Cultivation-independent assessment of the bathypelagic archaeal diversity of Tyrrhenian Sea: Comparative study of rDNA and rRNA-derived libraries and influence of sample decompression

Deep-Sea Research Part II: Topical Studies in Oceanography

Volumn 56, Issue 11-12, 2009, Pages 768-773

  La Cono, Violetta ^a   Tamburini, Christian ^b   Genovese, Lucrezia ^a   Spada, Gina La ^a   Denaro, Renata ^a   Yakimov, Michail M ^a  

^a CNR   (Italy)

^b AIX MARSEILLE UNIVERSITY   (France)

Author keywords

16S rRNA; Crenarchaeota Marine Group I; Deep Tyrrhenian Sea; Euryarchaeota Marine Group II; Phylogeny

Indexed keywords

16S RRNA; CRENARCHAEOTA MARINE GROUP I; DEEP TYRRHENIAN SEA; EURYARCHAEOTA MARINE GROUP II; PHYLOGENY;

DNA; GENES; LIBRARIES; RNA; SAMPLING; SEAWATER;

NUCLEIC ACIDS;

BACTERIOPLANKTON; COMPARATIVE STUDY; DEEP-SEA ORGANISM; DNA; PELAGIC ENVIRONMENT; PHYLOGENY; RNA;

MEDITERRANEAN SEA; TYRRHENIAN SEA;

ARCHAEA; CRENARCHAEOTA; EURYARCHAEOTA; MARINE GROUP II;

EID: 67349114821     PISSN: 09670645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dsr2.2008.07.025     Document Type: Article

References (40)

