Viruses in aquatic ecosystems: Important advancements of the last 20 years and prospects for the future in the field of microbial oceanography and limnology

Advances in Oceanography and Limnology

Volumn 1, Issue 1, 2010, Pages 97-141

  Jacquet, Stéphan ^a   Miki, Takeshi ^b   Noble, Rachel ^c   Peduzzi, Peter ^d   Wilhelm, Steven ^e  

^a UMR CARRTEL   (France)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d UNIVERSITY OF VIENNA   (Austria)

^e UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Abundances; Aquatic; Bacteria; Biogeochemistry; Diversity; Models; Mortality; Phage therapy; Phytoplankton; Viruses

Indexed keywords

ABUNDANCE; AQUATIC ECOSYSTEM; BACTERIUM; BIOGEOCHEMICAL CYCLE; COMMUNITY STRUCTURE; LIMNOLOGY; MORTALITY; OCEANOGRAPHY; PHYTOPLANKTON; VIRUS;

ALGAE; BACTERIA (MICROORGANISMS);

EID: 85069297488     PISSN: 19475721     EISSN: 1947573X     Source Type: Journal    
DOI: 10.1080/19475721003743843     Document Type: Review

References (269)

1. K.E. Wommack and R.R. Colwell, Virioplankton: Viruses in aquatic ecosystems, Microbiol. Mol. Biol. Rev. 64 (2000), pp. 69-114.
2. C.A. Suttle, Marine viruses-major players in the global ecosystem, Nature Rev. Microbiol. 5 (2007), pp. 801-812.
3. M. Middelboe, S. Jacquet, and M. Weinbauer, Viruses in freshwater ecosystems: an introduction to the exploration of viruses in new aquatic habitats, Fresh. Biol. 53 (2008), pp. 1069-1075.
4. S.W. Wilhelm and A.R. Matteson, Freshwater and marine virioplankton: a brief overview of commonalities and differences, Freshw. Biol. 53 (2008), pp. 1076-1089.
5. J.L. Clasen, S.M. Brigden, J.P. Payet, and C.A. Suttle, Evidence that viral abundance across oceans and lakes is driven by different biological factors, Fresh. Biol. 53 (2008), pp. 1090-1100.
6. M. Le Romancer, M. Gaiilard, C. Geslin, and D. Prieur, Viruses in extreme environments, Rev. Environ. Sci. Biotechnol. 6 (2007), pp. 17-31.
7. K. Porter, B.E. Russ, and M.L. Dyall-Smith, Virus-host interactions in salt lakes, Curr. Opin. Microbiol. 10 (2007), pp. 418-424.
8. D. Prangishvili, Evolutionary insights from studies on vorises of hyperthermophilic archaea, Res. Microbiol. 154 (2003), pp. 289-294.
9. D. Prangishvili, R.A. Garrett, and E.V. Koonin, Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life, Vir. Res. 117 (2006), pp. 52-67.
10. R. Rachel, M. Bettstetter, B.P. Hedlund, M. Häring, A. Kessler, K.O. Stetter, and D. Prangishvili, Remarkable morphological diversity of viruses and virus-like particles in hot terrestrial environments, Arch. Virol. 147 (2002), pp. 2419-2429.
11. G. Rice, K. Stedman, J. Snyder, B. Wiedenheft, and D. Willits, Viruses from extreme thermal environments, Proc. Nat. Acad. Sci. USA 98 (2001), pp. 13341-13345.
12. F. Torrella and R.Y. Morita, Evidence by electron micrographs for a high incidence of bacteriophage particles in the waters of Yaquina Bay, Oregon: Ecological and taxonomical implications, Appl. Environ. Microb. 37 (1979), pp. 774-778.
13. O. Bergh, K.Y. Borsheim, G. Bratbak, and M. Heldal, High abundance of viruses found in aquatic environments, Nature 340 (1989), pp. 467-468.
14. L.M. Proctor and J.A. Fuhrman, Viral mortality of marine bacteria and cyanobacteria, Nature 343 (1990), pp. 60-62.
15. G. Bratbak, M. Heldal, S. Norland, and T.F. Thingstad, Viruses as partners in spring bloom microbial trophodynamics, Appl. Environ. Microbiol. 56 (1990), pp. 1400-1405.
16. T.F. Thingstad, M. Heldal, G. Bratbak, and I. Dundas, Are viruses important partners in pelagic food webs?, Trends Ecol. Evol. 8 (1993), pp. 209-213.
17. T.F. Thingstad and R. Lignell, Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand, Aquat. Microb. Ecol. 13 (1997), pp. 19-27.
18. G. Bratbak, and M. Heldal, Viruses-The new players in the game, their ecological role and could they mediate genetic exchange by transduction? in Molecular Ecology of Aquatic Microbes, I. Joint, ed., 1995, pp. 249-264.
19. G. Bratbak and M. Heldal, Viruses rule the waves-the smallest and most abundant members of marine ecosystems, Microbiol. Today 27 (2000), pp. 171-173.
20. W.H. Wilson, J.L. van Etten, and M.J. Allen, The phycodnaviridae: the story of how tiny giants rule the world, in Lesser known Large dsDNA Viruses, J.L. van Etten, ed., Current Topics in Microbiology and Immunology, 2009, pp. 1-42.
21. F. Rohwer and R. Vega Thurber, Viruses manipulate the marine environment, Nature 459 (2009), pp. 207-212.
22. J.H. Paul, Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?, ISME J 2 (2008), pp. 579-589.
23. J.A. Fuhrman, Marine viruses and their biogeochemical and ecological effects, Nature 399 (1999), pp. 541-548.
24. S.W. Wilhelm and C.A. Suttle, Viruses and nutrient cycles in the sea, Bioscience 49 (1999), pp. 781-788.
25. M.G. Weinbauer, Ecology of prokaryotic viruses, FEMS Microbiol. Rev. 28 (2004), pp. 127-181.
26. M.G. Weinbauer and F. Rassoulzadegan, Are viruses driving microbial diversification and diversity?, Environ. Microbiol. 6 (2004), pp. 1-11.
27. C.P.D. Brussaard, Viral control of phytoplankton populations-A review, J. Eukaryot. Microbiol. 51 (2004), pp. 125-138.
28. C.A. Suttle, Cyanophages and their role in the ecology of cyanobacteria, in The Ecology of Cyanobacteria, B.A. Whitton and M. Potts, eds., Kluwer Academic Publ, Boston, 2000a, pp. 563-589.
29. C.A. Suttle, Ecological, evolutionary, and geochemical consequences of viral infection of cyanobacteria and eukaryotic algae, in Viral Ecology, C. Hurst, ed., Academic Press, London, 2000b, pp. 247-296.
30. C.A. Suttle, Viruses in the sea, Nature 437 (2005), pp. 356-361.
31. C.P.D. Brussaard and J. Martinez Martinez, Algal bloom viruses, Plant Vir 2 (2008), pp. 1-13.
32. M. Middelboe. Microbial disease in the sea: effects of viruses on carbon and nutrient cycling, in Infectious Disease Ecology: Effects of Ecosystems on Disease and of Disease on Ecosystems, R.S. Ostfeld, F. Keesing, and V.T. Eviner, eds., Princeton University Press, Princeton, NJ, 2008, pp. 242-259.
33. K. Nagasaki, Dinoflagellates, diatoms and their viruses, J. Microbiol. 46 (2008), pp. 235-243.
34. K. Nagasaki, and C. Brussaard Algal viruses, in Encyclopedia of Virology, 3rd ed., Vol. 1, 2008, pp. 97-105.
35. R.A. Sandaa, Burden or benefit? Virus-hot interactions in the marine environment, Res. Microbiol. 159 (2008), pp. 374-381.
