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Isolation Independent Methods of Characterizing Phage Communities 1: Strain Typing Using Fingerprinting Methods

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Bacteriophages

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 502))

Abstract

Since most of the phage genomes isolated from natural samples are previously unknown sequences, an isolation-independent approach is necessary to quantify the diversity of natural viral communities. Currently, two different methodological approaches are widely used to obtain genetic fingerprints of natural phage communities. While the separation of different viral genomes with pulsed field gel electrophoresis (PFGE) is based on the size of the genome, denaturing gradient gel electrophoresis (DGGE) uses minor differences in gene base composition to separate fragments of amplified DNA from natural viral communities. Finger printing techniques are a relatively fast and cheap tool to assess the diversity of environmental viruses. Together, PFGE and DGGE provide useful tools to study viral ecology in natural habitats.

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References

  1. Suttle, C.A., Viruses in the sea. 2005. Nature, 437(7057): 356–361.

    Article  CAS  PubMed  Google Scholar 

  2. Bergh, Ø., et al., High abundance of viruses found in aquatic environments. Nature, 1989. 340: 467–468.

    Article  CAS  PubMed  Google Scholar 

  3. Proctor, L. and J. Fuhrman, Viral mortality of marine bacteria and cyanobacteria. Nature, 1990. 343: 60–62.

    Article  Google Scholar 

  4. Williamson, K.E., M. Radosevich, and K.E. Wommack, Abundance and diversity of viruses in six delaware soils. Applied Environmental Microbiology, 2005. 71(6): 3119–3125.

    Article  CAS  Google Scholar 

  5. Wommack, K.E., et al., Population dynamics of chesapeake bay virioplankton: total-community analysis by pulsed-field gel electrophoresis. Applied Environmental Microbiology, 1999. 65(1): 231–240.

    CAS  Google Scholar 

  6. Cochlan, W.P., et al., Spatial-distribution of viruses, bacteria and chlorophyll-a in neritic, oceanic and estuarine environments. Marine Ecology-Progress Series, 1993. 92(1–2): 77–87.

    Article  Google Scholar 

  7. Suttle, C.A., Cyanophages and their role in the ecology of cyanobacteria, in The Ecology of Cyanobacteria, B. Whitton and M. Potts, Editors. 2000, Kluwer Academic Publishers. 563–589.

    Google Scholar 

  8. Suttle, C., The significance of viruses to mortality in aquatic microbial communities. Microbial Ecology, 1994. 28: 237–243.

    Article  Google Scholar 

  9. Wilhelm, S.W. and C.A. Suttle, Viruses and Nutrient Cycles in the Sea. Bioscience, 1999. 49(10): 781–788.

    Article  Google Scholar 

  10. Middelboe, M., N. Jorgensen, and N. Kroer, Effects of viruses on nutrient turnover and growth efficiency of noninfected marine bacterioplankton. Applied Environmental Microbiology, 1996. 62(6): 1991–1997.

    CAS  Google Scholar 

  11. Gobler, C.J., et al., Release and bioavailability of C, N, P, Se, and Fe following viral lysis of a marine chrysophyte. Limnology and Oceanography., 1997. 42: 1492–1504.

    Article  CAS  Google Scholar 

  12. Middelboe, M. and p.G. Lyck, Regeneration of dissolved organic matter by viral lysis in marine microbial communities. Aquatic Microbial Ecology, 2002. 27(2): 187–194.

    Article  Google Scholar 

  13. Fuhrman, J., Marine vitruses and their biogeochemical and ecological effects. Nature, 1999. 399: 541–548.

    Article  CAS  PubMed  Google Scholar 

  14. Moebus, K., Further investigations on the concentration of marine bacteriophages in the water around helgoland, with reference to the phage-host systems encountered. Helgolander Meeresuntersuchungen, 1992. 46(3): 275–292.

    Article  Google Scholar 

  15. Sullivan, M.B., J.B. Waterbury, and S.W. Chisholm, Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature, 2003. 424(6952): 1047–1051.

    Article  CAS  PubMed  Google Scholar 

  16. Nagasaki, K., et al., Virus-like particles in Heterosigma akashiwo (Raphidophyceae): a possible red tide disintegration mechanism. Marine Biology, 1994. 119: 307–312.

    Article  Google Scholar 

  17. Tarutani, K., K. Nagasaki, and M. Yamaguchi, Viral impacts on total abundance and clonal composition of the harmful bloom-forming phytoplankton Heterosigma akashiwo. Applied and Environmental Microbiology, 2000. 66(11): 4916–4920.

    Article  CAS  PubMed  Google Scholar 

  18. Sahlsten, E., Seasonal abundance in Skagerrak-Kattegat coastal waters and host specificity of viruses infecting the marine photosynthetic flagellate Micromonas pusilla. Aquatic Microbial Ecology, 1998. 16(2): 103–108.

    Article  Google Scholar 

  19. Breitbart, M., et al., Genomic analysis of uncultured marine viral communities. Proceeding of the Natural Acadamy of Sciences, 2002. 99(22): 14250–14255.

