An investigation of the physiology and potential role of components of the deep ocean bacterial community (of the NE Atlantic) by enrichments carried out under minimal environmental change

Deep-Sea Research Part I: Oceanographic Research Papers

Volumn 61, Issue , 2012, Pages 11-20

  Egan, Simon T ^a   McCarthy, David M ^a   Patching, John W ^a   Fleming, Gerard T A ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

16S rDNA; Bacterial community; Deep sea; DGGE; Diversity; NE Atlantic; PCR; Pressure

Indexed keywords

16S RDNA; BACTERIAL COMMUNITY; DEEP-SEA; DGGE; DIVERSITY; PCR;

ELECTROPHORESIS; MICROBIOLOGY; NUTRIENTS; PRESSURE;

BACTERIA;

ATMOSPHERIC PRESSURE; AUTOCHTHON; BACTERIUM; COMMUNITY STRUCTURE; DEEP SEA; DEVELOPMENTAL BIOLOGY; DNA; ELECTROKINESIS; ENVIRONMENTAL CHANGE; GEL; GENETIC ANALYSIS; MAGNITUDE; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; PRESSURE EFFECT;

ATLANTIC OCEAN; ROCKALL TROUGH;

BACTERIA (MICROORGANISMS); BACTEROIDES; CYTOPHAGA; FLAVOBACTERIUM; OTUS; PROKARYOTA;

EID: 84857133544     PISSN: 09670637     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dsr.2011.11.005     Document Type: Article

References (92)