36. R.T. Noble and J.A. Fuhrman, Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria, Aquat. Microb. Ecol. 14 (1998), pp. 113-118.
37. M. Dominique, C.P.D. Brussaard, R. Thyrhaug, G. Bratbak, and D. Vaulot, Enumeration of marine viruses in culture and natural samples by flow cytometry, Appl. Environ. Microbiol. 65 (1) (1999), pp. 45-52.
38. F. Rohwer and R. Edwards, The phage proteomic tree: a genome based taxonomy for phage, J. Bact. 184 (2002), pp. 4529-4535.
39. R. Danovaro, C. Corinaldesi, M. Filippini, U.R. Fischer, M.O. Gessner, S. Jacquet, M. Magagnini, and B. Velimirov, Viriobenthos in freshwater and marine sediments: a review, Freshw. Biol. 53 (2008), pp. 1186-1213.
40. R. Maranger and D.F. Bird, Viral abundance in aquatic systems: a comparison between marine and freshwaters, Mar. Ecol. Progr. Ser. 121 (1995), pp. 217-226.
41. A.C. Ortmann and C.A. Suttle, High abundance of viruses in a deep-sea hydrothermal vent system indicates viral mediated microbial mortality, Deep-Sea Res. I 52 (2005), pp. 1515-1527.
42. M.G. Weinbauer and M.G. Höfle, Significance of viral lysis and flagellate grazing as factors controlling bacterioplankton production in eutrophic lake, Appl. Environ. Microbiol. 64 (1998), pp. 431-438.
43. J. Colombet, T. Sime-Ngando, H.M. Cauchie, G. Fonty, L. Hoffmann, and G. Demeure, Depth-related gradients of viral activity in Lake Pavin, Appl. Environ. Microbiol. 72 (2006), pp. 4440-4445.
44. C. Sawstrom, M.A. Anesio, W. Granéli, and J. Laybourn-Parry, Seasonal viral loop dynamics in two large ultraoligotrophic Antarctic freshwater lakes, Microb. Ecol. 53 (2007), pp. 1-11.
45. J.S. Hofer and R. Sommaruga, Seasonal dynamics of viruses in an alpine lake: importance of filamentous forms, Aquat. Microb. Ecol. 26 (2001), pp. 1-11.
46. N. Maurin, C. Amblard, and G. Bourdier, Phytoplanktonic excretion and bacterial reassimilation in an oligotrophic lake: molecular weight fractionation, J. Plank. Res. 19 (1997), pp. 1045-1068.
47. M. Filippini, N. Buesing, and M. Gessner, Temporal dynamics of freshwater bacterio-and virioplankton along a littoral-pelagial gradient, Fresh. Biol. 53 (2008), pp. 1114-1125.
48. M.G. Weinbauer and P. Peduzzi, Significance of viruses versus heterotrophic nanoflagellates for controlling bacterial abundance in the northern Adriatic Sea, J. Plankt. Res. 17 (1995), pp. 1851-1856.
49. Y. Bettarel, C. Amblard, T. Sime-Ngando, J.F. Carrias, D. Sargos, F. Garabetian, and P. Lavandier, Viral lysis, flagellate grazing potential, and bacterial production in Lake Pavin, Microb. Ecol. 45 (2003), pp. 119-127.
50. S. Personnic, I. Domaizon, T. Sime-Ngando, and S. Jacquet, Seasonal variations of microbial abundances and of virus-vs. flagellate-induced mortality of picoplankton in some peri-alpine lakes, J. Plank. Res. 31 (2009), pp. 1161-1177.
51. M.G. Weinbauer and C.A. Suttle, Comparison of epifluorescence and transmission electron microscopy for counting viruses in natural marine waters, Aquat. Microb. Ecol. 13 (1997), pp. 225-232.
52. R.A. Sandaa and A. Larsen, Seasonal variations in virus-host populations in Norwegian coastal waters: focusing on the cyanophage community infecting marine Synechococcus spp., Appl. Environ. Microbiol. 72 (2006), pp. 4610-4618.
53. D. Lymer, E.S. Lindström, and K.A. Vrede, Variable importance of viral-induced bacterial mortality along gradients of trophic status and humic content in lakes, Freshw. Biol. 53 (2008), pp. 1101-1113.
54. S. Jacquet, M. Heldal, D. Iglesias-Rodriguez, A. Larsen, W. Wilson, and G. Bratbak, Flow cytometric analysis of an Emiliana huxleyi bloom terminated by viral infection, Aquat. Microbial. Ecol. 27 (2002), pp. 111-124.
55. C. Winter, G.J. Herndl, and M.G. Weinbauer, Diel cycles in viral infection of bacterioplankton in the North Sea, Aquat. Microb. Ecol. 35 (2004), pp. 207-216.
56. D.M. Winget and K.E. Wommack, Diel and daily fluctuations in virioplankton production in coastal ecosystems, Environ. Microbiol. 11 (2009), pp. 2904-2914.
57. J.R. Seymour, L. Seuront, M. Doubell, R.L. Waters, and J.G. Mitchell, Microscale patchiness of virioplankton, J. Mar. Biol. Ass. UK 86 (2006), pp. 551-561.
58. F. Azam and F. Malfatti, Microbial structuring of marine ecosystems, Nature Rev. Microbiol. 5 (2007), pp. 782-791.
59. B. Luef, T.R. Neu, and P. Peduzzi, Imaging and quantifying virus fluorescence signals on aquatic aggregates: a new method and its implication for aquatic microbial ecology, FEMS Microbiol. Ecol. 68 (2009), pp. 372-380.
60. B. Luef, T.R. Neu, I. Zweimüller, and P. Peduzzi, Structure and composition of aggregates in two large European rivers, based on Confocal Laser Scanning Microscopy and image and statistical analysis, Appl. Environ. Microbiol. 75 (2009), pp. 5952-5962.
61. M.A. Tapper and R.E. Hicks, Temperate viruses and lysogeny in Lake Superior bacterioplankton, Limnol. Oceanogr. 43(1) (1998), pp. 95-103.
62. S.C. Jiang and J.H. Paul, Seasonal and diel abundance of viruses and occurrence of lysogeny/ bacteriocinogeny in the marine environment, Mar. Ecol. Progr. Ser. 104 (1994), pp. 163-172.
63. S.C. Jiang, C.A. Kellogg, and J.H. Paul, Characterization of marine temperate phage-host systems isolated from Mamala Bay, Oahu, Hawaii, Appl. Environ. Microbiol. 64 (1998), pp. 535-542.
64. D. Stopar, A. Cěrne, M. Zěigman, M. Poljsǎk-Prijatelj, and V. Turk, Viral abundance and a high proportion of lysogens suggest that viruses are important members of the microbial community in the Gulf of Trieste, Microb. Ecol. 47 (2004), pp. 1-8.
65. J.T. Lisle and J.C. Priscu, The occurrence of lysogenic bacteria and microbial aggregates in the lakes of the McMurdo Dry Valleys, Antarctica, Microb. Ecol. 47 (2004), pp. 427-439.
66. M.K. Waldor and J.J. Mekalanos, Lysogenic conversion by filamentous phage encoding cholera toxin, Science 272 (1996), pp. 1910-1914.
67. K.Y. Børsheim, Native marine bacteriophages, FEMS Microbiol. Ecol. 102 (1993), pp. 141-159.
68. L.M. Proctor, Advances in the study of marine viruses, Microsc. Res. Tech. 37 (1997), pp. 136-161.
69. T. Sime-Ngando and J. Colombet, Virus et prophages dans les écosystèmes aquatiques, Rev. Can. Microb. 55 (2009), pp. 95-109.
