Selective Enrichment of Methylococcaceae Versus Methylocystaceae Methanotrophs Via Control of Methane Feeding Schemes

Methanotrophs are crucial in keeping environmental CH4 emissions in check. However, the contributions of different groups of methanotrophs at terrestrial CH4-oxidation hotspots, such as the oxic-anoxic interface of rice paddies, have shown considerable inconsistency across observations. To address the knowledge gap regarding this inconsistency, methanotrophic microbiomes were enriched from paddy soils in well-mixed CH4-fed batch reactors under six different incubation conditions, prepared as combinations of two CH4 mixing ratios (0.5 and 10%) and three supplemented Cu2+ concentrations (0, 2, and 10 μM). Monitoring of temporal community shifts in these cultures revealed a dominance of Methylocystis spp. in all 0.5%-CH4 cultures, while methanotrophs affiliated to Gammaproteobacteria dominated the 10%-CH4 cultures that were less consistent both temporally and across conditions. The shotgun metagenome analyses of the 0.5%-CH4 cultures corroborated the Methylocystis dominance and, interestingly, showed that copper deficiency did not select for mmoXYZ-possessing methanotrophs. Instead, a mbn cluster, accounting for approximately 5% of the Methylocystis population, was identified, suggesting the ecological significance of methanobactin in Cu-deficient methanotrophy. These findings underscore the important role of Methylocystis spp. in mitigating emissions from terrestrial CH4 hotspots and suggest the feasibility of directed enrichment and/or isolation of Methylocystis spp. for utilization in, for example, methanobactin and polyhydroxybutyrate production.