1. Achenbach L., Woese C. 16S and 23S rRNA-like primers. In Archaea: A Laboratory Manual 1995, 201-203. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. F.T. Robb, A.R. Place, K.R. Sowers, H.J. Schreier, S. DasSarma, E.M. Fleischmann (Eds.).
2. Acinas S.G., Rodríguez-Valera F., Pedrós-Alió C. Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiol. Ecol 1997, 24:27-40.
3. Agogué H., Lamy D., Neal P.R., Sogin M.L., Herndl G.J. Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Mol. Ecol. 2011, 20:258-274.
4. Alonso C., Pernthaler J. Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. EMI 2006, 8:2022-2030.
5. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
6. Aminot A., Kérouel R. Dissolved organic carbon, nitrogen and phosphorus in the N-E Atlantic and the N-W Mediterranean with particular reference to non-refractory fractions and degradation. Deep-Sea Res. I: Oceanographic Research Papers 2004, 51(12):1975-1999.
7. Bano N., Hollibaugh J.T. Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Arctic Ocean. Appl. Environ. Microbiol. 2000, 66:1960-1969.
8. Bianchi A., Garcin J., Tholosan O. A high-pressure serial sampler to measure microbial activity in the deep sea. Deep-Sea Res. I 1999, 46:2129-2142.
9. Bodungen B., Kahler P. Dissolved organic carbon in the Atlantic-seasonal and regional patterns. Eos, Trans., Am. Geophys. Union 1994, (Suppl. 75):106.
10. Brown M.V., Philip G.K., Bunge J.A., Smith M.C., Bissett A., Lauro F.M., Fuhrman J.A., Donachie S.P. Microbial community structure in the North Pacific Sea. ISME J. 2009, 3:1374-1386.
11. Bruggemann J., Stephen J.R., Chang Y.J., Macnaughton S.J., Kowalchuk G.A., Kline E., White D.C. Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy. J. Microbiol. Methods 2000, 40:111-123.
12. Casamayor E.O., Pedros-Alio C., Muyzer G., Amann R. Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations. Appl. Environ. Microbiol. 2002, 68:1706-1714.
13. Chastain R.A., Yayanos A.A. Ultrastructural changes in an obligately barophilic marine bacterium after decompression. Appl. Environ. Microbiol. 1991, 57:1489-1497.
14. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., Thompson J.D. Multiple sequence alignment with the clustal series of programs. Nucl. Acids Res. 2003, 31(13):3497-3500.
15. Cho J.C., Giovannoni D.J. Cultivation and characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl. Environ. Microbiol. 2004, 423-440.
16. Church M.J., Delong E.F., Ducklow H.W., Karner M.B., Preston C.M., Karl D.M. Abundance and distribution of planktonic Archaea and Bacteria in the waters west of the Antarctic Peninsula. Limnol. Oceanogr. 2003, 48(5):1893-1902.
17. Church M.J. The tropic tapestry of the sea. Proc. Natl. Acad. Sci. (USA) 2009, 15:15519-15520.
18. Cottrell M.T., Kirchman D.L. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 2000, 66:1692-1697.
19. Crump B.C., Kling G.W., Bahar M., Hobbie J.E. Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl. Environ. Microbiol. 2003, 69:2253-2268.
20. Danovaro R., Company J.B., Corinaldesi C., D'Onghia G., Galil B., Gambi C., Gooday A.J., Lampadariou N., Luna G.M., Morigi C., Olu K., Polymenakou P., Ramirez-Llodra E., Sabbatini A., Sard F., Sibuet M., Tselepides A. Deep-sea biodiversity in the Mediterranean Sea: the known, the unknown, and the unknowable. PLoS ONE 2010, 5(8):e11832.
21. De Long E.F., Franks D.G., Alldredge A.L. Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol. Oceanogr. 1993, 38:924-934.
22. De Long E.F., Franks D.G., Yayanos A.A. Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl. Environ. Microbiol. 1997, 63:2105-2108.
23. Deuser W.G. Seasonal and interannual variations in deep-water particle fluxes in the Sargasso Sea and their relation to surface hydrography. Deep-Sea Res. 1986, 33:225-246.
24. Eardly D.F., Carton M.W., Gallagher J.M., Patching J.W. Bacterial abundance and activity in deep-sea sediments from the eastern North Atlantic. Prog. Oceanogr. 2001, 50:245-259.
