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

Methanotrophs are crucial in keeping environmental CH ₄ 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 CH ₄ -containing gas, methanotrophic microbiomes were enriched from paddy soils under six different incubation conditions prepared as combinations of two different CH ₄ mixing ratios (0.5% and 10% v/v) and three supplemented Cu ²⁺ concentrations (0, 2, and 10 μM). 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 CH ₄ 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.