RNA Stable Isotope Probing, a Novel Means of Linking Microbial Community Function to Phylogeny

TLDR

Identifying microorganisms responsible for environmental processes is challenging, but recent methodological innovations now link community function to phylogeny. The study aimed to identify the bacteria responsible for phenol degradation in an aerobic industrial bioreactor by feeding stable‑isotope‑labeled 13C phenol and tracking the resulting 13C‑labeled RNA. Stable‑isotope‑labeled RNA was isolated by equilibrium density centrifugation and characterized using reverse transcription‑PCR and denaturing gradient gel electrophoresis. The method revealed that phenol degradation is dominated by a Thauera species, highlighting its key role in the bioreactor and contradicting results from conventional approaches.

Abstract

ABSTRACT Identifying microorganisms responsible for recognized environmental processes remains a great challenge in contemporary microbial ecology. Only in the last few years have methodological innovations provided access to the relationship between the function of a microbial community and the phylogeny of the organisms accountable for it. In this study stable-isotope-labeled [ 13 C]phenol was fed into a phenol-degrading community from an aerobic industrial bioreactor, and the 13 C-labeled RNA produced was used to identify the bacteria responsible for the process. Stable-isotope-labeled RNA was analyzed by equilibrium density centrifugation in concert with reverse transcription-PCR and denaturing gradient gel electrophoresis. In contradiction with findings from conventional methodologies, this unique approach revealed that phenol degradation in the microbial community under investigation is dominated by a member of the Thauera genus. Our results suggest that this organism is important for the function of this bioreactor.