25. Etter R.J., Mullineaux L.S. Deep-sea communities. Marine Community Ecology 2001, 367-393. Sinauer Associates, Inc., Sunderlands, Massachusetts. M.D. Bertness, S.D. Gaines, M.E. Hay (Eds.).
26. Fang J., Zang L., Bazylinsky D.A. Deep-sea piezosphere and piezophiles: geomicrobiology and biochemistry. Trends Microbiol. 2010, 18:413-422.
27. Fellows D.A., Karl D.M., Knauer G.A. Large particle fluxes and the vertical transport of living carbon in the upper 1500m of the northeast Pacific Ocean. Deep-Sea Res. 1981, 28:921-936.
28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
29. Fuhrman J.A., Azam F. Adaptations of bacteria to marine subsurface waters studied by temperature response. Mar. Ecol. Prog. Ser. 1983, 13:95-98.
30. Fuhrman J.A. Microbial community structure and its functional implications. Nat. Rev. Insight 2009, 459:193-199.
31. Fuhrman J.A., Comeau D.E., Hagström Å., Chan A.M. Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl. Environ. Microbiol. 1988, 54:1426-1429.
32. Giovannoni, S.J., Rappe', M.S., Vergin, K.L., Adair, N.L., 1996. 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the green non-sulfur bacteria. In: The Proceedings of the National Academy of Sciences (USA), vol. 93, pp. 7979-7984.
33. Gómez-Pereira P.R., Fuchs B.M., Alonso C., Oliver M.J., van Beusekom J.E., Amann R. Distinct flavobacterial communities in contrasting water masses of the north Atlantic Ocean. ISME J. 2010, 4(4):472-487.
34. Grossart H.P., Gust G. Hydrostatic pressure affects physiology and community structure of marine bacteria during settling to 4000m: an experimental approach. Mar. Ecol.-Prog. Ser. 2009, 390:97-104.
35. Hansell D.A., Ducklow H.W. Bacterioplankton distribution and production in the bathypelagic ocean: directly coupled to particulate organic carbon export?. Limnol. Oceanogr. 2003, 48(1):150-156.
36. Hansell D.A., Carlson C.A., Repeta D.J., Schlitzer R. Dissolved organic matter in the ocean. A controversy stimulates new insights. Oceanography 2009, 22:202-211.
37. Herndl G.J., Reinthaler T., Teira E., van Aken H., Veth C., Pernthaler A., Pernthaler J. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 2005, 71:2303-2309.
38. Jannasch H.W., Wirsen C.O. Microbial activities in undecompressed microbial populations from the deep seawater samples. Appl. Environ. Microbiol. 1982, 43:1116-1124.
39. Jannasch H.W., Wirsen C.O. Variability of pressure adaptation in deep sea bacteria. Arch. Microbiol. 1984, 139:281-288.
40. Jiang H.C., Dong H.L., Ji S., Ye Y., Wu N.Y. Microbial diversity in the deep marine sediments from the Qiongdongnan Basin in South China Sea. Geomicrobiol. J. 2007, 24(6):505-517.
41. Kato C., Sato T., Horikoshi K. Isolation and properties of barophilic and barotolerant bactria from dep-sea mud samples. Biodiversity Conserv. 1995, 4:1-9.
42. Kato C., Li L., Nogi Y., Nakamura Y., Tamaoka J., Horikoshi K. Extremely barophilic bacteria isolated from the Mariana Trench, Challenger deep, at a depth of 11,000m. Appl. Environ. Microbial 1998, 64:1510-1513.
43. Katano T., Fukui M., Watanabe Y. Identification of cultured and uncultured picocyanobacteria from a mesotrophic freshwater lake based on the partial sequences of 16S rDNA. Limnology 2001, 2:213-218.
44. Kuznetsov S.L., Dubinia G.A., Lapteva N.A. Biology of oligotrophic bacteria. Annu. Rev. Microbiol. 1979, 33:377-387.
45. Lai X.T., Zeng X.F., Fang S., Huang Y.L., Cao L.X., Zhou S.N. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial community composition in deep-sea sediments of the South China Sea. World J. Microbiol. Biol. 2006, 22(12):1337-1345.
46. Langenheder S., Lindstrom E.S., Tranvik L.J. Weak coupling between community composition and functioning of aquatic bacteria. Limnol. Oceanogr. 2005, 50(3):957-967.
47. Li L., Kato C., Horikoshi K. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan. Trench. Mar. Biotechnol. 1999, 1(4):391-400.
48. Li L., Kato C., Horikoshi K. Bacterial diversity in deep-sea sediments from different depths. Biodiversity Conserv. 1999, 8(5):659-677.