    Article  CAS  Google Scholar 

  20. Steward, G.F., J.L. Montiel, and F. Azam, Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments. Limnology and Oceanography, 2000. 45(8): 1697–1706.

    Article  Google Scholar 

  21. Steward, G.F., Fingerprinting viral assemblages by pulsed field gel electrophoresis (PFGE). In Methods in Microbiology, ed. J.H. Paul, Vol. 30, p. 666, 2001, San Diego: Academic Press.

    Google Scholar 

  22. Myers, R., T. Maniatis, and L. Lerman, Detecting and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol, 1987(155): 501–527.

    Article  CAS  PubMed  Google Scholar 

  23. Frederickson, C.M., S.M. Short, and C.A. Suttle, The physical environment affects cyanophage communities in british columbia inlets. Microbial Ecology, 2003. 46(3): 348–357.

    Article  CAS  PubMed  Google Scholar 

  24. Short, S.M. and C.A. Suttle, Use of the polymerase chain reaction and denaturing gel electrophoresis to study diversity in natural virus communities. Hydrobiologia, 1999. 00: 1–15.

    Google Scholar 

  25. Wommack, K.E. and R.R. Colwell, Virioplankton: Viruses in Aquatic Ecosystems. Microbiology and Molecular Biology Reviews, 2000. 64(1): 69–114.

    Article  CAS  PubMed  Google Scholar 

  26. Short, C.M. and C.A. Suttle, Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Applied Environmental Microbiology, 2005. 71(1): 480–486.

    Article  CAS  Google Scholar 

  27. Zhong, Y., et al., Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20. Applied Environmental Microbiology, 2002. 68(4): 1576–1584.

    Article  CAS  Google Scholar 

  28. Suttle, C., A. Chan, and M. Cottrell, Use of ultrafiltration to isolate viruses from seawater which are pathogens to marine phytoplankton. Applied Environmental Microbiology, 1991. 57: 721–726.

    CAS  Google Scholar 

  29. Short, S.M. and C.A. Suttle, Sequence analysis of marine virus communities reveals that groups of related algal viruses are widely distributed in nature. Applied Environmental Microbiology, 2002. 68(3): 1290–1296.

    Article  CAS  Google Scholar 

  30. Hennes, K., C. Suttle, and A. Chan, Fluorescently labeled virus probes show that natural virus populations can control the structure of marine microbial communities. Applied Environmental Microbiology, 1995. 61(10): 3623–3627.

    CAS  Google Scholar 

  31. Noble, R.T. and J.A. Fuhrman, Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquatic Microbial Ecology, 1998. 14(2): 113–118.

    Article  Google Scholar 

  32. Wen, K., A.C. Ortmann, and C.A. Suttle, Accurate estimation of viral abundance by epifluorescence microscopy. Applied Environmental Microbiology, 2004. 70(7): 3862–3867.

    Article  CAS  Google Scholar 

  33. Williamson, K.E., K.E. Wommack, and M. Radosevich, Sampling natural viral communities from soil for culture-independent analyses. applied environmental microbiology, 2003. 69(11): 6628–6633.

    Article  CAS  Google Scholar 

  34. Chen, F. and C. Suttle, Amplification of DNA polymerase gene fragments from viruses infecting microalgae. Applied Environmental Microbiology, 1995. 61(4): 1274–1278.

    CAS  Google Scholar 

  35. Chen, F., C. Suttle, and S. Short, Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes. Applied Environmental Microbiology, 1996. 62(8): 2869–2874.

    CAS  Google Scholar 

  36. Birren, B. and E. Lai, Pulsed field electrophoresis: A practical guide. 1993, San Diego: Academic Press.

    Google Scholar 

  37. BioRad, DCodeTm Universal Mutation Detection System instruction manual. 1996, Hercules, Ca: BioRad.

    Google Scholar 

  38. Fuller, N.J., et al., Occurrence of a sequence in marine cyanophages similar to that of t4 g20 and its application to PCR-based detection and quantification techniques. Applied Environmental Microbiology, 1998. 64(6): 2051–2060.

    CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Earth & Ocean Sciences, University of British Columbia, Vancouver, BC, Canada

    Clemens Pausz, Jessica L. Clasen & Curtis A. Suttle

Authors
  1. Clemens Pausz
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  2. Jessica L. Clasen
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  3. Curtis A. Suttle
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Editor information

Editors and Affiliations

  1. University of Leicester, Leicester, UK

    Martha R.J. Clokie

  2. Public Health Agency of Canada, Guelph, Ontario, Canada

    Andrew M. Kropinski

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Pausz, C., Clasen, J.L., Suttle, C.A. (2009). Isolation Independent Methods of Characterizing Phage Communities 1: Strain Typing Using Fingerprinting Methods. In: Clokie, M.R., Kropinski, A.M. (eds) Bacteriophages. Methods in Molecular Biology™, vol 502. Humana Press. https://doi.org/10.1007/978-1-60327-565-1_15

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  • DOI: https://doi.org/10.1007/978-1-60327-565-1_15

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-564-4

  • Online ISBN: 978-1-60327-565-1

  • eBook Packages: Springer Protocols

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