1. Acinas S.G., Antón J., and Rodríguez-Valera F. Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA. Applied and Environmental Microbiology 65 (1999) 514-522
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 25 (1997) 3389-3402
3. Bianchi A., Garcin J., and Tholosan O. Effects of hydrostatic pressure on microbial activity through a 2000 m deep water column in the NW Mediterranean Sea. Marine Ecology Progress Series 183 (1999) 49-57
4. DeLong, E.F., 1992. Archaea in coastal marine environments. In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, pp. 5685-5689.
5. DeLong E.F., Franks D.G., and Alldredge A.L. Phylogenetic diversity of aggregate-attached vs. free-living marine bacteria assemblages. Limnology and Oceanography 38 (1993) 924-934
6. DeLong E.F., Preston C.M., Mincer T., Rich V., Hallam S.J., Frigaard N.U., Martinez A., Sullivan M.B., Edwards R., Brito B.R., Chisholm S.W., and Karl D.M. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311 (2006) 496-503
7. Felske A., Rheims H., Wolterin k.A., Stackebrandt E., and Akkermans A.D. Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology 143 (1997) 2983-2989
8. Frigaard N.U., Martinez A., Mincer T.J., and DeLong E.F. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 439 (2006) 847-850
9. Fuhrman J.A., Mccallum K., and Davis A.A. Novel major archaebacterial group from marine plankton. Nature 356 (1992) 148-149
10. Gentile G., Giuliano L., D'Auria G., Smedile F., Azzaro M., De Domenico M., and Yakimov M.M. Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing. Environmental Microbiology 8 (2006) 2150-2161
11. Gillan D., and Danis B. The archaebacterial communities in Antarctic bathypelagic sediments. Deep-Sea Research II 54 (2007) 1682-1690
12. Good I.J. The population frequencies of species and the estimation of the population parameters. Biometrika 40 (1953) 237-264
13. Hallam S.J., Girguis P.R., Preston C.M., Richardson P.M., and DeLong E.F. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Applied Environmental Microbiology 69 (2003) 5483-5491
14. Hallsworth J.E., Yakimov M.M., Golyshin P.N., Gillion J.L., D'Auria G., de Lima A.F., La Cono V., Genovese M., McKew B., Hayes S.L., Harris G., Giuliano L., Timmis K.N., and McGenity T.J. Limits of life in MgCl2-containing environments: Chaotropicity defines the window. Environmental Microbiology 9 (2007) 801-813
15. Karner M.B., DeLong E.F., and Karl D.M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409 (2001) 507-510
16. Kendall M.M., Wardlaw G.D., Tang C.F., Bonin A.S., Liu Y., and Valentine D.L. Diversity of Archaea in marine sediments from Skan Bay, Alaska, including cultivated methanogens, and description of Methanogenium boonei sp. nov. Applied and Environmental Microbiology 73 (2007) 407-414
17. Lauro F.M., and Bartlett D.H. Prokaryotic lifestyles in deep sea habitats. Extremophiles 12 (2008) 15-25
18. Lauro F.M., Chastain R.A., Blankenship L.E., Yayanos A.A., and Bartlett D.H. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Applied and Environmental Microbiology 73 (2007) 838-845
19. Martin-Cuadrado A.-B., Lòpez-Garcia P., Alba J.-C., Moreira D., Monticelli L., Srittmatter A., Gottschalk G., and Rodriguez-Valera F. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. Public Library of Science One 9 (2007) e914
20. Mills H.J., Martinez R.M., Story S., and Sobecky P. Identification of members of the metabolically active microbial populations associated with Beggiatoa species mat communities from Gulf of Mexico cold-seep sediments. Applied and Environmental Microbiology 70 (2004) 5447-5458
21. Mills H.J., Martinez R.J., Story S., and Sobecky P.A. Characterization of microbial community structure in Gulf of Mexico gas hydrates: Comparative analysis of DNA- and RNA-derived clone libraries. Applied and Environmental Microbiology 71 (2005) 3235-3247
22. Mincer T.J., Church M.J., Taylor L.T., Preston C., Karl D.M., and DeLong E.F. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environmental Microbiology 9 (2007) 116-1175
23. Miskin I.P., Farrimond P., and Head I.M. Identification of novel bacterial lineages as active members of microbial populations in a freshwater sediment using a rapid RNA extraction procedure and RT-PCR. Microbiology 145 (1999) 1977-1987
24. Moeseneder M.M., Arrieta J.M., and Herndl G.J. A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community. FEMS Microbiology Ecology 51 (2005) 341-352
25. Nogales B., Moore E.R., Abraham W.R., and Timmis K.N. Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. Environmental Microbiology 1 (1999) 199-212
26. Olsen G.J., Lane D.J., Giovannoni S.J., Pace N.R., and Stahl D.A. Microbial ecology and evolution: A ribosomal RNA approach. Annual Reviews in Microbiology 40 (1986) 337-365
27. Poulsen L.K., Ballard G., and Stahl D.A. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Applied and Environmental Microbiology 59 (1993) 1354-1360
28. Rajagopal I. SOFTWARE: Genomics made easy. Science 290 (2000) 474
29. Rossello-Mora R., and Amann R. The species concept for prokaryotes. FEMS Microbiology Review 25 (2001) 39-67
30. Simonato F., Campanaro S., Lauro F.M., Vezzi A., D'Angelo M., Vitulo N., Valle G., and Bartlett D.H. Piezophilic adaptation: a genomic point of view. Journal of Biotechnology 126 (2006) 11-25
31. Singleton D.R., Furlong M.A., Rathbun S.L., and Whitman W.B. Quantitative comparisons of 16S rDNA sequence libraries from environmental samples. Applied and Environmental Microbiology 67 (2001) 4373-4376
32. Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., Arrieta, J.M., Herndl, G.J., 2006. Microbial diversity in the deep sea and the underexplored ''rare biosphere''. In: Proceeding of National Academy of Science USA, vol. 103, pp. 12115-12120.
33. Stackebrandt E., and Goebel B.M. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in Bacteriology. International Journal of Systematic and Evolutionary Microbiology 44 (1994) 846-849
34. van der Wielen P.W., Bolhuis H., Borin S., Daffonchio D., Corselli C., Giuliano L., D'Auria G., de Lange G.J., Huebner A., Varnavas S.P., Thomson J., Tamburini C., Marty D., McGenity T.J., Timmis K.N., and BioDeep Scientific Party. The enigma of prokaryotic life in deep hypersaline anoxic basins. Sciente 307 (2005) 121-123
35. Vetriani C., Jannasch H.W., MacGregor B.J., Stahl D.A., and Reysenbach A.L. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Applied and Environmental Microbiology 65 (1999) 4375-4384
36. Wawer C., Jetten M.S., and Muyzer G. Genetic diversity and expression of the [NiFe] hydrogenase large-subunit gene of Desulfovibrio spp. In environmental samples. Applied and Environmental Microbiology 63 (1997) 4360-4369
37. Whitman, W.B., Coleman, D.C., Wiebe, W.J., 1998. Prokaryotes: the unseen majority. In: Proceeding of National Academy of Science USA 95, pp. 6578-6583.
38. Yakimov M.M., La Cono V., Denaro R., D'Auria G., Decembrini F., Timmis K.N., Golyshin P.N., and Giuliano L. Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic lake L'Atalante, Eastern Mediterranean Sea. The ISME Journal 1 (2007) 743-755
39. Yayanos A.A. Microbiology to 10,500 m in the deep-sea. Annual Reviews in Microbiology 49 (1995) 777-805
40. Zaballos M., Lopez-Lopez A., Ovreas L., Bartual S.G., D'Auria G., Alba J.C., Legault B., Pushker R., Daae F.L., and Rodriguez-Valera F. Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea. FEMS Microbial Ecology 56 (2006) 389-405