Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

ISME Journal

Volumn 4, Issue 11, 2010, Pages 1431-1442

  De Corte, Daniele ^a,b   Sintes, Eva ^a   Winter, Christian ^c   Yokokawa, Taichi ^a   Reinthaler, Thomas ^c   Herndl, Gerhard J ^a,c  

^a ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c UNIVERSITY OF VIENNA   (Austria)

Author keywords

atlantic; deep sea; prokaryotes; romanche fracture zone; viruses

Indexed keywords

ARCHAEAL DNA; BACTERIAL DNA; SEA WATER; VIRUS DNA;

ABUNDANCE; BIOLOGICAL PRODUCTION; DEEP SEA; FRACTURE ZONE; HETEROTROPHY; PROKARYOTE; SPECIES DIVERSITY; VIRUS; WATER COLUMN;

ARCHAEBACTERIUM; ARTICLE; ATLANTIC OCEAN; BACTERIAL LOAD; BACTERIUM; BIODIVERSITY; CLASSIFICATION; CLUSTER ANALYSIS; DNA FINGERPRINTING; GENETIC POLYMORPHISM; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; METAGENOME; MICROBIOLOGY; RANDOM AMPLIFIED POLYMORPHIC DNA; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; TROPIC CLIMATE; VIROLOGY; VIRUS; VIRUS LOAD;

ARCHAEA; ATLANTIC OCEAN; BACTERIA; BACTERIAL LOAD; BIODIVERSITY; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, VIRAL; GENOTYPE; METAGENOME; POLYMORPHISM, GENETIC; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; SEAWATER; TROPICAL CLIMATE; VIRAL LOAD; VIRUSES;

ATLANTIC OCEAN; ATLANTIC OCEAN (SUBTROPICAL);

ARCHAEA; BACTERIA (MICROORGANISMS); OTUS; PROKARYOTA;

EID: 77958478635     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.65     Document Type: Article

References (58)

