, Suttle C. 2007. Viral Community Structure, p 445-453. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch36
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Adams, M. H. 1959. Bacteriophages. John Wiley & Sons, New York, N.Y.
2. Angly, F.,, B. Rodriguez-Brito,, D. Bangor,, P. Mcnairnie,, M. Breitbart,, P. Salamon,, B. Felts,, J. Nulton,, J. Mahaffy, and, F. Rohwer. 2005. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 6: 41.
3. Bergh, O.,, K. Y. Børsheim,, G. Bratbak, and, M. Heldal. 1989. High abundance of viruses found in aquatic environments. Nature 340: 467468.
4. Bettarel, Y.,, C. Amblard,, T. Sime-Ngando,, J. F. Carrias,, D. Sargos,, F. Garabetian, and, P. Lavandier. 2003. Viral lysis, flagellate grazing potential, and bacterial production in Lake Pavin. Microb. Ecol. 45: 119127.
5. Bettarel, Y.,, T. Sime-Ngando,, C. Amblard, and, H. Laveran. 2000. A comparison of methods for counting viruses in aquatic systems. Appl. Environ. Microbiol. 66: 22832289.
6. Børsheim, K. Y. 1993. Native marine bacteriophages. FEMS Microbiol. Lett. 102: 141159.
7. Børsheim, K. Y.,, G. Bratbak, and, M. Heldal. 1990. Enumeration and biomass estimation of planktonic bacteria and viruses by transmission electron microscopy. Appl. Environ. Microbiol. 56: 352356.
8. Bratbak, G.,, J. K. Egge, and, M. Heldal. 1993. Viral mortality of the marine alga Emiliania huxleyi (Haptophyceae) and termination of algal blooms. Mar. Ecol. Prog. Ser. 93: 3948.
9. Bratbak, G.,, M. Heldal,, S. Norland, and, T. Thingstad. 1990. Viruses as partners in spring bloom microbial trophodynamics. Appl. Environ. Microbiol. 56: 14001405.
10. Breitbart, M.,, B. Felts,, S. Kelley,, J. M. Mahaffy,, J. Nulton,, P. Salamon, and, F. Rohwer. 2004. Diversity and population structure of a near-shore marine-sediment viral community. Proc. R. Soc. London B 271: 565574.
11. Breitbart, M.,, I. Hewson,, B. Felts,, J. M. Mahaffy,, J. Nulton,, P. Salamon, and, F. Rohwer. 2003. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185: 62206223.
12. Breitbart, M.,, J. H. Miyake, and, F. Rohwer. 2004. Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol. Lett. 236: 249256.
13. 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: 1425014255.
14. Brussaard, C. P. D. 2004. Optimization of procedures for counting viruses by flow cytometry. Appl. Environ. Microbiol. 70: 15061513.
15. Brussaard, C. P. D.,, D. Marie, and, G. Bratbak. 2000. Flow cytometric detection of viruses. J. Virol. Methods 85: 175182.
16. Brussaard, C. P. D.,, D. Marie,, R. Thyrhaug, and, G. Bratbak. 2001. Flow cytometric analysis of phytoplankton viability following viral infection. Aquat. Microb. Ecol. 26: 157166.
17. Cann, A. J.,, S. E. Fandrich, and, S. Heaphy. 2005. Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes 30: 151156.
18. Castberg, T.,, A. Larsen,, R. A. Sandaa,, C. P. D. Brussaard,, J. K. Egge,, M. Heldal,, R. Thyrhaug,, E. J. Van Hannen, and, G. Bratbak. 2001. Microbial population dynamics and diversity during a bloom of the marine coccolithophorid Emiliania huxleyi (Haptophyta). Mar. Ecol. Prog. Ser. 221: 3946.
19. Chen, F.,, J.-R. Lu,, B. J. Binder,, Y.-C. Liu, 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: 539545.
20. 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: 28692874.
21. Cochlan, W. P.,, J. Wikner,, G. F. Steward,, D. C. Smith, and, F. Azam. 1993. Spatial distribution of viruses, bacteria and chlorophyll a in neritic, oceanic and estuarine environments. Mar. Ecol. Prog. Ser. 92: 7787.
