RNA stable isotope probing and high-throughput sequencing to identify active microbial community members in a methane-driven denitrifying biofilm

Aims Aerobic methane oxidation coupled to denitrification (AME-D) is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. This study used RNA stable isotope probing (RNA-SIP) and high-throughput sequencing to identify the micro-organisms that are actively involved in aerobic methane oxidation within a denitrifying biofilm. Methods and Results Two RNA-SIP experiments were conducted to investigate labelling of RNA and methane monooxygenase (pmoA) transcripts when exposed to C-13-labelled methane over a 96-hour time period and to determine active bacteria involved in methane oxidation in a denitrifying biofilm. A third experiment was performed to ascertain the extent of C-13 labelling of RNA using isotope ratio mass spectrometry (IRMS). All experiments used biofilm from an established packed bed reactor. IRMS confirmed C-13 enrichment of the RNA. The RNA-SIP experiments confirmed selective enrichment by the shift of pmoA transcripts into heavier fractions over time. Finally, high-throughput sequencing identified the active micro-organisms enriched with C-13. Conclusions Methanotrophs (Methylovulum spp. and Methylocystis spp.), methylotrophs (Methylotenera spp.) and denitrifiers (Hyphomicrobium spp.) were actively involved in AME-D. Significance and Impact of the Study This is the first study to use RNA-SIP and high-throughput sequencing to determine the bacteria active within an AME-D community.

Automated summary

This study identified the active micro-organisms involved in aerobic methane oxidation coupled to denitrification (AME-D) using RNA-SIP and high-throughput sequencing techniques. Methanotrophs, methylotrophs, and denitrifiers were found to be actively participating in the AME-D process. It is the first study to utilize RNA-SIP and high-throughput sequencing to determine the active bacteria within an AME-D community.