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Keywords:

  • stable-isotope probing;
  • DNA;
  • marine sediments;
  • Bacteria;
  • Archaea;
  • PCR-DGGE

Abstract

Stable isotope probing of prokaryotic DNA was used to determine active prokaryotes using 13C-labelled substrates (glucose, acetate, CO2) in sediment slurries from different biogeochemical zones of the Severn Estuary, UK. Multiple, low concentrations (5 × 100 μM) of 13C-substrate additions and short-term incubations (7 days) were used to minimize changes in the prokaryotic community, while achieving significant 13C-incorporation. Analysis demonstrated clear metabolic activity within all slurries, although neither the net sulphate removal nor CH4 production occurred in the anaerobic sulphate reduction and methanogenesis zone slurries. Some similarities occurred in the prokaryotic populations that developed in different sediment slurries, particularly in the aerobic and dysaerobic zone slurries with 13C-glucose, which were dominated by Gammaproteobacteria and Marine Group 1 Archaea, whereas both anaerobic sediment slurries incubated with 13C-acetate showed incorporation into Epsilonproteobacteria and other bacteria, with the sulphate reduction zone slurry also showing 13C-acetate utilization by Miscellaneous Crenarchaeotic Group Archaea. The lower potential energy methanogenesis zone slurries were the only conditions where no 13C-incorporation into Archaea occurred, despite Bacteria being labelled; this was surprising because Archaea have been suggested to be adapted to low-energy conditions. Overall, our results highlight that uncultured prokaryotes play important ecological roles in tidal sediments of the Severn Estuary, providing new metabolic information for novel groups of Archaea and suggesting broader metabolisms for largely uncultivated Bacteria.