Selective Enrichment of Methylococcaceae versus Methylocystaceae Methanotrophs via Control of Methane Feeding Schemes

Methanotrophs are crucial in keeping environmental CH emissions in check. However, the contributions of different groups of methanotrophs at terrestrial CH-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 CH-fed batch reactors under six different incubation conditions, prepared as combinations of two CH mixing ratios (0.5 and 10%) and three supplemented Cu concentrations (0, 2, and 10 μM). Monitoring of temporal community shifts in these cultures revealed a dominance of Methylocystis spp. in all 0.5%-CH cultures, while methanotrophs affiliated to Gammaproteobacteria dominated the 10%-CH cultures that were less consistent both temporally and across conditions. The shotgun metagenome analyses of the 0.5%-CH 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 CH hotspots and suggest the feasibility of directed enrichment and/or isolation of Methylocystis spp. for utilization in, for example, methanobactin and polyhydroxybutyrate production.