Reference Work Entry

Handbook of Hydrocarbon and Lipid Microbiology

pp 3503-3511

In Situ Microcosm Studies to Characterize Microbial Processes in the Field

  • M. Kästner
  • , H. H. Richnow


A concept of in situ microcosms, which allows analyzing structure, function, and activity of microbial communities in situ, as well as the enrichment of microorganisms for subsequent cultivation in laboratory experiments is described. The concept is based on the application of stable isotope-labeled compounds supplied within the microcosm system. Microorganisms capable of utilizing these substrates as carbon or nitrogen sources become labeled upon metabolism and biosynthesis. Stable isotope probing (SIP) of biomarker molecules such as fatty acids, proteins, or nucleic acids allows tracing the flux of the label into the biomass and offers potential for linking structure and function of the active microbial communities.