1. Ackermann HW, DuBow MS. (1987). Viruses of prokaryotes. In: General Properties of Bacteriophages. CRC, Boca Raton, FL, USA, Vol 1.
2. Allen EE, Bartlett DH. (2002). Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology 148: 1903-1913.
3. Allen EE, Facciotti D, Bartlett DH. (1999). Monounsaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium photobacterium profundum SS9 at high pressure and low temperature. Appl Environ Microbiol 65: 1710-1720.
4. Anderson MJ, Ford RB, Feary DA, Honeywill C. (2004). Quantitative measures of sedimentation in an estuarine system and its relationship with intertidal soft-sediment infauna. Mar Ecol-Prog Ser 272: 33-48.
5. Aristegui J, Gasol JM, Duarte CM, Herndl GJ. (2009). Microbial oceanography of the dark ocean's pelagic realm. Limnol Oceanog 54: 1501-1529.
6. Avaniss-Aghajani E, Jones K, Chapman D, Brunk C. (1994). A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences. BioTechniques 17: 144-149. (Pubitemid 2114974)
7. Borneman J, Triplett EW. (1997). Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63: 2647-2653.
8. Bouvier T, del Giorgio PA. (2007). Key role of selective viral-induced mortality in determining marine bacterial community composition. Environ Microbiol 9: 287-297.
9. Breitbart M, Middelboe M, Rohwer F. (2008). Marine viruses: community dynamics, diversity and impact on microbial processes. In: Kirchmam DL (ed). Microbial Ecology of the Oceans. John Wiley & Sons Inc.: Hoboken, NJ, USA, pp 443-479.
10. Brussaard CPD. (2004). Optimization of procedures for counting viruses by flow cytometry. Appl Environ Microbiol 70: 1506-1513.
11. Cardinale M, Brusetti L, Quatrini P, Borin S, Puglia AM, Rizzi A et al. (2004). Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70: 6147-6156.
12. Danovaro R, Luna GM, Dell-Anno A, Pietrangeli B. (2006). Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. Appl Environ Microbiol 72: 5982-5989.
13. De Corte D, Yokokawa T, Varela MM, Agogue H, Herndl GJ. (2009). Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eaastern Mediterranean Sea. ISME J 3: 147-158.
14. Del Giorgio PA, Bird DF, Prairie YT, Planas D. (1996). Flow cytometric determination of bacterial abundance in lake plankton with the green nucleic acid stain SYTO 13. Limnol Oceanogr 41: 783-789.
15. DeLong EF. (1992). Archaea in coastal marine environments. Proc Natl Acad Sci USA 89: 5685-5689.
16. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N-U et al. (2006). Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
17. Fisher MM, Triplett EW. (1999). Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65: 4630-4636.
18. Fuhrman JA. (1999). Marine viruses and their biogeochemical and ecological effects. Nature 399: 541-548.
19. Fuhrman JA. (2000). Impact of viruses on bacterial processes. In: Kirchmam DL (ed). Microbial Ecology of the Oceans. Wiley-Liss Inc.: Hoboken, NJ, USA, pp 327-350.
20. Hammer Ø., Harper DAT, Ryan PD (2001). PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4: 9 pp.
21. Hara S, Koike I, Terauchi K, Kamiya H, Tanoue E. (1996). Abundance of viruses in deep oceanic waters. Mar Ecol Prog Ser 145: 269-277.
22. Herndl GJ, Agogue H, Baltar F, Reinthaler T, Sintes E, Varela MM. (2008). Regulation of aquatic microbial processes: the A 0microbial loop0 of the sunlit surface waters and the dark ocean dissected. Aquat Microb Ecol 53: 59-68.
23. Holmfeldt K, Middelboe M, Nybroe O, Riemann L. (2007). Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Appl Environ Microbiol 73: 6730-6739.
24. Kent AD, Jones SE, Yannarell AC, Graham JM, Lauster GH, Kratz TK et al. (2004). Annual patterns in bacterioplankton community variability in a humic lake. Microb Ecol 48: 550-560.
25. Kimmance SA, Wilson WH, Archer SD. (2007). Modified dilution technique to estimate viral versus grazing mortality of phytoplankton: limitations associated with method sensitivity in natural waters. Aquat Microb Ecol 49: 207-222.
26. Klieve AV, Bauchop T. (1988). Morphological diversity of ruminal bacteriophages from sheep and cattle. Appl Environ Microbiol 54: 1637-1641.
27. Larsen A, Castberg T, Sandaa RA, Brussaard CPD, Egge J, Heldal M et al. (2001). Population dynamics and diversity of phytoplankton, bacteria and viruses in a seawater enclosure. Mar Ecol Prog Ser 221: 47-57.
28. Lauro FM, Bartlett DH. (2008). Prokaryotic lifestyles in deep sea habitats. Extremophiles 12: 15-25.
29. Lee S, Fuhrman JA. (1987). Relationships between biovolume and biomass of naturally-derived marine bacterioplankton. Appl Environ Microbiol 53: 1298-1303.
