Microbial diversity in Cenozoic sediments recovered from the Lomonosov Ridge in the Central Arctic Basin

Environmental Microbiology

Volumn 11, Issue 3, 2009, Pages 630-639

  Forschner, Stephanie R ^a   Sheffer, Roberta ^a   Rowley, David C ^a   Smith, David C ^b  

^a UNIVERSITY OF RHODE ISLAND   (United States)

^b UNIVERSITY OF RHODE ISLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL DNA; ARCHAEAL RNA; BACTERIAL DNA; BACTERIAL RNA; RIBOSOME DNA; RNA 16S;

ARCHAEBACTERIUM; ARCTIC; ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA GENE; SEDIMENT; SEQUENCE HOMOLOGY;

ARCHAEA; ARCTIC REGIONS; BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, RRNA; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 61449165890     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2008.01834.x     Document Type: Article

References (39)

1. Abulencia, C.B., Wyborski, D.L., Garcia, J.A., Podar, M., Chen, W., Chang, S.H., et al. (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72 : 3291 3301.
2. Backman, J., Jackobsson, M., Frank, M., Sangiorgi, F., Brinkhuis, H., Stickley, C., et al. (2008) Age model and core-seismic integration for the Cenozoic Arctic Coring Expedition sediments from the Lomonosov Ridge. Paleoceanography 23 : PA1S03. doi: 10.1029/2007PA001476
3. Banning, N., Brock, F., Fry, J.C., Parkes, R.J., Hornibrook, E.R.C. Weightman, A.J. (2005) Investigation of the methanogen population structure and activity in a brackish lake sediment. Environ Microbiol 7 : 947 960.
4. Biddle, J.F., Lipp, J.S., Lever, M.A., Lloyd, K.G., Sørensen, K.B., Anderson, R., et al. (2006) Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Nat Acad Sci USA 103 : 3846 3851.
5. Coolen, M.J.L., Cypionka, H., Sass, A.M., Sass, H. Overmann, J. (2002) Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296 : 2407 2410.
6. D'Hondt, S., Jorgensen, B.B., Miller, D.J., Batzke, A., Blake, R., Cragg, B.A., et al. (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306 : 2216 2221.
7. DeLong, E.F. (1992) Archaea in coastal marine environments. Proc Nat Acad Sci USA 89 : 5685 5689.
8. Expedition 302 Scientists (2005) Arctic Coring Expedition (ACEX): paleoceanographic and tectonic evolution of the central Arctic Ocean. IODP Prel. Rept., 302. doi:10.2204/iodp.pr.302.2005.
9. Expedition 302 Scientists (2006) Expedition 302 summary. In Backman, J., Moran, K., McInroy, D.B., Mayer, L.A. the Expedition 302 Scientists. Proc. IODP, 302 : Edinburgh (Integrated Ocean Drilling Program Management International). doi: 10.2204/iodp.proc.2302.2101.2006
10. Gonzalez, J.M., Portillo, M.C. Saiz-Jimenez, C. (2005) Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments. Environ Microbiol 7 : 1024 1028.
11. Grosskopf, R., Janssen, P.H. Liesack, W. (1998) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 64 : 960 969.
12. Inagaki, F., Suzuki, M., Takai, K., Oida, H., Sakamoto, T., Aoki, K., et al. (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69 : 7224 7235.
13. Inagaki, F., Nunoura, T., Nakagawa, S., Teske, A., Lever, M., Lauer, A., et al. (2006) Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments, on the Pacific Ocean Margin. Proc Nat Acad Sci USA 103 : 2815 2820.
14. Kallmeyer, J., Smith, D.C., Spivack, A.J. D'Hondt, S. (2008) A new cell extraction procedure applied to deep subsurface sediments. Limnol Oceanogr Methods 6 : 236 245.
15. Knies, J., Mann, U., Popp, B.N., Stein, R. Brumsack, H.J. (2008) Surface water productivity and paleoceanographic implications in the Cenozoic Arctic Ocean. Paleoceanography 23 : PA1S16. doi: 10.1029/2007PA001455