49. Menezes C.B., Bonugli-Santos R.C., Miqueletto P.B., Passarini M.R., Silva C.H., Justo M.R., Leal R.R., Fantinatti-Garboggini F., Oliveira V.M., Berlinck R.G., Sette L.D. Microbial diversity associated with algae, ascidians and sponges from the north coast of São Paulo state, Brazil. Microbiol. Res. 2009, 165:466-482.
50. Moeseneder M.M., Winter C., Herndl G.J. 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. 2001, 46:95-107.
51. Murray A.E., Hollibaugh J.T., Orrego C. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 1996, 62:2676-2680.
52. Murray A.E., Preston C.M., Massana R., Taylor L.T., Blakis A., Wu K., DeLong E.F. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl. Environ. Microbiol. 1998, 64:2585-2595.
53. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
54. Nagata T., Tamburini C., Arìstegui J., Baltar F., Bochdansky A.B., Fonda-Umani S., Fukuda H., Gogou A., Hansell D.A., Hansman R.L., Herndl G.J., Panagiotopoulos C., Reinthaler T., Sohrin R., Verdugo P., Yamada N., Yamashita Y., Yokokawa T., Bartlett D.H. Emerging concepts on microbial processes in the bathypelagic ocean-ecology, biogeochemistry, and genomics. Deep Sea Res. II 2010, 57:1519-1536.
55. Nercessian O., Fouquet Y., Pierre C., Prieur D., Jeanthon C. Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge. EMI 2005, 7(5):698-714.
56. Ogawa H., Amagai Y., Koike I., Kaiser K., Benner R. Production of refractory dissolved organic matter by bacteria. Science 2001, 292(5518):917-920.
57. Oger P.M., Jebbar M. The many ways of coping with pressure. Res. Microbiol. 2010, 161(10):799-809.
58. Orcutt B., Sylvan J., Knab N., Katrina J., Edwards K.J. Microbial ecology of the Dark Ocean above, at, and below the seafloor. Microbiol. Mol. Biol. Rev. 2011, 75:361-422.
59. Park C.B., Clark D.S. Rupture of the cell envelope by decompression of the deep-sea methanogen Methanococcus jannaschii. Appl. Environ. Microbiol. 2002, 68:1458-1463.
60. Parkes R.J., Cragg B.A., Getliff J.M., Harvey S.M., Fry J.C., Lewis C.A., Rowland S.J. A quantitative study of microbial decomposition of biopolymers in recent sediments from the Peru Margin. Mar. Geol. 1993, 113:55-66.
61. Patching J.W., Eardly D. Bacterial biomass and activity in the deep waters of the eastern Atlantic-evidence of a barophilic community. Deep-Sea Res. I: Oceanogr. Res. Papers 1997, 44(9-10):1655-1670.
62. Polymenakou P.N., Bertilsson S., Tselepides A., Stephanou E.G. Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries. Microb. Ecol. 2005, 50(3):447-462.
63. Ramirez-Llodra E., Brandt A., Danovaro R., De Mol B., Escobar E., German C.R., Levin L.A., Martinez Arbizu, P., Menot L., Buhl-Mortensen P., Narayanaswamy B.E., Smith C.R., Tittensor D.P., Tyler P.A., Vanreusel A., Michael Vecchione Deep, diverse and definitely different: unique attributes of the world's largest ecosystem. Biogeosciences 2010, 7(9):2851-2899.
64. Riemann, L., Fandino, L.B., Steward, G.F., Smith, D.C., Ducklow, H.W., Azam, F., 1998. Variability of bacterial community composition in the Arabian Sea during the 1995 JGOFS program. EOS 79: OS 68.
65. Riemann L., Steward G.F., Fandino L.B., Campbell L., Landry M.R., Azam F. Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes. Deep-Sea Res. 1999, 46:1791-1811.
66. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
67. Sheffield V.C., Cox D.R., Lerman L.S., Myers R.M. Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. (USA) 1989, 86:232-236.
68. Schut F., Prins R.A., Gottschal J.C. Oligotrophy and pelagic marine bacteria: facts and fiction. Aquat. Microbiol. Ecol. 1997, 12:177-202.
69. Sigler W.V., Zeyer M.J. Electrophoresis time impacts the denaturing gradient gel electrophoresis-based assessment of bacterial community structure. J. Microbiol. Meth. 2004, 57:17-22.
70. Swan B.K., Martinez-Garcia M., Preston C.M., Sczyrba A., Woyke T., Lamy D., Reinthaler T., Poulton N.J., Masland E.D., Gomez M.L., Sieracki M.E., DeLong E.F., Herndl G.J., Stepanauskas R. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 2011, 333(6047):1296-1300.
