Selective enrichment of Methylococcaceae versus Methylocystaceae methanotrophs via control of methane feeding scheme

Methanotrophs are crucial in keeping environmental CH4 emissions in check. However, how different groups of methanotrophs contribute to this important role in different environmental settings remain ambiguous. Here, in a simplified laboratory setting of well-mixed batch reactors fed continuous flow of CH4-containing gas, methanotrophic microbiomes were enriched from paddy soils under six different incubation conditions prepared as combinations of two different CH4 mixing ratios (0.5% and 10% v/v) and three supplemented Cu2+ concentrations (0, 2, and 10 M). Monitoring of the temporal community shifts in the reactor microbiomes observed domination of Methylocystis spp. in all three reactors fed 0.5% v/v, as further supported by the analyses of pmoCAB genes in the shotgun metagenomes of the single-point samples from the same reactors. Copper deficiency did not select for mmoXYZ-possessing methanotrophs. Instead, a cluster of mbn genes with an abundance accounting for approximately 5% of Methylocystis population was identified, suggesting a comparative ecological importance of methanobactin in Cu-deficient methanotrophy over soluble methane monooxygenases. These findings highlight the importance of Methylocystis spp. in mitigating emissions from CH4 hotspots, e.g., landfills and rice paddies, and suggest the feasibility of directed enrichment/isolation of Methylocystis spp. for utilization in, for example, methanobactin and polyhydroxybutyrate production. SynopsisThis study reports enrichment of a complex soil microbiota with 0.5% methane resulting in dominance of a specific group of methane-consuming bacteria Methylocystis, highlighting their ecological significance as CH4 sink.