Nematoda from the terrestrial deep subsurface of South Africa

Journal name:
Nature
Volume:
474,
Pages:
79–82
Date published:
DOI:
doi:10.1038/nature09974
Received
Accepted
Published online

Since its discovery over two decades ago, the deep subsurface biosphere has been considered to be the realm of single-cell organisms, extending over three kilometres into the Earth’s crust and comprising a significant fraction of the global biosphere1, 2, 3, 4. The constraints of temperature, energy, dioxygen and space seemed to preclude the possibility of more-complex, multicellular organisms from surviving at these depths. Here we report species of the phylum Nematoda that have been detected in or recovered from 0.9–3.6-kilometre-deep fracture water in the deep mines of South Africa but have not been detected in the mining water. These subsurface nematodes, including a new species, Halicephalobus mephisto, tolerate high temperature, reproduce asexually and preferentially feed upon subsurface bacteria. Carbon-14 data indicate that the fracture water in which the nematodes reside is 3,000–12,000-year-old palaeometeoric water. Our data suggest that nematodes should be found in other deep hypoxic settings where temperature permits, and that they may control the microbial population density by grazing on fracture surface biofilm patches. Our results expand the known metazoan biosphere and demonstrate that deep ecosystems are more complex than previously accepted. The discovery of multicellular life in the deep subsurface of the Earth also has important implications for the search for subsurface life on other planets in our Solar System.

At a glance

Figures

  1. General morphology of H. mephisto.
    Figure 1: General morphology of H. mephisto.

    Light microscopy drawings of female holotype and scanning electron microscopy photograph of head. a, Entire body; b, neck region; c, anterior region; d, scanning electron microscope face view (scale bar, 1μm; black arrowheads indicate the positions of two cephalic papillae; black arrow indicates amphid opening); e, reproductive system; f, tail. SE, secretory–excretory.

  2. Bayesian-interference 50%-majority-rule consensus phylogenies based
on small-subunit rDNA data.
    Figure 2: Bayesian-interference 50%-majority-rule consensus phylogenies based on small-subunit rDNA data.

    H. mephisto with GenBank sequences of closely related taxa. Branch support is indicated with posterior probability values. Scale bar, expected substitutions per site. SSU, small subunit.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