16. Kormas, K.A., Smith, D.C., Edgcomb, V. Teske, A. (2003) Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176). FEMS Microbiol Ecol 45 : 115 125.
17. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E. Goodfellow, M. (eds). New York, USA : Wiley, pp. 115 175.
18. Liao, P., Huang, B. Huang, S. (2007) Microbial community composition of the Danshui River estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding. Microb Ecol 54 : 497 507.
19. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32 : 1363 1371.
20. Mauclaire, L., Zepp, K., Meister, P. McKenzie, J.A. (2004) Direct in situ detection of cells in deep-sea sediment cores from the Peru Margin (ODP Leg 201, Site 1229). Geobiology 2 : 217 223.
21. Maymo-Gatell, X., Chien, Y.T., Gossett, J.M. Zinder, S.H. (1997) Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276 : 1568 1571.
22. Mincer, T.J., Fenical, W. Jensen, P.R. (2005) Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora. Appl Environ Microbiol 71 : 7019 7028.
23. Moran, K., Backman, J., Brinkhuis, H., Clemens, S.C., Cronin, T., Dickens, G.R., et al. (2006) The Cenozoic palaeoenvironment of the Arctic Ocean. Nature 441 : 601 605.
24. Ovreas, L., Forney, L., Daae, F.L. Torsvik, V. (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63 : 3367 3373.
25. Parkes, R.J., Cragg, B.A. Wellsbury, P. (2000) Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol J 8 : 11 28.
26. Parkes, R.J., Webster, G., Cragg, B.A., Weightman, A.J., Newberry, C.J., Ferdelman, T.G., et al. (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436 : 390 394.
27. Ravenschlag, K., Sahm, K. Amann, R. (2001) Quantitative molecular analysis of the microbial community in marine Arctic sediments (Svalbard). Appl Environ Microbiol 67 : 387 395.
28. Reed, D.W., Fujita, Y., Delwiche, M.E., Blackwelder, D.B., Sheridan, P.P., Uchida, T. Colwell, F.S. (2002) Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl Environ Microbiol 68 : 3759 3770.
29. Roussel, E.G., Bonavita, M.-A.C., Querellou, J., Cragg, B.A., Webster, G., Prieur, D. Parkes, R.J. (2008) Extending the sub-sea-floor biosphere. Science 320 : 1046.
30. Schippers, A., Neretin, L.N., Kallmeyer, J., Ferdelman, T.G., Cragg, B.A., Parkes, R.J. Jorgensen, B.B. (2005) Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433 : 861 864.
31. Smith, D.C. D'Hondt, S. (2006) Exploration for life in deep subseafloor sediments. Oceanography 19 : 58 70.
32. Sørensen, K.B. Teske, A. (2006) Stratified communities of active Archaea in deep marine subsurface sediments. Appl Environ Microbiol 72 : 4596 4603.
33. Sørensen, K.B., Lauer, A. Teske, A. (2004) Archaeal phylotypes in a metal-rich and low-activity deep subsurface sediment of the Peru Basin, ODP Leg 201, Site 1231. Geobiology 2 : 151 161.
34. Stein, R. (2007) Upper Cretaceous/lower Tertiary black shales near the North Pole: organic-carbon origin and source-rock potential. Mar Petrol Geol 24 : 67 73.
35. Swofford, D. (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 10. Sunderland, MA, USA : Sinauer.
36. Teske, A. Sørensen, K.B. (2008) Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J 2 : 3 18.
37. Teske, A., Hinrichs, K.-U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S.P., et al. (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68 : 1994 2007.
38. Webster, G., Newberry, C.J., Fry, J.C. Weightman, A.J. (2003) Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale. J Microbiol Methods 55 : 155 164.
39. Wellsbury, P., Mather, I. Parkes, R.J. (2002) Geomicrobiology of deep, low organic carbon sediments in the Woodlark Basin, Pacific Ocean. FEMS Microbiol Ecol 42 : 59 70.