22. Comeau, A. M.,, S. Short, and, C. A. Suttle. 2004. The use of degenerate-primed random amplification of polymorphic DNA (Dp-Rapd) for strain-typing and inferring the genetic similarity among closely related viruses. J. Virol. Methods 118: 95100.
23. Cottrell, M. T.,, and 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: 19.
24. Cottrell, M. T.,, and C. A. Suttle. 1995. Dynamics of a lytic virus infecting the photosynthetic marine picoflagel-late, Micromonas pusilla. Limnol. Oceanogr. 40: 730739.
25. Culley, A. I.,, A. S. Lang, and, C. A. Suttle. 2003. High diversity of unknown picorna-like viruses in the sea. Nature 424: 10541057.
26. Culley, A. I.,, and N. A. Welschmeyer. 2002. The abundance, distribution, and correlation of viruses, phytoplankton, and prokaryotes along a Pacific Ocean transect. Limnol. Oceanogr. 47: 15081513.
27. Danovaro, R.,, and M. Serresi. 2000. Viral density and virus-to-bacterium ratio in deep-sea sediments of the eastern Mediterranean. Appl. Environ. Microbiol. 66: 18571861.
28. Drake, L. A.,, K. H. Choi,, A. G. E. Haskell, and, F. C. Dobbs. 1998. Vertical profiles of virus-like particles and bacteria in the water column and sediments of Chesapeake Bay, USA. Aquat. Microb. Ecol. 16: 1725.
29. Edwards, R. A.,, and F. Rohwer. 2005. Viral metagenomics. Nat. Rev. Microbiol. 3: 504510.
30. Ferrari, V. C.,, and J. T. Hollibaugh. 1999. Distribution of microbial assemblages in the central Arctic Ocean Basin studied by PCR/DGGE: analysis of a large data set. Hydrobiologia 401: 5568.
31. Frederickson, C. M.,, S. M. Short, and, C. A. Suttle. 2003. The physical environment affects cyanophage communities in British Columbia inlets. Microb. Ecol. 46: 348357.
32. 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: 20512060.
33. Gowing, M. M.,, B. E. Riggs,, D. L. Garrison,, A. H. Gibson, and, M. O. Jeffries. 2002. Large viruses in Ross Sea late autumn pack ice habitats. Mar. Ecol. Prog. Ser. 241: 111.
34. Hara, S.,, K. Terauchi, and, I. Koike. 1991. Abundance of viruses in marine waters: assessment by epifluorescence and transmission electron microscopy. Appl. Environ. Microbiol. 57: 27312734.
35. Heldal, M.,, and G. Bratbak. 1991. Production and decay of viruses in aquatic environments. Mar. Ecol. Prog. Ser. 72: 205212.
36. Hennes, K. P.,, and C. A. Suttle. 1995. Direct counts of viruses in natural waters and laboratory cultures by epifluorescence microscopy. Limnol. Oceanogr. 40: 10501055.
37. Hennes, K.,, and M. Simon. 1995. Significance of bacteriophages for controlling bacterioplankton growth in a mesotrophic lake. Appl. Environ. Microbiol. 61: 333340.
38. Hurley, M. A.,, and M. E. Roscoe. 1983. Automated statistical analysis of microbial enumeration by dilution series. J. Appl. Bacteriol. 55: 159164.
39. Jiang, S.,, W. Fu,, W. Chu, and, J. A. Fuhrman. 2003. The vertical distribution and diversity of marine bacteriophage at a station off Southern California. Microb. Ecol. 45: 399410.
40. Jiang, S.,, G. Steward,, R. Jellison,, W. Chu, and, S. Choi. 2004. Abundance, distribution, and diversity of viruses in alkaline, hypersaline Mono Lake, California. Microb. Ecol. 47: 917.
41. Kellogg, C. A.,, J. B. Rose,, S. C. Jiang,, J. Thurmond, and, J. H. Paul. 1995. Genetic diversity of related vibriophages isolated from marine environments around Florida and Hawaii, USA. Mar. Ecol. Prog. Ser. 120: 8998.
