Combined genome-centric metagenomics and stable isotope probing unveils the microbial pathways of aerobic methane oxidation coupled to denitrification process under hypoxic conditions

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

“…This is the first study to use RNA‐SIP in combination with high‐throughput sequencing to determine the bacteria actively involved in aerobic methane oxidation within a denitrifying biofilm community. Previous studies investigating methane oxidation coupled to denitrification have used high‐throughput 16S rRNA gene sequencing (Alrashed et al, 2018; Cao et al, 2019; Lee et al, 2019; Siniscalchi et al, 2017; Sun et al, 2013) and DNA‐SIP (Zhang et al, 2020) to determine the communities present when this process is occurring in both aerobic and anaerobic environments. In comparison to using 16S rRNA gene sequencing techniques alone or with DNA‐SIP, 13 CH 4 RNA‐SIP enables the active members, directly involved in the metabolism of methane or methane oxidation metabolites to be identified.…”

“…AME‐D is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. DNA stable isotope probing (DNA‐SIP) was recently used to investigate aerobic methane oxidation coupled to denitrification under hypoxia (Zhang et al, 2020). RNA stable isotope probing (RNA‐SIP) was developed to identify the active members of a microbial community in situ (Ghori et al, 2019; Manefield et al, 2002a).…”

Intermediates Production in Methane Oxidation Coupled with Denitrification: Current Status, Challenges, and Future Opportunities

“…However, the process of MOD is usually completed by a biological community, part of which cannot however be separated and purified presently. Therefore, the use of metagenomic sequencing technology could obtain the whole genome of cultured/uncultured microorganisms in the community, which is favorable in terms of grasping the interaction between the species of a community and between species and the environment, as well as genetic characteristics and metabolic pathways [189,190]. However, the large and complete information acquisition method of metagenomics brings difficulties in subsequent analysis.…”