Gene expression in the deep biosphere


Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles1,2,3, but deep biosphere activities are not well understood1. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles1. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations1 and models4 of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

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Figure 1: Biogeochemical and gene-expression profiles of the deep biosphere from Peru Margin sediment, Ocean Drilling Program Site 1229D.
Figure 2: Profiles of deep biosphere metabolic activities in Peru Margin sediment.
Figure 3: Transcripts involved in cell motility and DNA repair.
Figure 4: A comparison of gene-expression data to existing metagenomic studies13,29 from Ocean Drilling Program Site 1229.

Accession codes


Sequence Read Archive

Data deposits

Data has been deposited in the NCBI Short Read Archive under accession number SRA058813 and in MG RAST ( under accession numbers 4515478.3, 4515477.3, 4515476.3, 4510337.3, 4510336.3 and 4510335.3.


  1. 1

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

    ADS  Article  Google Scholar 

  2. 2

    Schrenk, M. O., Huber, J. A. & Edwards, K. J. Microbial provinces in the subseafloor. Annu. Rev. Mar. Sci. 2, 279–304 (2010)

    ADS  Article  Google Scholar 

  3. 3

    Jørgensen, B. B. & D’Hondt, S. A starving majority deep beneath the seafloor. Science 314, 932–934 (2006)

    Article  Google Scholar 

  4. 4

    Lomstein, B. A., Langerhuus, A. T., D’Hondt, S., Jorgensen, B. B. & Spivack, A. J. Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment. Nature 484, 101–104 (2012)

    CAS  ADS  Article  Google Scholar 

  5. 5

    Parkes, J., Cragg, B. & Wellsbury, P. Recent studies on bacterial populations and processes in subseafloor sediments: a review. Hydrogeol. J. 8, 11–28 (2000)

    ADS  Article  Google Scholar 

  6. 6

    Biddle, J. F. et al. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl Acad. Sci. USA 103, 3846–3851 (2006)

    CAS  ADS  Article  Google Scholar 

  7. 7

    Kallmeyer, J., Pockalny, R., Adhikari, R., Smith, D. C. & D’Hondt, S. Global distributions of microbial abundance and biomass in subseafloor sediment. Proc. Natl Acad. Sci. USA 109, 16213–16216 (2012)

    CAS  ADS  Article  Google Scholar 

  8. 8

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

    CAS  ADS  Article  Google Scholar 

  9. 9

    Biddle, J. F., House, C. H. & Brenchley, J. E. Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology 3, 287–295 (2005)

    CAS  Article  Google Scholar 

  10. 10

    D’Hondt, S. et al. Subseafloor sedimentary life in the South Pacific Gyre. Proc. Natl Acad. Sci. USA 106, 11651–11656 (2009)

    ADS  Article  Google Scholar 

  11. 11

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

    ADS  Article  Google Scholar 

  12. 12

    Hinrichs, K. U. & Inagaki, F. Downsizing the deep biosphere. Science 338, 204–205 (2012)

    CAS  ADS  Article  Google Scholar 

  13. 13

    Biddle, J. F., Fitz-Gibbon, S., Schuster, S. C., Brenchley, J. E. & House, C. H. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc. Natl Acad. Sci. USA 105, 10583–10588 (2008)

    CAS  ADS  Article  Google Scholar 

  14. 14

    Teske, A. in Proceedings of the Ocean Drilling Program Vol. 201 (eds Jørgensen, B. B. et al.) Ch. 2, 1–19 (ODP, 2006)

  15. 15

    Lipp, J. S., Morono, Y., Inagaki, F. & Hinrichs, C. H. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature 454, 991–994 (2008)

    CAS  ADS  Article  Google Scholar 

  16. 16

    Moran, M. A. et al. Sizing up metatranscriptomics. ISME J. 7, 237–243 (2013)

    CAS  Article  Google Scholar 

  17. 17

    Gao, H. et al. Global transcriptome analysis of the heat shock response of Shewanella oneidensis . J. Bacteriol. 186, 7796–7803 (2004)

    CAS  Article  Google Scholar 

  18. 18

    Jørgensen, B. B., D’Hondt, S. & Miller, D. J. in Proceedings of the Ocean Drilling Program Vol. 201 (eds Jørgensen, B. B. et al.) Ch. 1, 1–45 (ODP, 2006)

  19. 19

    Milucka, J. et al. Zero valent sulphur is a key intermediate in marine methane oxidation. Nature 491, 541–546 (2012)

    CAS  ADS  Article  Google Scholar 

  20. 20

    Lever, M. Functional gene surveys from ocean drilling expeditions — a review and perspective. FEMS Microbiol. Ecol. 84, 1–23 (2013)

    CAS  Article  Google Scholar 

  21. 21

    Webster, G. et al. Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol. Ecol. 58, 65–85 (2006)

    CAS  Article  Google Scholar 

  22. 22

    Oremland, R. S. & Polcin, S. Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in estuarine sediments. Appl. Environ. Microbiol. 44, 1270–1276 (1982)

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Valentine, D. L. Emerging topics in marine methane biogeochemistry. Annu. Rev. Mar. Sci. 3, 147–171 (2011)

    ADS  Article  Google Scholar 

  24. 24

    Lloyd, K. G. et al. Predominant archaea in marine sediments degrade detrital proteins. Nature 496, 215–218 (2013)

    CAS  ADS  Article  Google Scholar 

  25. 25

    Jørgensen, B. B. Deep subseafloor microbial cells on physiological standby. Proc. Natl Acad. Sci. USA 108, 18193–18194 (2011)

    ADS  Article  Google Scholar 

  26. 26

    Hoehler, T. M. & Jorgensen, B. B. Microbial life under extreme energy limitation. Nature Rev. Microbiol. 11, 83–94 (2013)

    CAS  Article  Google Scholar 

  27. 27

    Orsi, W., Biddle, J. & Edgcomb, V. Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across multiple subsurface provinces. PLoS ONE 8, e56335 (2013)

    CAS  ADS  Article  Google Scholar 

  28. 28

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

    Google Scholar 

  29. 29

    Martino, A. J. et al. Novel degenerate PCR method for whole-genome amplification applied to Peru Margin (ODP Leg 201) subsurface samples. Front. Microbiol. 3, 17 (2012)

    Article  Google Scholar 

  30. 30

    Brady, A. & Salzberg, S. L. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature Methods 6, 673–676 (2009)

    CAS  Article  Google Scholar 

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This work was fostered by a Center for Dark Energy Biosphere Investigations (CDEBI) grant OCE-0939564 to W.D.O. and a National Science Foundation IOS grant 1238801 to J.F.B. We thank C. House and A. Teske for providing samples. We also thank M. Sogin and R. Fox at the Josephine Bay Paul Center for providing access to computing resources. E. Leadbetter and S. Hallam provided comments on the manuscript, and we also thank S. D’Hondt for discussions on the deep biosphere. This is CDEBI contribution 137.

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W.D.O. performed experiments, analysed data and wrote the paper; W.D.O., J.F.B. and V.P.E. designed experiments and developed ideas. W.D.O. and G.D.C. developed analytical tools. All authors participated in data interpretation and provided editorial comments on the manuscript.

Corresponding author

Correspondence to William D. Orsi.

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The authors declare no competing financial interests.

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Orsi, W., Edgcomb, V., Christman, G. et al. Gene expression in the deep biosphere. Nature 499, 205–208 (2013).

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