Determination of viral production in aquatic sediments using the dilution-based approach

Nature Protocols

Volumn 4, Issue 7, 2009, Pages 1013-1022

  Dell'Anno, Antonio ^a   Corinaldesi, Cinzia ^a   Magagnini, Mirko ^a   Danovaro, Roberto ^a  

^a UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

FRESH WATER;

ARTICLE; CALCULATION; DILUTION; EPIFLUORESCENCE MICROSCOPY; EXPERIMENTAL DESIGN; FOOD WEB; INCUBATION TIME; MARINE ENVIRONMENT; POPULATION ABUNDANCE; PRIORITY JOURNAL; RELIABILITY; SEDIMENT; VIROGENESIS; VIRUS GENOME; VIRUS PARTICLE;

BIOMASS; FOOD CHAIN; GEOLOGIC SEDIMENTS; MICROSCOPY, FLUORESCENCE; VIROLOGY; VIRUSES;

EID: 68149164591     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2009.82     Document Type: Article

References (38)

1. Fuhrman, J.A. Marine viruses and their biogeochemical and ecological effects. Nature 399, 541-548 (1999).
2. Suttle, C.A. Viruses in the sea. Nature 437, 356-361 (2005).
3. Danovaro, R. et al. Major viral impact on the functioning of benthic deep-sea ecosystems. Nature 454, 1084-1087 (2008).
4. Heldal, M. & Bratbak, G. Production and decay of viruses in aquatic environments. Mar. Ecol. Prog. Ser. 72, 205-212 (1991).
5. Waterbury, J.B. & Valois, F.W. Resistance to co-occurring phages enables marine Synechococcus communities to coexist with cyanophages abundant in seawater. Appl. Environ. Microbiol. 59, 3393-3399 (1993).
6. Proctor, L.M. & Fuhrman, J.A. Viral mortality of marine bacteria and cyanobacteria. Nature 343, 60-62 (1990).
7. Weinbauer, M.G., Fuks, D. & Peduzzi, P. Distribution of viruses and dissolved DNA along a coastal trophic gradient in the northern Adriatic sea. Appl. Environ. Microbiol. 59, 4074-4082 (1993).
8. Steward, G.F., Wikner, J., Smith, D.C., Cochlan, W.P. & Azam, F. Estimation of virus production in the sea. 1. Method development. Mar. Microb. Food Webs 6, 57-78 (1992).
9. Wilhelm, S.W., Briden, S. & Suttle, C.A. A dilution technique for the direct measurement of viral production: A comparison in stratified and tidally mixed coastal waters. Microb. Ecol. 43, 168-173 (2002).
10. Noble, R.T. & Fuhrman, J.A. Rapid virus production and removal as measured with fluorescently labeled viruses as tracers. Appl. Environ. Microbiol. 66, 3790-3797 (2000).
11. Binder, B. Reconsidering the relationship between virally induced prokaryotic mortality and frequency of infected cells. Aquat. Microb. Ecol. 18, 207-215 (1999).
12. Winget, D.M., Williamson, K.E., Helton, R.R. & Wommack, K.E. Tangential flow diafiltration: An improved technique for estimation of virioplankton production. Aquat. Microb. Ecol. 41, 221-232 (2005).
13. Helton, R.R., Cottrell, M.T., Kirchman, D.L. & Wommack, K.E. Evaluation of incubation-based methods for estimating virioplankton production in estuaries. Aquat. Microb. Ecol. 41, 209-219 (2005).
14. Fischer, U.R., Wieltschnig, C., Kirschner, A.K.T. & Velimirov, B. Does virus-induced lysis contribute significantly to prokaryotic mortality in the oxygenated sediment layer of shallow oxbow lakes? Appl. Environ. Microbiol. 69, 5281-5289 (2003).
15. Fischer, U.R., Weisz, W., Wieltsching, C., Kirschner, A.K.T. & Velimirov, B. Benthic and pelagic viral decay experiments: A model-based analysis and its applicability. Appl. Environ. Microbiol. 70 6706-6713 (2004).
16. Fischer, U.R., Wieltschnig, C., Kirschner, A.K.T. & Velimirov, B. Contribution of virus-induced lysis and protozoan grazing to benthic prokaryotic mortality estimated simultaneously in microcosms. Environ. Microbiol. 8, 1394-1407 (2006).
17. Bettarel, Y., Bouvy, M., Dumont, C. & Sime-Ngando, T. Virus-bacterium interactions in water and sediment of West African inland aquatic systems. Appl. Environ. Microbiol. 72, 5274-5282 (2006).
