Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190

Authors

  • Carole J. Newberry,

    1. Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, PO Box 915, Cardiff CF10 3TL, Wales, UK.
    Search for more papers by this author
  • Gordon Webster,

    1. Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, PO Box 915, Cardiff CF10 3TL, Wales, UK.
    Search for more papers by this author
  • Barry A. Cragg,

    1. Department of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK.
    Search for more papers by this author
    • Present address: School of Earth, Ocean and Planetary Sciences, Cardiff University, PO Box 914, Cardiff CF10 3YE, Wales, UK.

  • R. John Parkes,

    1. Department of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK.
    Search for more papers by this author
    • Present address: School of Earth, Ocean and Planetary Sciences, Cardiff University, PO Box 914, Cardiff CF10 3YE, Wales, UK.

  • Andrew J. Weightman,

    1. Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, PO Box 915, Cardiff CF10 3TL, Wales, UK.
    Search for more papers by this author
  • John C. Fry

    Corresponding author
    1. Cardiff School of Biosciences, Cardiff University, Main Building, Park Place, PO Box 915, Cardiff CF10 3TL, Wales, UK.
    Search for more papers by this author

*E-mail fry@cardiff.ac.uk; Tel. (+44) 29 2087 4190; Fax (+44) 29 2087 4305.

Summary

Diversity of Bacteria and Archaea was studied in deep marine sediments by PCR amplification and sequence analysis of 16S rRNA and methyl co-enzyme M reductase (mcrA) genes. Samples analysed were from Ocean Drilling Program (ODP) Leg 190 deep subsurface sediments at three sites spanning the Nankai Trough in the Pacific Ocean off Shikoku Island, Japan. DNA was amplified, from three depths at site 1173 (4.15, 98.29 and 193.29 mbsf; metres below the sea floor), and phylogenetic analysis of clone libraries showed a wide variety of uncultured Bacteria and Archaea. Sequences of Bacteria were dominated by an uncultured and deeply branching ‘deep sediment group’ (53% of sequences). Archaeal 16S rRNA gene sequences were mainly within the uncultured clades of the Crenarchaeota. There was good agreement between sequences obtained independently by cloning and by denaturing gradient gel electrophoresis. These sequences were similar to others retrieved from marine sediment and other anoxic habitats, and so probably represent important indigenous bacteria. The mcrA gene analysis suggested limited methanogen diversity with only three gene clusters identified within the Methanosarcinales and Methanobacteriales. The cultivated members of the Methanobacteriales and some of the Methanosarcinales can use CO2 and H2 for methanogenesis. These substrates also gave the highest rates in 14C-radiotracer estimates of methanogenic activity, with rates comparable to those from other deep marine sediments. Thus, this research demonstrates the importance of the ‘deep sediment group’ of uncultured Bacteria and links limited diversity of methanogens to the dominance of CO2/H2 based methanogenesis in deep sub-seafloor sediments.

Ancillary