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Deep sub-seafloor prokaryotes stimulated at interfaces over geological time


The sub-seafloor biosphere is the largest prokaryotic habitat on Earth1 but also a habitat with the lowest metabolic rates2. Modelled activity rates are very low, indicating that most prokaryotes may be inactive or have extraordinarily slow metabolism2. Here we present results from two Pacific Ocean sites, margin and open ocean, both of which have deep, subsurface stimulation of prokaryotic processes associated with geochemical and/or sedimentary interfaces. At 90 m depth in the margin site, stimulation was such that prokaryote numbers were higher (about 13-fold) and activity rates higher than or similar to near-surface values. Analysis of high-molecular-mass DNA confirmed the presence of viable prokaryotes and showed changes in biodiversity with depth that were coupled to geochemistry, including a marked community change at the 90-m interface. At the open ocean site, increases in numbers of prokaryotes at depth were more restricted but also corresponded to increased activity; however, this time they were associated with repeating layers of diatom-rich sediments (about 9 Myr old). These results show that deep sedimentary prokaryotes can have high activity, have changing diversity associated with interfaces and are active over geological timescales.

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Figure 1: Biogeochemical process and prokaryotic biodiversity profiles at the Peru margin site (ODP 1229).
Figure 2: Prokaryotic biodiversity at the Peru margin site (ODP Leg 201, site 1229).
Figure 3: Biogeochemical processes and prokaryotic populations at the Pacific open ocean site (ODP 1226).


  1. Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: The unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998)

    Article  ADS  CAS  Google Scholar 

  2. D'Hondt, S., Rutherford, S. & Spivack, A. J. Metabolic activity of subsurface life in deep-sea sediments. Science 295, 2067–2070 (2002)

    Article  ADS  CAS  Google Scholar 

  3. Parkes, R. J. & Wellsbury, P. in Microbial Diversity and Bioprospecting (ed. Bull, A. T.) 120–129 (ASM Press, Washington DC, 2004)

    Book  Google Scholar 

  4. Chapelle, F. H. & Lovley, D. R. Rates of microbial-metabolism in deep coastal-plain aquifers. Appl. Environ. Microbiol. 56, 1865–1874 (1990)

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Lovley, D. R. & Chapelle, F. H. Deep subsurface microbial processes. Rev. Geophys. 33, 365–381 (1995)

    Article  ADS  Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  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)

    Google Scholar 

  8. Wellsbury, P. et al. Deep marine biosphere fuelled by increasing organic matter availability during burial and heating. Nature 388, 573–576 (1997)

    Article  ADS  CAS  Google Scholar 

  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)

    Article  ADS  Google Scholar 

  10. Teske, A., Wawer, C., Muyzer, G. & Ramsing, N. B. Distribution of sulfate-reducing bacteria in a stratified Fjord (Mariager 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)

    CAS  PubMed  PubMed Central  Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  13. D'Hondt, S. et al. Distributions of microbial activities in deep subseafloor sediments. Science 306, 2216–2221 (2004)

    Article  ADS  CAS  Google Scholar 

  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)

    Google Scholar 

  15. Mitterer, R. M. et al. Co-generation of hydrogen sulfide and methane in marine carbonate sediments. Geophys. Res. Lett. 28, 3931–3934 (2001)

    Article  ADS  CAS  Google Scholar 

  16. Boetius, A. et al. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623–626 (2000)

    Article  ADS  CAS  Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  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)

    Google Scholar 

  19. Wellsbury, P., Herbert, R. A. & Parkes, R. J. Incorporation of [methyl-3H]thymidine by obligate and facultative anaerobic bacteria when grown under defined culture conditions. FEMS Microbiol. Ecol. 12, 87–95 (1993)

    Article  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  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)

    Article  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  23. Schippers, A. et al. Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria. Nature 433, 861–864 (2005)

    Article  ADS  CAS  Google Scholar 

  24. Ibarki, M. Eocene through Pleistocene planktonic Foraminifers off Peru, Leg 112—Biostratigraphy and Paleoceanography. Proc. ODP Sci Results 112, 239–262 (1990)

    Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  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)

    Article  CAS  Google Scholar 

  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)

    Google Scholar 

  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)

    Article  Google Scholar 

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We thank members of the Leg 201 cruise for assistance in obtaining and processing samples, and T. Daniell for assistance with DNA sequencing. This research used samples and data provided by the ODP. The ODP is sponsored by the US National Science Foundation (NSF) and participating countries under the management of Joint Oceanographic Institutions (JOI), Inc. We thank the European Union and the Natural Environment Research Council (Marine and Freshwater Microbial Biodiversity Programme) for supporting this research financially.

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Correspondence to R. John Parkes.

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Reprints and permissions information is available at The authors declare no competing financial interests.

Supplementary information

Supplementary Figures S1-S4

Figures showing rarefaction curves and phylogenetic trees of representative sequences from 12 prokaryotic gene libraries from Peru Margin site 1229 (ODP Leg 201) deep sub-seafloor sediment. (PDF 84 kb)

Supplementary Figure Legends S1-S4 (PDF 69 kb)

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Parkes, R., Webster, G., Cragg, B. et al. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436, 390–394 (2005).

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