70. C.B. Mathias, A.K.T. Kirschner, and B. Velimirov, Seasonal variations of virus abundance and viral control of the prokaryotic production in the backwater system of the Danube River, Appl. Environ. Microbiol. 61 (1995), pp. 3734-3740.
71. R. Sommaruga, M. Krössbacher, W. Salvenmoser, J. Catalan, and R. Psenner, Presence of large virus-like particles in a eutrophic reservoir, Aquat. Microb. Ecol. 9 (1995), pp. 305-308.
72. R.L. Kepner, R.A. Wharton, and C.A. Suttle, Viruses in Antarctic lakes, Limnol. Oceanogr. 43 (1998), pp. 1754-1761.
73. S. Pina, A. Creus, N. Gonzalze, R. Gironés, M. Felip, and R. Sommaruga, Abundance, morphology and distribution of planktonic virus-like particles in two high-mountain lakes, J. Plank. Res. 20 (1998), pp. 2413-2421.
74. M.M. Gowing, Large virus-like particles from vacuoles of Phaeodarian radiolarians and from the marine samples, Mar. Ecol. Prog. Ser. 101 (1993), pp. 33-43.
75. A. Monier, J.B. Larsen, R.A. Sandaa, G. Bratbak, J.M. Claverie, and H. Ogata, Marine mimivirus relatives are probably large algal viruses, Virol. J. 5 (2008), pp. 1-12.
76. J.M. Claverie, and H. Ogata, Ten good reasons not to exclude giruses from the evolutionary picture, Nat. Rev. Microbiol. (2009).
77. J. Lu, F. Chen, and R.E. Hodson, Distribution, isolation, host specificity, and diversity of cyanophages infecting marine Synechococcus spp. in river estuaries, Appl. Environ. Microbiol. 67 (2001), pp. 3285-3290.
78. R. Maranger, D.F. Bird, and S.R. Juniper, Viral and bacterial dynamics in Arctic sea ice during the spring algal bloom near Resolute, N.W.T. Canada, Mar. Ecol. Prog. Ser. 111 (1994), pp. 121-127.
79. M.G. Weinbauer and P. Peduzzi, Frequency, size and distribution of bacteriophages in different marine bacterial morphotypes, Mar. Ecol. Prog. Ser. 108 (1994), pp. 11-20.
80. K. Wommack, J. Ravel, R. Hill, J. Chun, and R. Colwell, Population dynamics of Chesapeake Bay virioplankton, Appl. Environ. Microbiol. 65 (1999), pp. 241-250.
81. S.M. Short and C.A. Suttle, Nearly identical bacteriophage structrural gene sequences are widely distributed in marine and freshwater environments, Appl. Environ. Microbiol. 71 (2005), pp. 480-486.
82. W. Wilson, N. Fuller, I. Joint, and N. Mann, Analyse of cyanophage diversity and population structure in a south-north transect of the Atlantic ocean, Bull. Inst. Océano Monaco 19 (1999), pp. 209-216.
83. A.I. Culley, A.S. Lang, and C.A. Suttle, High diversity of unlnown picorna-like viruses in the sea, Nature 424 (2003), pp. 1054-1057.
84. A.I. Culley, A.S. Lang, and C.A. Suttle, Metagenomic analysis of coastal RNA virus communities, Science 312 (2006), pp. 1795-1798.
85. A.I. Culley and G.F. Steward, New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences, Appl. Environ. Microbiol. 73 (2007), pp. 5937-5944.
86. I. Hewson, D.M. Winget, K.E. Williamson, J.A. Fuhrman, and K.E. Wommack, Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida Shelf (Gulf of Mexico), J. Mar. Biol. Ass. UK 86 (2006), pp. 591-603.
87. R.A. Sandaa, L. Gomez-Consarnau, J. Pinhassi, L. Riemann, A. Maltis, M.G. Weinbauer, J.M. Gasol, and T.F. Thingstad, Viral control of bacterial biodiversity-evidence from a nutrient-enriched marine mesocosm experiment, Environ. Microbiol. 11 (2009), pp. 2585-2597.
88. J.C. Auguet, H. Montanié, and P. Lebaron, Structure of virioplankton in the Charente Estuary (France): transmission electron microscopy versus pulse field gel electrophoresis, Microb. Ecol. 51 (2005), pp. 197-208.
89. M. Breitbart and F. Rohwer, Here a virus, there a virus, everywhere the same virus?, Trends Microbiol. 13 (2005), pp. 278-284.
90. A. Lopez-Bueno, J. Tamames, D. Velazquez, A. Moya, A. Quesada, and A. Alcami, High diversity of the viral community from an Antarctic lake, Science 326 (2009), pp. 858-861.
91. F.E. Angly et al., The marine viromes of four oceanic regions, Plos. Biol. 4 (11) (2006), p. e368.
92. M. Breitbart, P. Salamon, B. Andresen, J.M. Mahaffy, A.M. Segall, D. Mead, F. Azam, and F. Rohwer, Genomic analysis of uncultured marine viral communities, Proc. Natl. Acad. Sci. USA 99 (2002), pp. 14250-14255.
93. M. Breitbart, B. Felts, S. Kelley, J.M. Mahaffy, J. Nulton, P. Salamon, and F. Rohwer, Diversity and population structure of a near-shore marine sediment viral community, Proc. Roy Soc. Lon. Ser. B 271 (2004), pp. 565-574.
94. S.J. Williamson, S. Craig Cary, K.E. Williamson, R.R. Helton, S.R. Bench, D. Winget, and K.E. Wommack, Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents, ISME J. 2 (2008), pp. 1112-1121.
95. M.R. Henn, et al., Analaysis of high-throughput sequencing and annotation strategies for phage genomics, Plos One 5 (2) (2010), p. e9083.
96. R.R. Helton and K.E. Wommack, Seasonal dynamics and metagenomic characterization of estuarine viriobenthos assemblages by Randomly Amplified Polymorphic DNA PCR, Appl. Environ. Microbiol. 75 (2009), pp. 2259-2265.
97. D.M. Winget and K.E. Wommack, Randomly Amplified Polymorphic DNA PCR as a tool for assessment of marine viral richness, Appl. Environ. Microbiol. 74 (2008), pp. 2612-2618.
98. M. Tijdens, H.L. Hoogveld, M. Kamst-van Agterveld, S.G.H. Simis, A.C. Baudoux, H.J. Laanbroek, and H.J. Gons, Population dynamics and diversity of viruses, bacteria and phytoplankton in shallow eutrophic lake, Microb. Ecol. 56 (2008), pp. 29-42.
99. M. Tijdens, D.B. van de Waal, H. Slovacckova, H.L. Hoogveld, and H.J. Gons, Estimates of bacterial and phytoplankton mortality caused by viral lysis and microzooplankton grazing in a eutrophic lake, Fresh Biol. 53 (2008), pp. 1126-1141.
100. T. Catsberg, A. Larsen, R.A. Sandaa, C.P.D. Brussaard, J.K. Egge, M. Heldal, R. Thyrhaug, E.J. van Hannen, and G. Bratbak, Microbial population dynamics and diversity during a bloom of the marine coccolithophorid Emiliania huxleyi (Haptophyta), Marine Ecol.-Progress Ser. 221 (2001), pp. 39-43.
101. A. Larsen, T. Castberg, R.A. Sandaa, C.D.P. Brussaard, J.K. Egge, M. Heldal, A. Paulino, R. Thyrhaug, E. van Hannen, and G. Bratbak, Population dynamics and diversity of phytoplankton, bacteria and viruses in a seawater enclosure, Mar. Ecol. Prog. Ser. 221 (2001), pp. 47-57.