71. Snelgrove P.V.R., Smith C.R. A riot of species in an environmental calm: the paradox of the species-rich deep-sea. Oceanogr. Mar. Biol. 2002, 40:311-342.
72. Steinberg D.K., Van Mooy B.A.S., Buesseler K.O., Boyd P.W., Kobari T., Karl D.M. Bacterial vs. zooplankton control of sinking particle flux in the ocean's twilight zone. Limnol. Oceanogr. 2008, 53(4):1327-1338.
73. Stuart C.T., Rex M.A., Etter R.J. Large-scale spatial and temporal patterns of deepsea benthic species diversity. Ecosystems of the Deep Oceans. 10 Ecosystems of the World 2003, 295-313. Elsevier, Amsterdam. P.A. Tyler (Ed.).
74. Tabor P.S., Deming J.W., Ohwada K., Davis H., Waxman M., Colwell R.R. A pressure-retaining deep ocean sampler and transfer system for measurement of microbial activity in the deep sea. Microb. Ecol. 1981, 7:51-65.
75. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, In press. http://10.1093/molbev/msr121.
76. Tamburini C., Garcin J., Bianchi A. Role of deep-sea bacteria in organic matter mineralization and adaptation to hydrostatic pressure conditions in the NW Mediterranean Sea. Aquat. Microb. Ecol. 2003, 32(3):209-218.
77. Tamburini C., Garcin J., Grégori G., Leblanc K., Rimmelin P., Kirchman D.L. Pressure effects on surface Mediterranean prokaryotes and biogenic silica dissolution during a diatom sinking experiment. Aquat. Microb. Ecol. 2006, 43(3):267-276.
78. Turley C.M., Lochte K. Microbial response to the input of fresh detritus to the deep-sea bed. Palaeogeogr. Palaeoclimatogr. Palaeoecol. 1990, 89:3-23.
79. Turley C.M., Lochte K., Lampitt R.S. Transformations of biogenic particles during sedimentation in the Northeastern Atlantic. Phil. Trans. Roy. Soc. London Ser. B-Biol. Sci. 1995, 348(1324):179-189.
80. Tyagi A., Saravanan V., Karunasagar I., Karunasagar I. Detection of Vibrio parahaemolyticus in tropical shellfish by SYBR green real-time PCR and evaluation of three enrichment media. Int. J. Food Microbiol. 2009, 129:124-130.
81. Wright T.D., Vergin K.L., Boyd P.W., Giovannoni S.J. A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer. Appl. Environ. Microbiol. 1997, 63:1441-1448.
82. Xu Y., Nogi Y., Kato C., Liang Z.Y., Ruger H.J., De Kegel D., Glansdorff N. Moritella profunda sp nov and Moritella abyssi sp nov., two psychropiezophilic organisms isolated from deep Atlantic sediments. Int. J. Syst. Evol. Microbiol. 2003, 53:533-538.
83. Xu M.X., Wang P., Wang F.P., Xiao X. Microbial diversity at a deep-sea station of the Pacific nodule province. Biodiversity Conserv. 2005, 14(14):3363-3380.
84. Xu M.X., Wang F.P., Meng J., Xiao X. Construction and preliminary analysis of a metagenomic library from a deep-sea sediment of east Pacific Nodule Province. FEMS Microbiol. Ecol. 2007, 62:233-241.
85. Yayanos, A.A. 1998. Empirical and Theoretical Aspects of Life at High Pressure in the Deep Sea. Extremophiles. Microbial life in Extreme Environments.Wiley and Sons, Inc., New York. p. 47-92.
86. Yayanos A.A., Dietz A.S., Van Boxtel R. Isolation of a deep-sea barophilic bacterium and some of its growth characteristics. Science 1979, 205:808-810.
87. Yayanos A.A., Dietz A.S. Thermal inactivation of a deep-sea barophilic bacterium, isolate CNPT-3. Appl. Environ. Microbiol. 1982, 43:1481-1489.
88. Yayanos A.A., Dietz A.S. Death of a Hadal deep-sea bacterium after decompression. Science 1983, 220:497-498.
89. Yokokawa T., Nagata T. Linking bacterial community structure to carbon fluxes in marine environments. J. Oceanogr. 2010, 66:1-12.
90. Zhang X., Yao T., An L., Tian L., Xu S. A study on the vertical profile of bacterial DNA structure in the Puruogangri (Tibetan Plateau) ice core using denaturing gradient gel electrophoresis. Ann. Glaciol. 2006, 43(160-166):2006.
91. Zobell C.E. Apparatus for collecting water samples from different depths for bacteriological analysis. J. Mar. Res. 1941, 4:173-188.
92. ZoBell C.E., Anderson D.Q. Observations on the multiplication of bacteria in different volumes of sea water and the influence of oxygen tension and solid surfaces. Biol. Bull. (Woods Hole) 1936, 71:324-342.