Deep sub-seafloor prokaryotes stimulated at interfaces over geological time

Nature

Volumn 436, Issue 7049, 2005, Pages 390-394

  Parkes, R John ^a   Webster, Gordon ^a,b   Cragg, Barry A ^a   Weightman, Andrew J ^b   Newberry, Carole J ^b   Ferdelman, Timothy G ^c   Kallmeyer, Jens ^c,e   Jørgensen, Bo B ^c   Aiello, Ivano W ^d   Fry, John C ^b  

^a CARDIFF UNIVERSITY   (United Kingdom)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^d MOSS LANDING MARINE LABORATORIES   (United States)

^e UNIVERSITY OF RHODE ISLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; DNA; GEOLOGIC MODELS; METABOLISM; OCEAN HABITATS; SEDIMENTS;

BIOSPHERES; EARTH; METABOLIC RATES; PROKARYOTES;

MANGANESE NODULES;

DNA; METHANE; SEA WATER; SULFATE;

METABOLISM; PROKARYOTE; REACTION RATE; SEAFLOOR;

ARTICLE; BIODIVERSITY; GEOLOGICAL TIME; MOLECULAR WEIGHT; NONHUMAN; PACIFIC OCEAN; PRIORITY JOURNAL; PROKARYOTE; ARCHAEBACTERIUM; BACTERIAL COUNT; BACTERIUM; CHEMISTRY; CLASSIFICATION; CYTOLOGY; DIATOM; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PERU; PROKARYOTIC CELL; SEDIMENT; TIME;

BACILLARIOPHYTA; CELLULAR ORGANISMS; PROKARYOTA;

ARCHAEA; BACTERIA; BIODIVERSITY; COLONY COUNT, MICROBIAL; DIATOMS; DNA; GEOLOGIC SEDIMENTS; METHANE; MOLECULAR WEIGHT; PACIFIC OCEAN; PERU; PROKARYOTIC CELLS; SEAWATER; SEQUENCE ANALYSIS, DNA; SULFATES; TIME FACTORS;

EID: 22944465797     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03796     Document Type: Article

References (30)

1. Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: The unseen majority. Proc. Natl Acad. Sci. USA 95, 6578-6583 (1998).
2. D'Hondt, S., Rutherford, S. & Spivack, A. J. Metabolic activity of subsurface life in deep-sea sediments. Science 295, 2067-2070 (2002).
3. Parkes, R. J. & Wellsbury, P. in Microbial Diversity and Bioprospecting (ed. Bull, A. T.) 120-129 (ASM Press, Washington DC, 2004).
4. Chapelle, F. H. & Lovley, D. R. Rates of microbial-metabolism in deep coastal-plain aquifers. Appl. Environ. Microbiol. 56, 1865-1874 (1990).
5. Lovley, D. R. & Chapelle, F. H. Deep subsurface microbial processes. Rev. Geophys. 33, 365-381 (1995).
6. Krumholz, L. R., Mckinley, J. P., Ulrich, G. A. & Suflita, J. M. Confined subsurface microbial communities in Cretaceous rock. Nature 386, 64-66 (1997).
7. McMahon, P. B., Chapelle, F. H., Falls, W. F. & Bradley, P. M. Role of microbial processes in linking sandstone diagenesis with organic rich clays. J. Sedim. Petrol. 62, 1-10 (1992).
8. Wellsbury, P. et al. Deep marine biosphere fuelled by increasing organic matter availability during burial and heating. Nature 388, 573-576 (1997).
9. Parkes, R. J., Cragg, B. A. & Wellsbury, P. Recent studies on bacterial populations and processes in subseafloor sediments: A review. Hydrogeol. J. 8, 11-28 (2000).
10. Teske, A., Wawer, C., Muyzer, G. & Ramsing, N. B. Distribution of sulfate-reducing bacteria in a stratified Fjord (Manager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62, 1405-1415 (1996).
11. Coolen, M. J. L., Cypionka, H., Sass, A. M., Sass, H. & Overmann, J. Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes. Science 296, 2407-2410 (2002).
12. Inagaki, F. et al. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microbiol. 69, 7224-7235 (2003).
13. D'Hondt, S. et al. Distributions of microbial activities in deep subseafloor sediments. Science 306, 2216-2221 (2004).
14. Whelan, J. K., Kanyo, Z., Tarafa, M. & McCaffrey, M. A. Organic matter in Peru Upwelling sediments-analysis by pyrolysis, pyrolysis-gas chromatography, and pyrolysis-gas chromatography mass spectrometry. Proc. ODP Sci. Results 112, 573-587 (1990).
15. Mitterer, R. M. et al. Co-generation of hydrogen sulfide and methane in marine carbonate sediments. Geophys. Res. Lett. 28, 3931-3934 (2001).
16. Boetius, A. et al. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623-626 (2000).
17. Iversen, N. & Jorgensen, B. B. Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark). Limnol. Oceanogr. 30, 944-955 (1985).
18. Wellsbury, P., Goodman, K., Cragg, B. A. & Parkes, R. J. The geomicrobiology of deep marine sediments from Blake Ridge containing methane hydrate (Sites 994, 995 and 997). Proc. ODP Sci. Results 164, 379-391 (2000).
19. 3H]thymidine by obligate and facultative anaerobic bacteria when grown under defined culture conditions. FEMS Microbiol. Ecol. 12, 87-95 (1993).
20. Webster, G., Newberry, C. J., Fry, J. C. & Weightman, A. J. 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 (2003).
21. Newberry, C. J. et al. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ. Microbiol. 6, 274-287 (2004).
22. Webster, G., Parkes, R. J., Fry, J. C. & Weightman, A. J. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl. Environ. Microbiol. 70, 5708-5713 (2004).
23. Schippers, A. et al. Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433, 861-864 (2005).
24. Ibarki, M. Eocene through Pleistocene planktonic Foraminifers off Peru, Leg 112-Biostratigraphy and Paleoceanography. Proc. ODP Sci Results 112, 239-262 (1990).
25. Parkes, R. J., Cragg, B. A., Fry, J. C., Herbert, R. A. & Wimpenny, J. W. T. Bacterial biomass and activity in deep sediment layers from the Peru Margin. Phil. Trans. R. Soc. Lond. A 331, 139-153 (1990).
26. Marchesi, J. R., Weightman, A. J., Cragg, B. A., Parkes, R. J. & Fry, J. C. Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis. FEMS Microbiol. Ecol. 34, 221-228 (2001).
27. Kemp, P. F. & Aller, J. Y. Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol. Ecol. 47, 161-177 (2004).
28. Leloup, J., Quillet, L., Oger, C., Boust, D. & Petit, F. Molecular quantification of sulfate-reducing microorganisms (carrying dsrAB genes) by competitive PCR in estuarine sediments. FEMS Microbiol. Ecol. 47, 207-214 (2004).
29. Shipboard Scientific Party, Controls on microbial communities in deeply buried sediments, eastern Equatorial Pacific and Peru Margin sites 1225-1231, 27 January - 29 March 2002. Proc. ODP Init. Rep. 201, 1-81 (2003).
30. Kallmeyer, J., Ferdelman, T. G., Weber, A., Fossing, H. & Jørgensen, B. B. A cold chromium distillation procedure for radiolabeled sulfide applied to sulfate reduction measurements. Limnol. Oceanogr. Methods 2, 171-180 (2004).