102. M. Ohnishi, K. Kuokawa, and T. Hayashi, Diversification of Escherichia coli genomes: are bacteriophages the main contributors?, Trends Microbiol. 9 (2001), pp. 481-485.
103. D.W. Griffin, K.A. Donaldson, J.H. Paul, and J.B. Rose, Pathogenic human viruses in coastal waters, Clinical. Microbiol. Rev. 16 (2003), pp. 129-143.
104. E.V. Koonin, Y.I. Wolf, K. Nagasaki, and V.V. Dolja, The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups, Nature Rev. Microbiol. 6 (2008), pp. 925-939.
105. L.M. Proctor and J.A. Fuhrman, Roles of viral infection in organic particles flux, Mar. Ecol. Prog. Ser. 69 (1991), pp. 133-142.
106. K.P. Hennes and M. Simon, Significance of bacteriophages for controlling bacterioplankton growth in mesotrophic lake, Appl. Environ. Microb. 61 (1995), pp. 333-340.
107. M.G. Weinbauer, C. Winter, and M.G. Höflel, Reconsidering transmission electron microscopy based estimates of viral infection of bacterioplankton using conversion factors derived from natural communities, Aquat. Microb. Ecol. 27 (2002), pp. 103-110, 2002.
108. B. Binder, Reconsidering the relationship between virally induced bacterial mortality and frequency of infected cells, Aquat. Microb. Ecol. 18 (1999), pp. 207-2015.
109. M. Heldal and G. Bratbak, Production and decay of viruses in aquatic environments, Mar. Ecol. Progr. Ser. 72 (1991), pp. 205-212.
110. M.G. Weinbauer, U. Christaki, A. Nedoma, and K. Simek, Comparing the effects of resource enrichment and grazing on viral production in meso-eutrophic reservoir, Aquat. Microbial. Ecol. 31 (2003a), pp. 137-144.
111. S.W. Wilhelm, M.G. Weinbauer, C.A. Suttle, and W.H. Jeffrey, The role of sunlight in the removal and repair of viruses in the sea, Limnol. Oceanogr. 43 (1998), pp. 586-592.
112. P.K. Cochran, C.A. Kellogg, and J.H. Paul, Prophage induction of indigenous marine lysogenic bacteria by environmental pollutants, Mar. Ecol. Prog. Ser. 164 (1998), pp. 125-133.
113. V. Parada, G.J. Herndl, and M.G. Weinbauer, Viral burst size of heterotrophic prokaryotes in aquatic ecosystems, J. Mar. Biol. Ass. UK 86 (2006), pp. 613-621.
114. M.G. Weinbauer, D. Fuks, and P. Peduzzi, Distribution of viruses and dissolved DNA along a coastal trophic gradient in the northern Adriatic Sea, Appl. Environ. Microbiol. 59 (1993), pp. 4074-4082.
115. V. Parada, E. Sintes, H.M. van Aken, M.G. Weinbauer, and G.J. Herndl, Viral abundance, decay, and diversity in the meso-and bathypelagic waters of the North Atlantic, Appl. Environ. Microbiol. 73 (2007), pp. 4429-4438.
116. L. Bongiorni, M. Armeni, C. Corinaldesi, A. Del'Anno, A. Pusceddu, and R. Danovaro, Viruses, prokaryotes and biochemical composition of organic matter in different types of mucilage aggregates, Aquat. Microb. Ecol. 49 (2007), pp. 15-23.
117. S.W. Wilhelm, S.M. Brigden, and C.A. Suttle, A dilution technique for the direct measurement of viral production: a comparison in stratified and tidally mixed coastal waters, Microbial. Ecol. 43 (2002), pp. 168-173.
118. G.F. Steward, J. Wikner, D.C. Smith, W.P. Cochlan, and F. Azam, Estimation of virus production in the sea: I. Method development, Mar. Microb. Food Webs 6 (1992), pp. 57-78.
119. R.T. Noble and J.A. Fuhrman, Rapid virus production and removal as measured with fluorescently labeled viruses as tracers, Appl. Environ. Microbiol. 66 (2000), pp. 3790-3797.
120. A. Comeau, and R.T. Noble, Preparation and application of fluorescently labeled virus particles, in Limnol Oceangr, Manual of Aquatic Viral Ecology, Chapter 3, 2009, pp. 19-29.
121. C. Evans, S.D. Archer, S. Jacquet, and W.H. Wilson, Direct estimates of the contribution of viral lysis and microzooplankton grazing to the decline of a Micromonas spp. population, Aquat. Microb. Ecol. 30 (2003), pp. 207-219.
122. A.C. Baudoux, M.J.W. Veldhuis, A.A.M. Noordeloos, G. van Noort, and C.P.D. Brussaard, Estimates of virus-vs. grazing induced mortality of picophytoplankton in the North Sea during summer, Aquat. Microb. Ecol. 52 (2008), pp. 68-82.
123. S. Jacquet, I. Domaizon, S. Personnic, A.S. Pradeep-Ram, M. Heldal, S. Duhamel, and T. Sime-Ngando, Estimates of protozoan-and viral-mediated mortality of bacterioplankton in Lake Bourget (France), Fresh. Biol. 50 (2005), pp. 627-645.
124. R. Thomas, L. Berdjeb, T. Sime-Ngando, and S. Jacquet. Viral abundance, production, decay rates and life strategies (lytic vs. lysogeny) in Lake Bourget, Environ. Microb. (in revision).
125. J.A. Fuhrman and R.T. Noble, Viruses and protists cause similar bacterial mortality in coastal seawater, Limnol. Oceanogr. 40(7) (1995), pp. 1236-1242.
126. K. Simek, M.G. Weinbauer, K. Hornak, J. Jezbera, J. Nedoma, and J. Dolan, Grazer and virus induced mortality of bacterioplankton accelerates development of Flectobacillus populations in freshwater community, Environ. Microbiol. 9 (2007), pp. 789-800.
127. M. Middelboe, Bacterial growth rate and marine virus-host dynamics, Microb. Ecol. 40 (2000), pp. 114-124.
128. T. Miki and S. Jacquet, Complex interactions in the microbial world: underexplored key links between viruses, bacteria and protozoan grazers in aquatic environments, Aquat. Microb. Ecol. 51 (2008), pp. 195-208.
129. C.P.D. Brussaard, S.W. Wilhelm, F. Thingstad, M.G. Weinbauer, G. Bratbak, M. Heldal, S.A. Kimmance, M. Middelboe, K. Nagasaki, J.H. Paul, D.C. Schroeder, C.A. Suttle, D. Vaque, and K.E. Wommack, Global scale processes with a nanoscale drive-from viral genes to oceanic biogeochemical cycles, ISME J. 2 (2008), pp. 575-578.
130. C.J. Gobler, D.A. Hutchins, N.S. Fisher, E.M. Cosper, and S.A. Sãnudo-Wilhelmy, Release and bioavailability of C, N, P, Se, and Fe following viral lysis of a marine chrysophyte, Limnol. Oceanogr. 42 (1997), pp. 1492-1504.
131. L. Poorvin, J.M. Rinta-Kanto, D.A. Hutchins, and S.W. Wilhelm, Viral release of Fe and its bioavailability to marine plankton, Limnol. Oceanogr. 49 (2004), pp. 1734-1741.
132. J.A. Fuhrman. Bacterioplankton roles in cycling of organic matter: the microbial food web, in Primary Productivity and Biogeochemical Cycles in the Sea, P.G. Falkowski and A. Woodhead, eds., Plenum, New York, NY, 1992, pp. 361-384.