18. Filippini, M., Buesing, N., Bettarel, Y., Sime-Ngando, T. & Gessner, M.O. Infection paradox: High abundance but low impact of freshwater benthic viruses. Appl. Environ. Microbiol. 72, 4893-4898 (2006).
19. Proctor, L.M., Okubo, A. & Fuhrman, J.A. Calibrating estimates of phage-induced mortality in marine bacteria: Ultrastructural studies of marine bacteriophage development from one-step growth experiments. Microb. Ecol. 25, 161-182 (1993).
20. Guixa-Boixareu, N., Calderón-Paz, J.I., Heldal, M., Bratbak, G. & Pedròs-Aliò, C. Viral lysis and bacterivory as prokaryotic loss factors along a salinity gradient. Aquat. Microb. Ecol. 11, 215-227 (1996).
21. Mei, M.L. & Danovaro, R. Virus production and life strategies in aquatic sediments. Limnol. Oceanogr. 49, 459-470 (2004).
22. Glud, R. & Middelboe, M. Virus and bacteria dynamics of a coastal sediment: Implication for benthic carbon cycling. Limnol. Oceanogr. 49, 2073-2081 (2004).
23. Middelboe, M., Glud, R.N., Wenzhofer, F., Ogurib, K. & Kitazato, H. Spatial distribution and activity of viruses in the deep-sea sediments of Sagami Bay, Japan. Deep Sea Res. I. 53, 1-13 (2006).
24. Hewson, I. & Fuhrman, J.A. Viriobenthos production and virioplankton sorptive scavenging by suspended sediment particles in coastal and pelagic waters. Microb. Ecol. 46, 337-347 (2003).
25. Danovaro, R. et al. Viriobenthos in freshwater and marine sediments: A review. Freshwat. Biol. 53, 1186-1213 (2008).
26. Corinaldesi, C., Dell'Anno, A. & Danovaro, R. Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems. Limnol. Oceanogr. 52, 508-516 (2007).
27. Chen, F., Lu, J.R., Binder, B., Liu, Y. & Hodson, R.E. Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR Gold. Appl. Environ. Microbiol. 67, 539-545 (2001).
28. Patel, A. et al. Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat. Protoc. 2, 269-276 (2007).
29. Danovaro, R., Dell'Anno, A., Trucco, A., Serresi, M. & Vanucci, S. Determination of virus abundance in marine sediments. Appl. Environ. Microbiol. 67, 1384-1387 (2001).
30. Wen, K., Ortmann, A.C. & Suttle, C.A. Accurate estimation of viral abundance by epifluorescence microscopy. Appl. Environ. Microbiol. 70, 3862-3867 (2004).
31. Helton, R.R., Liu, L. & Wommack, K.E. Assessment of factors influencing direct enumeration of viruses within estuarine sediments. Appl. Environ. Microbiol. 72, 4767-4774 (2006).
32. Middelboe, M., Glud, R.N. & Finster, K. Distribution of viruses and bacteria in relation to diagenic activity in an estuarine sediment. Limnol. Oceanogr. 48, 1447-1456 (2003).
33. Fischer, U.R., Kirschner, A.K.T. & Velimirov, B. Optimization of extraction and estimation of viruses in silty freshwater sediments. Aquat. Microb. Ecol. 40, 207-216 (2005).
34. Hewson, I., O'Neil, J.M., Heil, C., Bratbak, G. & Dennison, W. Effects of concentrated viral communities on photosynthesis and community composition of co-occurring benthic microalgae and phytoplankton. Aquat. Microb. Ecol. 25, 1-10 (2001).
35. Duhamel, S. & Jacquet, S. Flow cytometric analysis of bacteria and virus-like particles in lake sediments. J. Microbiol. Method 64 316-322 (2006).
36. Noble, R.T. & Fuhrman, J.A. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol. 14, 113-118 (1998).
37. Shibata, A. et al. Comparison of SYBR Green I and SYBR Gold stains for enumerating bacteria and viruses by epifluorescence microscopy. Aquat. Microb. Ecol. 43, 223-231 (2006).
38. Noble, R.T. & Fuhrman, J.A. Breakdown and microbial uptake of marine viruses and other lysis products. Aquat. Microb. Ecol. 20, 1-11 (1999).