Physical fractionation of aquatic viral assemblages

Limnology and Oceanography: Methods

Volumn 9, Issue APRIL, 2011, Pages 150-163

  Brum, Jennifer R ^a   Steward, Grieg F ^a  

^a UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79955416724     PISSN: 15415856     EISSN: 15415856     Source Type: Journal    
DOI: 10.4319/lom.2011.9.150     Document Type: Article

References (50)

1. Aasted, B., B. Avery, and A. Cohn. 1984. Serological analysis of different mink Aleutian disease virus strains. Arch. Virol. 80:11-22.
2. Barkley, M. B., and P. R. Desjardins. 1977. Simple, effective method for purifying the AS-1 cyanophage. Appl. Environ. Microbiol. 33:971-974.
3. Barton, R. J. 1977. An examination of permeation chromatography on columns of controlled pore glass for routine purification of plant viruses. J. Gen. Virol. 35:77-87.
4. Bell, L. C., A. M. Posner, and J. P. Quirk. 1972. Surface charge characteristics of hydroxyapatite and fluorapatite. Nature 239:515-517.
5. Bergeron, A., M. Belcaid, G. F. Steward, and G. Poisson. 2007. Divide and conquer: enriching environmental sequencing data. PLoS ONE 2:e830.
6. Bitton, G. 1975. Adsorption of viruses onto surfaces in soil and water. Water Res. 9:473-484.
7. Brum, J. R. 2005. Concentration, production, and turnover of viruses and dissolved DNA pools at Station ALOHA, North Pacific Subtropical Gyre. Aquat. Microb. Ecol. 41:103-113.
8. Brum, J. R.. 2009. Investigations into the ecology, morphology, and genetic diversity of viruses in saline environments. Ph. D. thesis, Univ. of Hawaii at Manoa.
9. Brum, J. R., G. F. Steward, S. C. Jiang, and R. Jellison. 2005. Spatial and temporal variability of prokaryotes, viruses, and viral infections of prokaryotes in an alkaline, hypersaline lake. Aquat. Microb. Ecol. 41:247-260.
10. Brussaard, C. P. D., J. P. Payet, C. Winter, and M. G. Weinbauer. 2010. Quantification of viruses by flow cytometry, p. 102-109. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of aquatic viral ecology. ASLO.
11. Colwell, R. K. 2009. EstimateS: Statistical estimation of species richness and shared species from samples, v. 8.2. .
12. Darling, T., J. Albert, P. Russell, D. M. Albert, and T. W. Reid. 1977. Rapid purification of an RNA tumor virus and proteins by high-performance steric exclusion chromatography on porous glass bead columns. J. Chromatogr. 131:383-390.
13. Dowd, S. E., S. D. Pillai, S. Wang, and M. Y. Corapcioglu. 1998. Delineating the specific influence of virus isoelectric point and size on virus adsorption and transport through sandy soils. Appl. Environ. Microbiol. 64:405-410.
14. Edwards, R. A., and F. Rohwer. 2005. Viral metagenomics. Nat. Rev. Microbiol. 3:504-510.
15. Feldman, S. P., J. Schlom, and S. Spiegelman. 1973. Further evidence for oncornaviruses in human milk: the production of cores. Proc. Nat. Acad. Sci. U.S.A. 70:1976-1980.
16. Fuhrman, J. A. 1999. Marine viruses and their biogeochemical and ecological effects. Nature 399:541-548.
17. Fuhrman, J. A., and M. Schwalbach. 2003. Viral influence on aquatic bacterial communities. Biol. Bull. 204:192-195.
18. Gschwender, H. H., W. Haller, and P. H. Hofschneider. 1969. Large-scale preparations of viruses by steric chromatography on columns of controlled pore glass Phi X 174, M13, M12, Q Beta, and T4 bacteriophages. Biochim. Biophys. Acta 190:460-469.
19. Fuhrman, J. A., M. Brummond, and F. Lehmann-Grube. 1975. Lymphocytic choriomeningitis virus I. Concentration and purification of the infectious virus. J. Virol. 15:1317-1322.
20. Haller, W. 1965. Chromatography on glass of controlled pore size. Nature 206:693-696.
21. 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.
22. Hewish, D. R., and D. D. Shukla. 1983. Purification of barley yellow dwarf virus by gel filtration on Sephacryl S-1000 Superfine. J. Virol. Methods 7:223-228.