133. C.E. Mioni, L. Poorvin, and S.W. Wilhelm, Virus and siderophore-mediated transfer of available Fe between heterotrophic bacteria: characterization using a Fe-specific bioreporter, Aquat. Microb. Ecol. 41 (2005), pp. 233-245.
134. R.T. Noble and J.A. Fuhrman, Breakdown and microbial uptake of marine viruses, Aquat. Microb. Ecol. 20 (1999), pp. 1-11.
135. M. Middelboe, T.G. Nielsen, and P.K. Bjørnsen, Viral and bacterial production in the North Water polynya: In situ measurements, batch culture experiments, and characterization and distribution of a virus-host system, Deep Sea Res. II 49 (2002), pp. 5063-5079.
136. M. Middelboe, L. Riemann, G.L. Steward, V. Hansen, and O. Nybroe, Virus-induced transfer of organic carbon between marine bacteria in a model community, Aquat. Microb. Ecol. 33 (2003), pp. 1-10.
137. M. Middelboe and N.O.G. Jorgensen, Viral lysis of bacteria: an important source of dissolved amino acids and cell wall compounds, J. Mar. Biol. Ass. UK 86 (2006), pp. 605-612.
138. R.T. Noble and J.A. Fuhrman, Viral decay and ist causes in coastal waters, Appl. Environ. Microbiol. 63 (1997), pp. 77-83.
139. J.L. Higgins, I. Kudo, J. Nishioka, A. Tsuda, and S.W. Wilhelm, The response of the virus community to a mesoscale iron fertilization in the sub-Arctic Pacific Ocean, Deep-Sea Res. II 56 (2009), pp. 2788-2795.
140. M.G. Weinbauer, J.M. Arrieta, C. Griebler, and G.J. Herndl, Enhanced virus production and infection of bacterioplankton during an iron-induced phytoplankton bloom in the Southern Ocean, Limnol. Oceanogr. 54 (2009), pp. 774-784.
141. A.L. Dean, J.L. Higgins, J.M. DeBruyn, J.M. Rinta-Kanto, R.A. Bourbonniere, and S.W. Wilhelm, A review of planktonic viruses in Lake Erie and their role in phosphorus cycling, in Checking the Pulse of Lake Erie, M. Munawar and R.T. Heath eds., Aquatic Ecosystem Health Management Society/Ecovision World Monographs, Burlington, ON, Canada, 2008, pp. 247-270.
142. R.M. Wilcox and J.A. Fuhrman, Bacterial viruses in coastal seawater: lytic rather than lysogenic production, Mar. Ecol. Progr. Ser. 114 (1994), pp. 35-45.
143. T.F. Thingstad, Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems, Limnol. Oceanogr. 45 (2000), pp. 1320-1328.
144. M.G. Weinbauer, K.N. Hornák, J. Jezbera, J. Nedoma, J.R. Dolan, and K. Šimek, Synergistic and antagonistic effects of viral lysis and protistan grazing on bacterial biomass, production and diversity, Environ. Microbiol. 9 (2007), pp. 777-788.
145. T. Bouvier and P.A. del Giorgio, Key role of selective viral-induced mortality in determining marine bacterial community composition, Environ. Microbiol. 9 (2007), pp. 287-297.
146. S.C. Jiang and J.H. Paul, Viral contribution to dissolved DNA in the marine environment as determined by differential centrifugation and kingdom probing, Appl. Environ. Microbiol. 57 (1995), pp. 2197-2204.
147. L. Riemann, K. Holmfeldt, and J. Titelman, Importance of viral lysis and dissolved DNA for bacterioplankton activity in a P-limited estuary, northern Baltic Sea, Microb. Ecol. 57 (2008), pp. 286-294.
148. E.A. Dinsdale et al., Functional metagenomic profiling of nine biomes, Nature 452 (2008), pp. 629-633.
149. R.V. Miller. Bacteriophage-mediated transduction: an engine for change and evolution, in Microbial Evolution: Gene Establishment, Survival, and Exchange, R.V. Miller and M.J. Day, eds., ASM Press, Washington, DC, 2004, pp. 144-157.
150. H.X. Chiura, Generalized gene transfer by virus-like particles from marine bacteria, Aquat. Microbial. Ecol. 13 (1997), pp. 75-83.
151. N. Mann, A. Cook, A. Millard, S. Bailey, and M. Clokie, Marine ecosystems: bacterial photosynthesis genes in a virus, Nature, 424 (2003), pp. 424-741.
152. D. Lindell, J.D. Jaffe, Z.I. Johnson, G.M. Church, and S.W. Chisholm, Photosynthesis genes in marine viruses yield proteins during host infection, Nature 438 (2005), pp. 86-89.
153. M.B. Sullivan, M.L. Coleman, P. Weigele, F. Rohwer, and S.W. Chisholm, Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations, PLoS Biol. 3 (5) (2005), p. e144.
154. M.B. Sullivan, D. Lindell, J.A. Lee, L.R. Thompson, J.P. Bielawski, and S.W. Chisholm, Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts, PLoS Biol. 4 (8) (2006), p. e234.
155. M.R.J. Clokie, A.D. Millard, J.Y. Metha, and N.H. Mann, Virus isolation studies suggest diel cycles in viral abundance in natural cyanophage population of the Indian Ocean, J. Marine Biol. Assoc. UK 86 (2006), pp. 499-505.
156. S.C. Jiang and J.H. Paul, Significance of lysogeny in the marine environments: studies with isolates and a model of lysogenic phage production, Microbial. Ecol. 35 (1998), pp. 235-243.
157. O.A. Ogunseitan, Genetic transduction in freshwater ecosystems, Fresh. Biol. 53 (2008), pp. 1228-1239.
158. M.G. Weinbauer, I. Brettar, and M.G. Höfle, Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters, Limnol. Oceanogr. 48 (2003b), pp. 1457-1465.
159. J. Haaber and M. Middelboe, Viral lysis of Phaeocystis pouchetii: implication for algal population dynamics and heterotrophic C, N and P cycling, The ISME J. 3 (2009), pp. 1751-7362.
160. B.R. Levin, F.M. Stewar, and L. Chao, Resource-limited growth, competition, and predation: a model and experimental studies with bacteria and bacteriophage, The American Naturalist 111 (1977), pp. 3-24.
161. B.J.M. Bohannan and R.E. Lenski, Effect of resource enrichment on a chemostat community of bacteria and bacteriophage, Ecology 78 (1997), pp. 2303-2315.
162. T. Yoshida, S.P. Ellner, L.E. Jones, J.M. Bohannan, R.E. Lenski, and N.G. Hairston, Cryptic population dynamics: rapid evolution masks trophic interactions, PLoS Biol. 5 (2007), pp. 1868-1879.
163. F.M. Stewart and B.R. Levin, The population biology of bacterial viruses: why be temperate?, Theoret. Pop. Biol. 26 (1973), pp. 93-117.
164. J.E. Mittler, Evolution of the genetic switch in temperate bacteriophage. 1. Basic theory, J. Theor. Biol. 179 (1996), pp. 161-172.
165. J.S. Weitz and J. Dusnhoff, Alternative stable states in host-phage dynamics, Theoret. Ecol. 1 (2008), pp. 13-19.
166. S. Pearl, C. Gabay, R. Kishony, A. Oppenheim, and N.Q. Balaban, Nongenetic individuality in the host-phage interaction, PLoS Biol. 6 (2008), pp. 0957-0964.
167. M. Middelboe, A. Hagström, N. Blackburn, B. Sinn, U. Fischer, N.H. Borch, J. Pinhassi, K. Simu, and M.G. Lorenz, Effects of bacteriophages on population dynamics of four strains of pelagic marine bacteria, Microb. Ecol. 42 (2001), pp. 395-406.