42. Klieve, A. V.,, and R. A. Swain. 1993. Estimation of ruminal bacteriophage numbers by pulsed-field gel electrophoresis and laser densitometry. Appl. Environ. Microbiol. 59: 22992303.
43. Lawrence, J. E.,, A. M. Chan, and, C. A. Suttle. 2002. Viruses causing lysis of the toxic bloom-forming alga, Heterosigma akashiwo (Raphidophyceae), are widespread in coastal sediments of British Columbia, Canada. Limnol. Oceanogr. 47: 545550.
44. Marie, D.,, C. P. D. Brussaard,, R. Thyrhaug,, G. Bratbak, and, D. Vaulot. 1999. Enumeration of marine viruses in culture and natural samples by flow cytometry. Appl. Environ. Microbiol. 65: 4552.
45. Moebus, K.,, and H. Nattkemper. 1983. Taxonomic investigations of bacteriophage sensitive bacteria isolated from marine waters. Helgol. Meeresunters. 36: 357373.
46. Nagasaki, K.,, Y. Tomaru,, K. Nakanishi,, N. Hata,, N. Katanozaka, and, M. Yamaguchi. 2004. Dynamics of Heterocapsa circularisquama (Dinophyceae) and its viruses in Ago Bay, Japan. Aquat. Microb. Ecol. 34: 219226.
47. Noble, R. T. 2001. Enumeration of viruses. Methods Microbiol. 30: 4350.
48. Noble, R. T.,, and J. A. Fuhrman. 1998. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol. 14: 113118.
49. Porter, K. G.,, and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25: 943948.
50. Proctor, L. M. 1997. Advances in the study of marine viruses. Microsc. Res. Technol. 37: 136161.
51. Proctor, L. M.,, and J. A. Fuhrman. 1990. Viral mortality of marine bacteria and cyanobacteria. Nature 343: 6062.
52. Rappe, M. S.,, and S. J. Giovannoni. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57: 369394.
53. Ricciardi-Rigault, M.,, D. F. Bird, and, Y. T. Prairie. 2000. Changes in sediment viral and bacterial abundances with hypolimnetic oxygen depletion in a shallow eutrophic Lac Brome (Quebec, Canada). Can. J. Fish. Aquat. Sci. 57: 12841290.
54. Riemann, L.,, and M. Middelboe. 2002. Stability of bacterial and viral community compositions in Danish coastal waters as depicted by DNA fingerprinting techniques. Aquat. Microb. Ecol. 27: 219232.
55. Schroeder, D. C.,, J. Oke,, M. Hall,, G. Malin, and, W. H. Wilson. 2003. Virus succession observed during an Emiliania huxleyi bloom. Appl. Environ. Microbiol. 69: 24842490.
56. 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: 480486.
57. Short, S. M.,, and C. A. Suttle. 2000. Denaturing gradient gel electrophoresis resolves virus sequences amplified with degenerate primers. BioTechniques 28: 2026.
58. 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: 12901296.
59. Short, S. M.,, and C. A. Suttle. 2003. Temporal dynamics of natural communities of marine algal viruses and eukaryotes. Aquat. Microb. Ecol. 32: 107119.
60. Steward, G. F. 2001. Fingerprinting viral assemblages by pulsed field gel electrophoresis (PFGE). Methods Microbiol. 30: 85103.
61. Steward, G. F.,, J. L. Montiel, and, F. Azam. 2000. Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments. Limnol. Oceanogr. 45: 16971706.
62. Sullivan, M. B.,, J. B. Waterbury, and, S. W. Chisholm. 2003. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 424: 10471051.
63. Suttle, C. A. 1993. Enumeration and isolation of viruses, p. 121–134. In P. F. Kemp,, B. F. Sherr,, E. B. Sherr, and, J. J. Cole (ed.), Handbook of Methods in Aquatic Microbial Ecology. Lewis Publishers, Boca Raton, Fla.
64. Suttle, C. A. 2005. Viruses in the sea. Nature 437: 356361.
65. Suttle, C. A.,, and A. M. Chan. 1994. Dynamics and distribution of cyanophages and their effect on marine Synechococcus spp. Appl. Environ. Microbiol. 60: 31673174.
