Gene expression in the deep biosphere

Nature. 2013 Jul 11;499(7457):205-8. doi: 10.1038/nature12230. Epub 2013 Jun 12.


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 cycles, but deep biosphere activities are not well understood. 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 profiles. 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 calculations and models of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anaerobiosis
  • Biomass
  • Cell Division / genetics
  • Colony Count, Microbial
  • DNA Repair / genetics
  • DNA, Complementary / analysis
  • DNA, Complementary / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial
  • Gene Expression Regulation, Fungal
  • Geologic Sediments / microbiology*
  • Metabolic Networks and Pathways / genetics
  • Oceans and Seas
  • Seawater / microbiology
  • Sequence Analysis, DNA
  • Sulfates / metabolism
  • Transcriptome / genetics*
  • Water Microbiology


  • DNA, Complementary
  • Sulfates