References

  1. Pedersen, K. The deep subterranean biosphere. Earth Sci. Rev. 34, 243260 (1993)
  2. Onstott, T. C. et al. in Enigmatic Microorganisms and Life in Extreme Environments (ed. Seckbach, J.) 487500 (Kluwer, 1998)
  3. Amend, J. P. & Teske, A. Expanding frontiers in deep subsurface microbiology. Palaeogeogr. Palaeoclimatol. Palaeoecol. 219, 131155 (2005)
  4. Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 65786583 (1998)
  5. Sinclair, J. L. & Ghiorse, W. C. Distribution of aerobic bacteria, protozoa, algae and fungi in deep subsurface sediments. Geomicrobiol. J. 7, 1531 (1989)
  6. Ekendahl, S., O’Neill, A., Thomsson, E. & Pedersen, K. Characterisation of yeasts isolated from deep igneous rock aquifers of the Fennoscandian shield. Microb. Ecol. 46, 416428 (2003)
  7. Heip, C., Vincx, M. & Vranken, G. The ecology of marine nematodes. Oceanogr. Mar. Biol. 23, 399489 (1985)
  8. Lambshead, P. in Nematode Morphology, Physiology and Ecology Vol. 1 (eds Chen, Z. X., Chen, S. Y. & Dickson, D. W.) 438492 (Tsinghua Univ. Press, 2004)
  9. Föll, R. L. et al. Anaerobiosis in the nematode Caenorhabditis elegans. Comp. Biochem. Physiol. 124B, 269280 (1999)
  10. Moser, D. P. et al. Desulfotomaculum spp. and Methanobacterium spp. dominate 4–5 km deep fault. Appl. Environ. Microbiol. 71, 87738783 (2005)
  11. Dorris, M., De Ley, P. & Blaxter, M. Molecular analysis of nematode diversity and the evolution of parasitism. Parasitol. Today 15, 188193 (1999)
  12. Holterman, M. et al. Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown clades. Mol. Biol. Evol. 23, 17921800 (2006)
  13. Lippmann, J. et al. Dating ultra-deep mine waters with noble gases and 36Cl, Witwatersrand Basin, South Africa. Geochim. Cosmochim. Acta 67, 45974619 (2003)
  14. Onstott, T. C. et al. The origin and age of biogeochemical trends in deep fracture water of the Witwatersrand Basin, South Africa. Geomicrobiol. J. 23, 369414 (2006)
  15. Gihring, T. M. et al. The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa. Geomicrobiol. J. 23, 415430 (2006)
  16. Michel, R. L. in Isotopes in the Water Cycle: Past, Present and Future of a Developing Science (eds Aggarwal, P. K., Gat, J. R. & Froelich, K. F. O.) Ch. 5, 5366 (Springer, 2005)
  17. Wanger, G., Onstott, T. C. & Southam, G. Structural and chemical characterization of a natural fracture surface from 2.8 kilometers below land surface: biofilms in the deep subsurface. Geomicrobiol. J. 23, 443452 (2006)
  18. Ferris, H., Venette, R. C. & Lau, S. S. Population energetics of bacterial-feeding nematodes: carbon and nitrogen budgets. Soil Biol. Biochem. 29, 11831194 (1997)
  19. van Voorhies, W. & Ward, S. Broad oxygen tolerance in the nematode Caenorhabditis elegans. J. Exp. Biol. 203, 24672478 (2000)
  20. Van Voorhies, W. A. & Ward, S. Genetic and environmental conditions that increase longevity in Caenorhabditis elegans decrease metabolic rate. Proc. Natl Acad. Sci. USA 96, 1139911403 (1999)
  21. Phelps, T. J., Murphy, E. M., Pfiffner, S. M. & White, D. C. Comparison between geochemical and biological estimates of subsurface microbial activities. Microb. Ecol. 28, 335349 (1994)
  22. Ocana, A. Relationship between nematode species and the physico-chemical characteristics of spring waters. II. Temperature. Nematol. Mediterr. 19, 2528 (1991)
  23. Neher, D. A. & Powers, T. O. in Encyclopedia of Soils in the Environment Vol. 3 (eds Hillel, D. et al.) 15 (Academic, 2004)
  24. Hoeppli, R. & Chu, H. J. Free-living nematodes from hot springs in China and Formosa. Hong Kong Nat. 1 (suppl.). 1529 (1932)
  25. Jana, B. B. The thermal springs of Bakreswar, India: physico-chemical conditions, flora and fauna. Hydrobiologia 41, 291307 (1973)
  26. Engel, A. S. Observations on the biodiversity of sulfidic karst habitats. J. Cave Karst Stud. 69, 187206 (2007)
  27. Edwards, K. J., Bach, W. & McCollom, T. M. Geomicrobiology in oceanography: microbe–mineral interactions at and below the seafloor. Trends Microbiol. 13, 449456 (2005)
  28. Danovaro, R. et al. The first metazoa living in permanently anoxic conditions. BMC Biol. 8, 3040 (2010)
  29. Yeates, G. W., Bongers, T., Goede, R. G. M., d, Freckman, D. W. & Georgieva, S. S. Feeding habits in nematode families and genera — an outline for soil ecologists. J. Nematol. 25, 315331 (1993)

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Author information

Affiliations

  1. Department of Biology, Nematology Section, Ghent University, Ledeganckstraat 35, B9000 Ghent, Belgium

    • G. Borgonie &
    • W. Bert
  2. Metagenomics Platform, Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa

    • A. García-Moyano,
    • D. Litthauer,
    • A. Bester,
    • E. van Heerden,
    • C. Möller &
    • M. Erasmus
  3. Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 Wageningen, The Netherlands

    • W. Bert
  4. Department of Geosciences, Princeton University, Princeton, New Jersey 08544, USA

    • T. C. Onstott
  5. Present address: Department of Biology, University of Bergen, Postbox 7803, N-5020 Bergen, Norway.

    • A. García-Moyano

Contributions

A.G.-M., D.L. and W.B. all contributed equally to this study. G.B., A.G.-M., D.L., A.B. and M.E. collected the filtered samples and the control samples and performed field analyses. G.B. carried out the enrichments. A.G.-M. performed microbial DNA extraction and 16S rRNA amplification, sequencing and tree construction. C.M. performed DNA analyses on filters of mining water. W.B. provided the nematode identification, their morphological description and their molecular analyses. T.C.O. modelled the geochemical, 3H and 14C data. G.B. wrote the paper with input from W.B., A.G.-M., T.C.O. and E.v.H.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

Sequence information for H. mephisto has been deposited at GenBank under accession number GQ918144.

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Supplementary information

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  1. Supplementary Figures (1.8M)

    This file contains Supplementary Figures 1-9 with legends.

  2. Supplementary Information (895K)

    This file contains Supplementary Tables 1-5, Supplementary Methods, a Supplementary Discussion and additional references.

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