168. T. Miki and N. Yamamura, Intraguild predation reduces bacterial species richness and loosens the viral loop in aquatic systems: 'kill the killer of the winner' hypothesis, Aquat. Microb. Ecol. 41 (2005), pp. 1-12.
169. S.E. Forde, R.E. Beardmore, I. Gudelj, S.S. Arkin, J.N. Thompson, and L.D. Hurst, Understanding the limits to generalizability of experimental evolutionary models, Nature 455 (2008), pp. 220-224.
170. A.G. Murray and G.A. Jackson, Viral dynamics-a model of the effects of size, shape, motion and abundance of single-celled planktonic organisms and other particles, Mar. Ecol. Progr. Ser. 89 (1992), pp. 103-116.
171. K.H. Hoffmann, B. Rodriguez-Brito, M. Breitbart, D. Bangor, F. Angly, S.B. Felt, J. Nulton, F. Rohwer, and P. Salamon, Power low rank-abundance models for marine phage communities, FEMS Microbiol. Lett. 273 (2007), pp. 224-228.
172. S.P. Hubbell, A unified theory of biogeography and relative species abundance and its application to trophical rain forests and coral reefs, Coral Reefs 16 (1997), pp. S9-S21.
173. A.G. Murray and P.M. Eldridge, Marine viral ecology: incorporation of bacteriophage into the microbial planktonic food web paradigm, J. Plank. Res. 16 (1994), pp. 627-641.
174. T.R. Anderson and H.W. Ducklow, Microbial loop carbon cycling in ocean environments studies using a simple steady-state model, Aquat. Microb. Ecol. 26 (2001), pp. 37-49.
175. O. Bonilla-Findji, A. Malits, D. Lefevre, E. Rochelle-Newall, R. Lemee, M.G. Weinbauer, and J.P. Gattuso, Viral effects on bacterial respiration, production and growth efficiency: consistent trends in the Southern Ocean and the Mediterranean Sea, Deep Sea Res. II 55 (2009), pp. 790-800.
176. C. Motegi, T. Nagata, T. Miki, M.G. Weinbauer, L. Legendre, and F. Rassoulzadegan, Viral control of bacterial growth efficiency in marine pelagic environments, Limnol. Oceanogr. (2009), in press.
177. T. Miki, T. Nakazawa, T. Yokokawa, and T. Nagata, Functional consequences of viral impacts on bacterial communities: a food-web model analysis, Freshw. Biol. 53 (2008), pp. 1142-1153.
178. J.S. Weitz, Y. Mileyko, R.I. Joh, and E.O. Voit, Collective decision making in bacterial viruses, Biophys. J. 95 (2008), pp. 2673-2680.
179. S.T. Abedon, Selection for bacteriophage latent period length by bacterial density-a theoretical examination, Microb. Ecol. 18 (1989), pp. 79-88.
180. S.T. Abedon, T.D. Herschler, and D. Stopar, Bacteriophage latent-period evolution as a response to resource availability, Appl. Environ. Microbiol. 6 (2001), pp. 4233-4241.
181. S.T. Abedon, P. Hyman, and C. Thomas, Experimental examination of bacteriaophage latentperiod evolution as a response to bacterial availability, Appl. Environ. Microbiol. 69 (2003), pp. 7499-7506.
182. F. Azam, Microbial control of oceanic carbon flux: the plot Thickens, Sceince 280 (1998), pp. 694-696.
183. N. Chanishvili, T. Chanishvili, M. Tediashvili, and P.A. Barrow, Phages and their application against drug resistant bacteria, J. Chem. Tech. Biot. 76 (2001), pp. 689-699.
184. A. Dublanchet, Des virus pour combattre les infections. La phagothérapie: renouveau d'un traitement au secours des antibiotiques, Editions Favre, Lausanne, 2009, 237 p.
185. S. Jacquet, Infectiologie Bactérienne: quelle place pour la phagothérapie?, Virologie 12 (2008), pp. 1-3.
186. T. Nakai and S.C. Park, Bacteriophage therapy of infectious diseases in aquaculture, Res. Microbiol. 153 (2002), pp. 13-18.
187. S. Morrison and D.J. Rainnie, Bacteriophage therapy: an alternative to antibiotic therapy in aquaculture?, Can. Tech. Rep. Fish. Aquat. Sci. 2532 (2004), p. p. 23.
188. I. Karunasagar, N.M. Shivu, S.R. Girisha, G. Krohne, and I. Karunasagar, Biocontrol of pathogens in shrimp hatcheries using bacteriophage, Aquaculture 268 (2007), pp. 1-4.
189. A. Almeida, A. Cunha, N.C.M. Gomes, E. Alves, L. Costa, and M.A.F. Faustino, Phage therapy and photodynamic therapy: low environmental impact approaches to inactivate microorganisms in fish farming plants, Mar. Drugs 7 (2009), pp. 268-313.
190. R.S. Safferman and M.E. Morris, Control of algae with viruses, J. Ann. Water Works Assoc. 56 (1964), pp. 1217-1224.
191. M. Shilo, Biological agents which cause lysis of blue-green algae, Vehr. Int. Verein. Limnol. 19 (1971), pp. 206-213.
192. P.R. Desjardins, and G.B. Olson. Viral control of nuisance cyanobacteria (blue green algae). II. Cyanophage strains, stability studies of phages and hosts, and effects of environmental factors on phage-host interactions, California Water Resources Center, Contribution N°185, University of California, Davis, 1983.
193. E.L. Martin, and R. Benson, Phages of cyanobacteria, in The Bacteriophages, R. Calendar, ed., Vol. 2, Plenum Publish Corp, pp. 607-645.
194. E.J. Philips, R.L. Monegue, and F.J. Aldridge, Cyanophages which impact bloom-forming cyanobacteria, J. Aquat. Plant. Manage. 28 (1990), pp. 92-97.
195. K. Nagasaki, M. Ando, S. Itakura, I. Imai, and Y. Ishida, Viral mortality in the final stage of Heterosigma akashiwo (Raphidopyceae) red tide, J. Plank. Res. 16 (1994), pp. 1595-1599.
196. W.D. Paterson, R.J. Douglas, I. Grinyer, and L.A. McDermott, Isolation and preliminary characterization of some Aeromonas salmonicida bacteriophages, J. Fish. Res. Board Can. 26 (1969), pp. 629-632.
197. S. Imbeault, S. Parent, J.F. Blais, M. Lagacé, and C. Uhland, Utilisation de bactériophages pour contrôler les populations de Aeromonas salmonicida résistantes aux antibiotiques, J. Wat. Sci. 19 (2006), pp. 275-282.
198. J.L. Wu and W.J. Chao, Isolation and application of a new bacteriophage, ΦET-1, which infect Edwardsiella tarda, the pathogen of Edwardsiellosis, CAPD Fish Ser 8.
199. S.C. Park, I. Shimamura, M. Fukunaga, K.I. Mori, and T. Nakai, Isolation of bacteriophages specific to a fish pathogen, Pseudomonas plecoglossicida, as a candidate for disease control, Appl. Environ. Microbiol. 66 (2000), pp. 1416-1422.
200. S.C. Park and T. Nakai, Bacteriophage control of Pseudomonas plecoglossicida infection in ayu Plecoglossus altivelis, Dis. Aquat. Organ. 53 (2003), pp. 33-39.
201. D.W. Verner-Jeffreys, M. Algoet, M.J. Pond, H.K. Virdee, N.J. Bagwell, and E.G. Roberts, Furunculosis in Atlantic Salmon (Salmo Salar L.) is not readily controllable by bacteriophage therapy, Aquaculture 270 (2007), pp. 1-4.