30. Magagnini M, Corinaldesi C, Monticelli LS, De Domenico E, Danovaro R. (2007). Viral abundance and distribution in mesopelagic and bathypelagic waters of the mediterranean sea. Deep-Sea Research Part I-Oceanographic Research Papers 54: 1209-1220.
31. Marie D, Brussaard CPD, Thyrhaug R, Bratbak G, Vaulot D. (1999). Enumeration of marine viruses in culture and natural samples by flow cytometry. Appl Environ Microbiol 65: 45-52.
32. Moeseneder MM, Winter C, Arrieta JM, Herndl GJ. (2001a). Terminal-restriction fragment length polymorphism (T-RFLP) screening of a marine archaeal clone library to determine the different phylotypes. J Microbiol Methods 44: 159-172.
33. Moeseneder MM,Winter C, Herndl GJ. (2001b). 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.
34. Murray AG, Jackson GA. (1992). Viral dynamics: a model of the effects size, shape, motion and abundance of single-celled planktonic organisms and other particles. Mar Ecol Prog Ser 89: 103-116.
35. Noble RT, Fuhrman JA. (1998). Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol 14: 113-118.
36. Ortmann AC, Lawrence JE, Suttle CA. (2002). Lysogeny and lytic viral production during a bloom of the cyanobacterium synechococcus spp. Microb Ecol 43: 225-231.
37. Pan LA, Zhang J, Zhang LH. (2007). Picophytoplankton, nanophytoplankton, heterotrohpic bacteria and viruses in the Changjiang Estuary and adjacent coastal waters. J Plankton Res 29: 187-197.
38. Parada V, Sintes E, van Aken HM, Weinbauer MG, Herndl GJ. (2007). Viral abundance, decay, and diversity in the meso- and bathypelagic waters of the North Atlantic. Appl Environ Microbiol 73: 4429-4438.
39. Reinthaler T, van Aken H, Veth C, Aristegui J, Robinson C, Williams PJLR et al. (2006). Prokaryotic respiration and production in the meso- and bathypelagic realm of the eastern and western North Atlantic basin. Limnol Oceanogr 51: 1262-1273.
40. Rohwer F. (2003). Global phage diversity. Cell 113: 141-141
41. Sano E, Carlson S, Wegley L, Rohwer F. (2004). Movement of viruses between biomes. Appl Environ Microbiol 70: 5842-5846.
42. Simon M, Azam F. (1989). Protein content and protein synthesis rates of planktonic marine bacteria. Mar Ecol Prog Ser 51: 201-213.
43. Sullivan MB, Waterbury JB, Chisholm SW. (2003). Cyanophages infecting the oceanic Cyanobacterium Prochlorococcus. Nature 424: 1047-1051.
44. Suttle CA. (1999). Do viruses control the oceans? Nat History 108: 48-51.
45. 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.
46. 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.
47. Weinbauer MG. (2004). Ecology of prokaryotic viruses. FEMS Microbiol Rev 28: 127-181.
48. Weinbauer MG, Brettar I, Hofle MG. (2003). Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic marine waters. Limnol Oceanogr 48: 1457-1465.
49. Weinbauer MG, Rassoulzadegan F. (2004). Are viruses driving microbial diversification and diversity? Environ Microbiol 6: 1-11.
50. 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. Microbial Ecol 43: 168-173.
51. Wilhelm SW, Suttle CA. (1999). Viruses and nutrient cycles in the sea-viruses play critical roles in the structure and function of aquatic food webs. Bioscience 49: 781-788.
52. Winget DM, Wommack KE. (2008). Randomly amplified polymorphic DNA PCR as a tool for assessment of marine viral richness. Appl Environ Microbiol 74: 2612-2618.
53. Winter C, Herndl GJ, Weinbauer MG. (2004a). Diel cycles in viral infection of bacterioplankton in the North Sea. Aquat Microb Ecol 35: 207-216.
54. Winter C, Moeseneder MM, Herndl GJ,Weinbauer MG. (2008). Relationship of geographic distance, depth, temperature, and viruses with prokaryotic communities in the eastern tropical Atlantic Ocean. Microb Ecol 56: 383-389.
55. Winter C, Smit A, Herndl GJ, Weinbauer MG. (2004b). Impact of virioplankton on archaeal and bacterial community richness assessed in seawater batch cultures. Appl Environ Microbiol 70: 804-813.
56. Winter C, Smit A, Herndl GJ, Weinbauer MG. (2005). Linking prokaryotic richness with viral abundance and prokaryotic activity. Limnol Oceanogr 50: 968-977.
57. Wommack KE, Ravel J, Hill RT, Chun JS, Colwell RR. (1999a). Population dynamics of Chesapeake bay virioplankton: total-community analysis by pulsed-field gel electrophoresis. Appl Environ Microbiol 65: 231-240.
58. Wommack KE, Ravel J, Hill RT, Colwell RR. (1999b). Hybridization analysis of Chesapeak Bay virioplankton. Appl Environ Microbiol 65: 241-250.