66. Suttle, C. A.,, A. M. Chan, and, M. T. Cottrell. 1990. Infection of phytoplankton by viruses and reduction of primary productivity. Nature 347: 467469.
67. Suttle, C. A.,, and F. Chen. 1992. Mechanisms and rates of decay of marine viruses in seawater. Appl. Environ. Microbiol. 58: 37213729.
68. Tapper, M. A.,, and R. E. Hicks. 1998. Temperate viruses and lysogeny in Lake Superior bacterioplankton. Limnol. Oceanogr. 43: 95103.
69. Tomaru, Y.,, K. Tarutani,, M. Yamaguchi, and, K. Nagasaki. 2004. Quantitative and qualitative impacts of viral infection on a Heterosigma akashiwo (Raphidophyceae) bloom in Hiroshima Bay, Japan. Aquat. Microb. Ecol. 34: 227238.
70. Vanucci, S.,, V. Bruni, and, G. Pulicano. 2005. Spatial and temporal distribution of virioplankton and bacterio-plankton in a brackish environment (Lake of Ganzirri, Italy). Hydrobiologia 539: 8392.
71. Wang, K.,, and F. Chen. 2004. Genetic diversity and population dynamics of cyanophage communities in the Chesapeake Bay. Aquat. Microb. Ecol. 34: 105116.
72. 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: 33933399.
73. Weinbauer, M. G. 2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28: 127181.
74. Weinbauer, M. G.,, C. Beckmann, and, M. G. Hofle. 1998. Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria. Appl. Environ. Microbiol. 64: 50005003.
75. Weinbauer, M. G.,, and P. Peduzzi. 1994. Frequency, size and distribution of bacteriophages in different marine bacterial morphotypes. Mar. Ecol. Prog. Ser. 108: 1120.
76. Weinbauer, M. G.,, and C. A. Suttle. 1997. Comparison of epifluorescence and transmission electron microscopy for counting viruses in natural marine waters. Aquat. Microb. Ecol. 13: 225232.
77. Weinbauer, M. G.,, C. Winter, and, M. G. Hofle. 2002. Reconsidering transmission electron microscopy based estimates of viral infection of bacterio-plankton using conversion factors derived from natural communities. Aquat. Microb. Ecol. 27: 103110.
78. Wen, K.,, A. C. Ortmann, and, C. A. Suttle. 2004. Accurate estimation of viral abundance by epifluorescence microscopy. Appl. Environ. Microbiol. 70: 38623867.
79. Wilhelm, S. W.,, and L. Poorvin. 2001. Quantification of algal viruses in marine samples. Methods Microbiol. 30: 5365.
80. Wilhelm, S. W.,, M. G. Weinbauer,, C. A. Suttle,, R. J. Pledger, and, D. L. Mitchell. 1998. Measurements of DNA damage and photoreactivation imply that most viruses in marine surface waters are infective. Aquat. Microb. Ecol. 14: 215222.
81. Wommack, K. E.,, and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64: 69114.
82. Wommack, K. E.,, R. T. Hill,, M. Kessel,, C. E. Russek, and, R. R. Colwell. 1992. Distribution of viruses in the Chesapeake Bay. Appl. Environ. Microbiol. 58: 29652970.
83. Wommack, K. E.,, J. Ravel,, R. T. Hill,, J. Chun, and, R. R. Colwell. 1999. Population dynamics of Chesapeake Bay virioplankton: total community analysis using pulsed-field gel electrophoresis. Appl. Environ. Microbiol. 65: 231240.
84. Wommack, K. E.,, J. Ravel,, R. T. Hill, and, R. R. Colwell. 1999. Hybridization analysis of Chesapeake Bay virioplankton. Appl. Environ. Microbiol. 65: 241250.
85. Xenopoulos, M. A.,, and D. F. Bird. 1997. Virus a la sauce Yo-Pro: microwave-enhanced staining for counting viruses by epifluorescence microscopy. Limnol. Oceanogr. 42: 16481650.
86. Zhong, Y.,, F. Chen,, S. W. Wilhelm,, L. Poorvin, and, R. E. Hodson. 2002. Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene G20. Appl. Environ. Microbiol. 68: 15761584.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error