202. A. Ronnest Stenholm, I. Dalsgaard, and M. Middelboe, Isolation and characterization of bacteriophages infecting the fish pathogen Flavobacterium psychophylum, Appl. Environ. Microbiol. 74 (2008), pp. 4070-4078.
203. C. Crothers-Stomps, L. Høj, D.G. Bourne, M.R. Hall, and L. Owens, Isolation of lytic bacteriophage against Vibrio harveyi, J. Appl. Microbiol. 105 (2009), pp. 2133-2142.
204. R. Weld, Bacteriophage on the menu, Pharm. Sci. Technol. Today 3 (2000), pp. 404-405.
205. K.E. Cerveny, A. Depaola, D.H. Duckworth, and P. Gulig, Phage therapy of local and systemic disease caused by Vibrio vulnificus in iron-dextran-treated mice, Infect. Immun. 70 (2002), pp. 6251-6262.
206. K.K. Jackson, R.L. Murphee, and M.L. Tamplin, Evidence that mortality from Vibrio vulnificus results from single strains among heterogeneous populations in shellfish, J. Clin. Microbiol. 35 (1997), pp. 2098-2101.
207. C.O. Tacket, F. Brenner, and P.A. Blake, Clinical features in an epidemiological study of Vibrio vulnificus infections, J. Infect. Dis. 149 (1984), pp. 558-567.
208. M. Teplitski and K. Ritchie, How feasible is the biological control of coral diseases?, Trends Ecol. Evol. 24 (2009), pp. 378-385.
209. R. Efrony, Y. Loya, E. Bacharach, and E. Rosenberg, Phage therapy of coral disease, Coral Reefs 26 (2007), pp. 7-13.
210. J. Bradbury, My enemy's enemy is my friend: using phages to fight bacteria, The Lancet 363 (2004), pp. 624-625.
211. C.B. Munn, Viruses as pathogens of marine organisms-from bacteria to whales, J. Mar. Biol. Ass. UK 86 (2006), pp. 453-467.
212. D. Secord, Biological control of marine invasive species: cautionary tables and land-based lessons, Biol. Inv. 5 (2003), pp. 117-131.
213. P. Peduzzi, and B. Luef, Viruses, In Encyclopedia of Inland Waters. Vol. 3, G.E. Likens, ed., Elsevier, Oxford, 2009, pp. 279-294.
214. C.R. Townsend, J.L. Harper, and M. Begon, Essentials of ecology. Blackwell Science, Malden, USA, 2000, p. 552.
215. S. Jiang, G. Steward, R. Jellison, W. Chu, and S. Choi, Abundance, distribution and diversity of viruses in alkaline, hypersaline Mono Lake, California, Microb. Ecol. 47 (2003), pp. 9-17.
216. U. Dorigo, S. Jacquet, and J.F. Humbert, Cyanophage diversity, inferred from g20 sequence analyses, in the largest French lake in France, Lake Bourget, Appl. Environ. Microbiol. 70 (2004), pp. 1017-1022.
217. S.W. Wilhelm, M.J. Carberry, M.L. Eldridge, L. Poorvin, M.A. Saxton, and M.A. Doblin, Marine and freshwater cyanophages in a Laurentian Great Lake: evidence from infectivity assays and molecular analyses of g20 genes, Appl. Environ. Microbiol. 72 (2006), pp. 4957-4963.
218. U.R. Fischer, C. Wiltschnig, A.K.T. Kirschner, and B. Velimirov, Contribution of virus-induced lysis and protozoan grazing to benthic bacterial mortality estimated simultaneously in microcosms, Environ. Microbiol. 8 (2006), pp. 1394-1407.
219. P. Peduzzi and B. Luef, Viruses, bacteria and suspended particles in a backwater and main channel site of the Danube (Austria), Aquat. Sci. 70 (2008), pp. 186-194.
220. B. Luef, F. Aspetsberger, T. Hein, F. Huber, and P. Peduzzi, Impact of hydrology on free living and particle-associated microorganisms in a river floodplain system (Danube, Austria), Freshw. Biol. 52 (2007), pp. 1043-1057.
221. L. Kernegger, I. Zweimüller, and P. Peduzzi, Effects of suspended matter quality and virus abundance on microbial parameters: experimental evidence from a large European river, Aquat. Microb. Ecol. 57 (2009), pp. 161-173.
222. J. Aristegui, J.M. Gasol, C.M. Duarte, and G.J. Herndl, Microbial oceanography of the dark ocean's pelagic realm, Limnol. Oceanogr. 54 (2009), pp. 1501-1529.
223. M.G. Weinbauer, I. Bettarel, R. Cattaneo, B. Luef, C. Maier, C. Motegi, P. Peduzzi, and X. Mari, Viral ecology of organic and inorganic particles in aquatic systems: avenues for further research, Aquat. Microb. Ecol. 57 (2009), pp. 321-341.
224. R. Danovaro, A. Dell'Anno, C. Corinaldesi, M. Magagnini, R. Noble, C. Tamburini, and M. Weinbauer, Major viral impact on the functioning of benthic deep-sea ecosystems, Nature 454 (2008), pp. 1084-1087.
225. A.S. Pradeep Ram, M. Sabart, D. Latour, and T. Sime-Ngando, Low effect of viruses on bacteria in deep anoxic water and sediment of a productive freshwater reservoir, Aquat. Microb. Ecol. 55 (2009), pp. 255-265.
226. M. Leroy, M. Prigent, M. Dutertre, F. Confalioneri, and M. Dubow, Bacteriophage morphotype and genome diversity in Seine River sediment, Fres. Biol. 53 (2008), pp. 1176-1185.
227. Y. Bettarel, M. Bouvy, C. Dumont, and T. Sime-Ngando, Virus-bacterium interactions in water and sediment of west African inland aquatic systems, Appl. Environ. Microbiol. 72 (2006), pp. 5274-5282.
228. M. Filippini, N. Buesing, Y. Bettarel, T. Sime-Ngando, and M.O. Gessner, Infection paradox: high abundance but low impact of freshwater benthic viruses, Appl. Environ. Microbiol. 72 (2006), pp. 4893-4898.
229. T.J. Battin, L.A. Kaplan, J.D. Newbold, and C.M.E. Hansen, Contributions of microbial biofilms to ecosystem processes in stream mesocosms, Nature 426 (2003), pp. 439-442.
230. I. Sutherland, K. Highes, L. Skillman, and K. Tait, The interaction of phage and biofilms, FEMS Microbiol. Lett. 232 (2004), pp. 1-6.
231. J.A. Flood and N.J. Ashbolt, Virus-sized particles are concentrated and maintained within wastewater wetland biofilms, Adv. Environ. Res. 3 (2000), pp. 403-411.
232. T.J. Battin, W.T. Sloan, S. Kjelleberg, H. Daims, I.M. Head, T.P. Curtis, and L. Eberl, Microbial landscapes: new paths to biofilm research, Nature Rev. 5 (2007), pp. 76-81.
233. X. Mari, M.-E. Kerros, and M.G. Weinbauer, Virus attachment to transparent exopolymeric particles along trophic gradients in the southwest lagoon of New Caledonia, Appl. Environ. Microbiol. 73 (2007), pp. 5245-5252.
234. C.A. Suttle and F. Chen, Mechanisms and rates of decay of marine viruses in seawater, Appl. Environ. Microbiol. 58 (1992), pp. 3721-3729.
235. M. Simon, H.-P. Grossart, B. Schweitzer, and H. Ploug, Microbial Ecology of organic aggregates in aquatic ecosystems, Aquat. Microb. Ecol. 28 (2002), pp. 175-211.
