Long-Term Cultivation and Metagenomics Reveal Ecophysiology of Previously Uncultivated Thermophiles Involved in Biogeochemical Nitrogen Cycle

Microbes Environ. 2018 Mar 29;33(1):107-110. doi: 10.1264/jsme2.ME17165. Epub 2018 Mar 16.


Many thermophiles thriving in a natural high-temperature environment remain uncultivated, and their ecophysiological functions in the biogeochemical cycle remain unclear. In the present study, we performed long-term continuous cultivation at 65°C and 70°C using a microbial mat sample, collected from a subsurface geothermal stream, as the inoculum, and reconstructed the whole genome of the maintained populations using metagenomics. Some metagenome-assembled genomes (MAGs), affiliated into phylum-level bacterial and archaeal clades without cultivated representatives, contained genes involved in nitrogen metabolism including nitrification and denitrification. Our results show genetic components and their potential interactions for the biogeochemical nitrogen cycle in a subsurface geothermal environment.

Keywords: long-term continuous cultivation; metagenomics; nitrogen cycle; subsurface geothermal groundwater; thermophiles.

MeSH terms

  • Archaea / genetics*
  • Archaea / physiology
  • Bacteria / genetics*
  • Bacteria / metabolism
  • Bacterial Physiological Phenomena*
  • Biodiversity
  • Denitrification
  • Ecosystem
  • Hot Springs / microbiology
  • Metagenome
  • Metagenomics*
  • Nitrification
  • Nitrogen / metabolism
  • Nitrogen Cycle*
  • Soil Microbiology


  • Nitrogen