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Bacterial diversity in a deep-subsurface clay environment

V Boivin-Jahns1, R Ruimy, A Bianchi

  • 1Observatoire Océanologique, Centre National de la Recherche Scientifique and Université Paris, France.

Applied and Environmental Microbiology
|September 1, 1996
PubMed
Summary
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Deep clay sediments harbor bacteria, but their numbers decrease away from a mine gallery. Molecular methods confirmed bacterial presence even when cultures failed, suggesting trapped ancient microbes.

Area of Science:

  • Geomicrobiology
  • Molecular Biology
  • Clay Sedimentology

Background:

  • Investigating microbial life in deep subsurface environments is crucial for understanding Earth's biosphere.
  • The Boom clay formation in Belgium, a 35-million-year-old marine deposit, offers a unique environment to study ancient microbial communities.
  • Challenges exist in culturing and detecting bacteria in low-biomass, deep subsurface samples.

Purpose of the Study:

  • To analyze the presence and activity of bacteria within a deep clay sediment core.
  • To determine bacterial distribution and density in relation to proximity to a mine gallery.
  • To identify bacterial populations using molecular techniques.

Main Methods:

  • Bacterial activity was assessed by measuring respiration using [14C]glucose.

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  • DNA was extracted from sediment samples for polymerase chain reaction (PCR) amplification.
  • Eubacterial 16S rRNA genes were amplified using universal primers, cloned, sequenced, and analyzed via molecular phylogeny.

    • Main Results:

    • Bacterial densities decreased with increasing distance from the mine gallery.
    • While cultures detected few bacteria beyond 80 cm, PCR confirmed bacterial presence in all samples.
    • Phylogenetic analysis allowed tentative identification of bacteria, despite low cell counts and activity.

    Conclusions:

    • Molecular methods are essential for detecting bacteria in low-biomass deep clay environments where culturing is ineffective.
    • Bacterial communities in the Boom clay are sparse and show reduced activity.
    • The low porosity of the clay suggests some bacteria may be ancient cells trapped during sedimentation.