Interactive effects of viral and bacterial production on marine bacterial diversity

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Motegi, Chiaki ^a,b,c,d   Nagata, Toshi ^a,b   Miki, Takeshi ^e   Weinbauer, Markus G ^c,d   Legendre, Louis ^c,d   Rassoulzadegan, Fereidoun ^c,d  

^a UNIVERSITY OF TOKYO   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c SORBONNE UNIVERSITÉ   (France)

^d LABORATOIRE D OCÉANOGRAPHIE DE VILLEFRANCHE   (France)

^e NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PHOSPHATE; RNA 16S; SEA WATER;

16S RRNA GENE; ARTICLE; BACTERIAL GROWTH; CONTROLLED STUDY; GENE AMPLIFICATION; INCUBATION TIME; MARINE ENVIRONMENT; MEDITERRANEAN SEA; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MORTALITY; NONHUMAN; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEASONAL VARIATION; VIROGENESIS;

AQUATIC ORGANISMS; BACTERIA; BIODIVERSITY; SEAWATER; VIRUSES; WATER MICROBIOLOGY;

EID: 84892427303     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0076800     Document Type: Article

References (46)

1. Motegi C, Nagata T, Miki T, Weinbauer MG, Legendre L, et al. (2009) Viral control of bacterial growth efficiency in marine pelagic environments. Limnol Oceanogr 54: 1901-1910.
2. Suttle CA (2007) Marine viruses-major players in the global ecosystem. Nat Rev Microbiol 5: 801-812.
3. Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Environ Microbiol 6: 1-11.
4. Winter C, Bouvier T, Weinbauer MG, Thingstad TF (2010) Trade-offs between competition and defense specialists among unicellular planktonic organisms: the "Killing the Winner" hypothesis revisited. Microbiol Mol Biol Rev 74: 42-57.
5. Thingstad TF, Lignell R (1997) Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat Microb Ecol 13: 19-27.
6. Thingstad TF (2000) Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol Oceanogr 45: 1320-1328.
7. Fuhrman JA, Schwalbach MS (2003) Viral influence on aquatic bacterial communities. Biol Bull 204: 192-195.
8. Zhang R, Weinbauer MG, Qian PY (2007) Viruses and flagellates sustain apparent richness and reduce biomass accumulation of bacterioplankton in coastal marine waters. Environ Microbiol 9: 3008-3018.
9. Hewson I, Fuhrman JA (2007) Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments. Deep-Sea Res Pt I 54: 811-830.
10. Schwalbach MS, Hewson I, Fuhrman JA (2004) Viral effects on bacterial community composition in marine plankton microcosms. Aquat Microb Ecol 34: 117-127.
11. Winter C, Smit A, Herndl GJ, Weinbauer MG (2004) Impact of virioplankton on archaeal and bacterial community richness as assessed in seawater batch cultures. Appl Environ Microbiol 70: 804-813.
12. Thingstad TF, Ovreas L, Egge JK, Lovdal T, Heldal M (2005) Use of non-limiting substrates to increase size; a generic strategy to simultaneously optimize uptake and minimize predation in pelagic osmotrophs? Ecol Lett 8: 675-682.
13. Connell JH (1978) Diversity in tropical rain forests and coral reefs. Science 199: 1302-1310.
14. Proulx M, Mazumder A (1998) Reversal of grazing impact on plant species richness in nutrient-poor vs. nutrient-rich ecosystems source. Ecology 79: 2581-2592.
15. Kondoh M (2001) Unifying the relationships of species richness to productivity and disturbance. Proc R Soc Lond B 268: 269-271.
16. Sousa WP (1984) The role of disturbance in natural communities. Annu Rev Ecol Syst 15: 353-391.
17. Huston M (1979) A general hypothesis of species diversity. Am Nat 113: 81-101.
18. Avaniss-Aghajani E, Jones K, Chapman D, Brunk CA (1994) A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. BioTechniques 17: 144-146, 148-149.
19. Kirchman DL (2001) Measuring of bacterial biomass production and growth rates from leucine incorporation in natural aquatic environment. In: Paul JH, editor. Methods in Microbiology. San Diego: Academic Press. pp. 227-237.
20. Wilhelm SW, Brigden SM, Suttle CA (2002) A dilution technique for the direct measurement of viral production: A comparison in stratified and tidally mixed coastal waters. Microb Ecol 43: 168-173.
21. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, et al. (1994) Current protocols in molecular biology. New York, NY: Wiley Interscience.
22. Moeseneder MM, Winter C, Herndl GJ (2001) Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints. Limnol Oceanogr 46: 95-107.
23. Ludwig JA, Reynolds JF (1988) Statistical ecology - A primer on methods and computing. New York: John Wiley and Sons. 337 p.
24. Zuur AF, Ieno EN, Walker NJ, Saveliev AA, Smith GM (2009) Mixed effects models and extension in Ecology with R. New York: Springer Science+Business Media, LLC. 574 p.
25. R Development Core Team (2011) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
26. Azam F, Malfatti F (2007) Microbial structuring of marine ecosystems. Nat Rev Microbiol 5: 782-791.
27. Weinbauer MG, Hornak K, Jezbera J, Nedoma J, Dolan JR, et al. (2007) Synergistic and antagonistic effects of viral lysis and protistan grazing on bacterial biomass, production and diversity. Environ Microbiol 9: 777-788.
28. von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
29. Moyer CL, Tiedje JM, Dobbs FC, Karl DM (1996) A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl Environ Microbiol 62: 2501-2507.
30. Abrams PS (1995) Monotonic or unimodal diversity-productivity gradients: What does competition theory predict? Ecology 76: 2019-2027.
31. Jürgens K, Massana R (2008) Protistan grazing on marine bacterioplankton. In: Kirchman DL, editor. Microbial Ecology of the Ocean. 2nd edition ed. New York: Wiley-Liss. pp. 383-441.
32. Jara VC, Henrique J, Miyamoto S, da Gama BAP, Molis M, et al. (2006) Limited evidence of interactive disturbance and nutrient effects on the diversity of macrobenthic assemblages. Mar Ecol Prog Ser 308: 37-48.
33. Svensson JR, Lindegarth M, Siccha M, Lenz M, Molis M, et al. (2007) Maximum species richness at intermediate frequencies of disturbance: consistency among levels of productivity. Ecology 88: 830-838.
34. Worm B, Lotze HK, Hillebrand H, Sommer U (2002) Consumer versus resource control of species diversity and ecosystem functioning. Nature 417: 848-851.
35. Kassen R, Llewellyn M, Rainey PB (2004) Ecological constraints on diversification in a model adaptive radiation. Nature 431: 984-988.
36. Jiang SC, Paul JH (1996) Occurrence of lysogenic bacteria in marine microbial communities as determined by prophage induction. Mar Ecol Prog Ser 142: 27-38.
37. Hewson I, Fuhrman JA (2007) Characterization of lysogens in bacterioplankton assemblages of the southern California borderland. Microb Ecol 53: 631-638.
38. Weinbauer MG, Brettar I, Höfle MG (2003) Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters. Limnol Oceanogr 48: 1457-1465.
39. Bouvier T, del Giorgio PA (2007) Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol 9: 287-297.
40. de Wit R, Bouvier T (2006) "Everything is everywhere, but, the environment selects"; what did Baas Becking and Beijerinck really say? Environ Microbiol 8: 755-758.
41. Miki T, Yokokawa T, Nagata T, Yamamura N (2008) Immigration of prokaryotes to local environments enhances remineralization efficiency of sinking particles: a metacommunity model. Mar Ecol Prog Ser 366: 1-14.
42. Sintes E, Witte H, Stodderegger K, Steiner P, Herndl GJ (2013) Temporal dynamics in the free-living bacterial community composition in the coastal North Sea. FEMS Microbiol Ecol 83: 413-424.
43. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
44. Middelboe M, Holmfeldt K, Riemann L, Nybroe O, Haaber J (2009) Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties. Environ Microbiol 11: 1971-1982.
45. Lennon JT, Khatana SAM, Marston MF, Martiny JBH (2007) Is there a cost of virus resistance in marine cyanobacteria? ISME J 1: 300-312.
46. Kadmon R, Benjamini Y (2006) Effects of productivity and disturbance on species richness: a neutral model. Am Nat 167: 939-946.