23. Hiatt, C. W., A. Shelokov, E. J. Rosenthal, and J. M. Galimore. 1971. Treatment of controlled pore glass with poly(ethylene oxide) to prevent adsorption of rabies viruses. J. Chromatogr. 56:362-364.
24. Himmel, M. E., and P. G. Squire. 1988. Size exclusion parameters. In P. L. Dubin [ed.], Aqueous size exclusion chromatography. J. Chromatogr. Library. Elsevier.
25. 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. 47:9-17.
26. Krebs, C. J. 1999. Ecological methodology, 2nd ed. Addison-Welsey Educational Publishers.
27. Larsen, A., and others. 2001. Population dynamics and diversity of phytoplankton, bacteria and viruses in a seawater enclosure. Mar. Ecol. Prog. Ser. 221:47-57.
28. Larsen, J. B., A. Larsen, R. Thyrhaug, G. Bratbak, and R.-A. Sandaa. 2008. Response of marine viral populations to a nutrient-induced phytoplankton bloom at different pCO2 levels. Biogeosciences 5:523-533.
29. Lawrence, J. E. 2010. Purification of viruses by centrifugation. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of aquatic viral ecology. ASLO.
30. Loa, C. C., T. L. Lin, C. C. Wu, T. A. Bryan, H. L. Thacker, T. Hooper, and D. Schrader. 2002. Purification of turkey coronavirus by Sephacryl size-exclusion chromatography. J. Virol. Methods 104:187-194.
31. 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. 65:45-52.
32. 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. 14:113-118.
33. Ollivon, M., A. Walter, and R. Blumenthal. 1986. Sizing and separation of liposomes, biological vesicles, and viruses by high-performance liquid chromatography. Anal. Biochem. 152:262-274.
34. Payet, J. P., and C. A. Suttle. 2008. Physical and biological correlates of virus dynamics in the southern Beaufort Sea and Amundsen Gulf. J. Mar. Sys. 74:933-945.
35. Primrose, S. B., N. D. Seeley, K. B. Logan, and J. W. Nicolson. 1982. Methods for studying aquatic bacteriophage ecology. Appl. Environ. Microbiol. 43:694-701.
36. Reynolds, J. A., Y. Nozaki, and C. Tanford. 1983. Gel-exclusion chromatography on S1000 Sephacryl: application to phospholipid vesicles. Anal. Biochem. 130:471-474.
37. Reynolds, J. A., Y. Nozaki, and C. Tanford. 1983. Gel-exclusion chromatography on S1000 Sephacryl: application to phospholipid vesicles. Anal. Biochem. 130:471-474.
38. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press.
39. Scopes, R. K. 1993. Protein purification: principles and practices, 3rd ed. Springer-Verlag.
40. Shields, P. A., and S. R. Farrah. 2002. Characterization of virus adsorption by using DEAE-Sepharose and octyl-Sepharose. Appl. Environ. Microbiol. 68:3965-3968.
41. Slepushkin, V., and others. 2003. Large-scale purification of a lentiviral vector by size exclusion chromatography or Mustang Q ion exchange capsule. BioProcessing September/October:89-95.
42. Smith, T. J. 1987. The isolation of the two electrophoretic forms of cowpea mosaic virus using fast protein liquid chromatography. J. Virol. Methods 16:263-269.
43. Steward, G. F. 2001. Fingerprinting viral assemblages by pulsed field gel electrophoresis (PFGE), p. 85-103. In J. H. Paul [ed.], Methods in microbiology. Atlantic Canada Society for Microbial Ecology, Halifax.
44. 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. 45:1697-1706.
45. Steward, G. F., and M. S. Rappé. 2007. What's the 'meta' with metagenomics? ISME J. 1:100-102.
46. Suttle, C. A. 2005. Viruses in the sea. Nature 437:356-361.
47. Trilisky, E. I., and A. M. Lenhoff. 2007. Sorption processes in ion-exchange chromatography of viruses. J. Chromatogr. A 1142:2-12.
48. Walin, L., R. Tuma, G. J. Thomas Jr., and D. H. Bamford. 1994. Purification of viruses and macromolecular assemblies for structural investigations using a novel ion exchange method. Virol. 201:1-7.
49. Wallis, C., J. L. Melnick, and C. P. Gerba. 1979. Concentration of viruses from water by membrane chromatography. Annu. Rev. Microbiol. 33:413-437.
50. Wommack, K. E., and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69-114.