Response of the Anaerobic Methanotroph Candidatus Methanoperedens nitroreducens to Oxygen Stress

Candidatus Methanoperedens nitroreducens is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of Ca. Methanoperedens nitroreducens could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a Ca. Methanoperedens nitroreducens culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, Candidatus Methanoperedens nitroreducens Verserenetto. RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of Ca. Methanoperedens nitroreducens revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of Ca. Methanoperedens nitroreducens Verserenetto to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion. IMPORTANCE Candidatus Methanoperedens nitroreducens is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, Ca. Methanoperedens nitroreducens is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery Ca. Methanoperedens nitroreducens possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.