236. C. Brussaard, B. Kuipers, and M. Veldhuis, A mesocosm study of Phaeocystis globosa (Prymnesiophyceae) population dynamics. I. Regulatory role of viruses in bloom control, Harmf Alg. 4 (2005), pp. 859-874.
237. R.B. Kapuscinski and R. Michell, Processes controlling virus inactivation in coastal waters, Wat. Res. 14 (1980), pp. 363-371.
238. L. Riemann and H.-P. Grossart, Elevated lytic phage production as a consequence of particle colonization by a marine Flavobacterium (Cellulophaga sp.), Microb. Ecol. 56 (2008), pp. 505-512.
239. P. Peduzzi and M.G. Weinbauer, Effect of concentrating the virus-rich 2-200 nm size fraction of seawater on the formation of algal flocs (marine snow), Limnol. Oceanogr. 38 (1993), pp. 1562-1565.
240. R. Cattaneo, C. Rouvière, A. Malits, E. Sintes, G. Herndl, and M. Weinbauer, Black carbon: a new player structuring microbial processes in marine coastal waters, ASLO Aquat. Sci. Meeting, Nice (France), 2009, 25-29 January (abstract).
241. W.P. Cochlan, J. Wikner, G.F. Steward, D.C. Smith, and F. Azam, Spatial distribution of viruses, bacteria and chlorophyll a in neritic, oceanic and estuarine environments, Mar. Ecol. Progr. Ser. 92 (1993), pp. 77-87.
242. N. Guixa-Boixereu, D. Vaqué, J.M. Gasol, and C. Pedrós-Alió, Distribution of viruses and their potential effect on bacterioplankton in an oligotrophic marine system, Aquat. Microb. Ecol. 19 (1999), pp. 205-213.
243. N. Jiao, Y. Zhao, T. Luo, and X. Wang, Natural and anthropogenic forcing on the dynamics of virioplankton in the Yangtze River estuary, J. Mar. Biol. Ass. UK 86 (2006), pp. 543-550.
244. A. Maltis and M.G. Weinbauer, Effect of turbulence and viruses on prokaryotic cell size, production and diversity, Aquat. Microb. Ecol. 54 (2009), pp. 243-254.
245. R. Hendrix, Bacteriophage genomics, Curr. Opin. Microbiol. 6 (2003), pp. 506-511.
246. E.F. Delong, Archaea in coastal marine environments, Proc. Natl. Acad. Sci. USA 89 (1992), pp. 5685-5689.
247. L. Jardillier, D. Boucher, S. Personnic, S. Jacquet, A. Thénot, D. Sargos, C. Amblard, and D. Debroas, Relative importance of nutrients and mortality factors on prokaryotic community composition in two lakes of different trophic status: microcosm experiments, FEMS Microbiol. Ecol. 53 (2005), pp. 429-443.
248. S. Etien, C. Lepère, C. Mallet, G. Bronner, and D. Debroas, Structure of planktonic archaeal communities in the oxic zone of a mesotrophic lake (Lac du Bourget, France), J. Plank. Res. (2009).
249. A.F. Andersson and J.F. Banfield, Virus population dynamics and acquired virus resistance in natural microbial communities, Science 320 (2008), pp. 1047-1049.
250. T. Fenchel and R.N. Glud, Benthic primary production and O2-CO2 dynamic in a shallow water sediment: spatial and temporal heterogeneity, Ophelia 53 (2000), pp. 159-171.
251. M. Frada, I. Probert, M.J. Allen, W.H. Wilson, and C. de Vargas, The 'Cheshire cat' strategy of the coccolithophoride Emiliana huxleyi in response to viral infection, Proc. Nat. Acad. Sci. USA 105 (2008), pp. 15944-15948.
252. I. Hewson and J.A. Fuhrman, Covariation between viral parameters with bacterial assemblage richness and diversity in the water column and sediments, Deep-Sea Res. I 54 (2007), pp. 811-830.
253. S. Jacquet, Virus planctoniques: des tueurs très utiles!, Biofutur 213 (2001), pp. 57-61.
254. R.E. Lenski, Experimental studies of pleiotropy and epistaisis in Escherischia coli 1. Variation in competitive fitness among mutants resistant to virs-T4, Evolution 42 (1988), pp. 425-432.
255. M. Middelboe and P.G. Lyck, Regeneration of dissolved organic matter by viral lysis in marine microbial communities, Aquat. Microbial. Ecol. 27 (2002), pp. 187-194.
256. M. Middelboe, R.N. Glud, and K. Finster, Spatial distribution of viruses and relation to bacterial activity in coastal marine sediment, Limnol. Oceanogr. 48 (2006), pp. 1447-1456.
257. R.L. Monegue and E.J. Phlips, The effect of cyanophages on the growth and survival of Lyngbia wollei, Anabaena flos-aquae and Anabaena circinalis, J. Aquat. Plant Manage. 29 (1991), pp. 88-93.
258. J.H. Paul, M.F. DeFlaun, W.H. Jeffrey, and A.W. David, Seasonal and diel variability in dissolved DNA and in microbial biomass and activity in subtropical estuary, Appl. Environ. Microbiol. 54 (1988), pp. 718-727.
259. S. Personnic and S. Jacquet, Les virus: chefs d'orchestre aquatiques, La Recherche 407 (2007), pp. 50-53.
260. S. Ripp, O.A. Ogunseitan, and R.V. Miller, Transduction of a freshwater microbial community by a new Pseudomonas aeruginosa generalized transducing phage, UT1, Mol. Ecol. 3 (1994), pp. 121-126.
261. S. Ripp and R.V. Miller, Effects of suspended particulates on the frequency of transduction among Pseudomonas aeruginosa in a freshwater environment, Appl. Environ. Microbiol. 61 (1995), pp. 1214-1219.
262. D.J. Saye, O.A. Ogunseintan, G.S. Sayler, and R.V. Miller, Potential for transduction of plasmids in natural freshwater environment: effect of plasmid donor concentration and a natural microbial community on transduction in Pseudomonas aeruginosa, Environ. Microbiol. 53 (1987), pp. 987-995.
263. D.J. Saye, O.A. Ogunseintan, G.S. Sayler, and R.V. Miller, Transduction of linked chromosomal genes between Pseudomonas aeruginosa strains during incubation in situ in a freshwater habitat, Appl. Environ. Microbiol. 56 (1990), pp. 140-145.
264. C. Winter, A. Smit, G.J. Herndl, and M.G. Weinbauer, Impact of virioplankton on archaeal and bacterial community richness as assessed in seawater batch cultures, Appl. Environ. Microbiol. 70 (2004), pp. 804-813.
265. C. Winter, A. Smit, G.J. Herndl, and M.G. Weinbauer, Linking bacterial richness with viral abundance and prokaryotic activity, Limnol. Oceanogr. 50 (2005), pp. 968-977.
266. M.V. Zubkov and G.A. Tarran, High bacterivory by the smallest phytoplankton in the North Atlantic Ocean, Nature 455 (2008), pp. 224-227.
267. R.A. Spencer, Marine bacteriophages, Nature 175 (1955), pp. 690-691.
268. T. Nakai, R. Sugimoto, K.H. Park, S. Matsuoka, K. Mori, T. Nishioka, and K. Maruyama, Protective effects of bacteriophage on experimental Lactococcus garvisae infection in yellow-tail, Dis. Aquat. Org. 37 (1999), pp. 33-41.
269. M.G. Vinod, M.M. Shivu, K.R. Umesha, B.C. Rajeeva, G. Krohne, and I. Karunasagar, Isolation of Vibrio harveyi bacteriophage with a potential for biocontrol of luminous vibriosis in hatchery environments, Aquaculuture 255 (2006), pp. 117-124.