Exploration and enrichment of methane-oxidizing bacteria derived from a rice paddy field emitting highly concentrated methane

Abstract

Methane-oxidizing bacteria (MOB) possess the metabolic potential to assimilate the highly potent greenhouse gas, CH₄, and can also synthesize valuable products. Depending on their distinct and fastidious metabolic pathways, MOB are mainly divided into Type I and Type II; the latter are known as producers of polyhydroxyalkanoate (PHA). Despite the metabolic potential of MOB to synthesize PHA, the ecophysiology of MOB, especially under high CH₄ flux conditions, is yet to be understood. Therefore, in this study, a rice paddy soil receiving a high CH₄ flux from underground was used as an inoculum to enrich MOB using fed-batch operation, then the enriched Type II MOB were characterized. The transitions in the microbial community composition and CH₄ oxidation rates were monitored by 16S rRNA gene amplicon sequencing and degree of CH₄ consumption. With increasing incubation time, the initially dominant Methylomonas sp., affiliated with Type I MOB, was gradually replaced with Methylocystis sp., Type II MOB, resulting in a maximum CH₄ oxidation rate of 1.40 g-CH₄/g-biomass/day. The quantification of functional genes encoding methane monooxygenase, pmoA and PHA synthase, phaC, by quantitative PCR revealed concomitant increases in accordance with the Type II MOB enrichment. These increases in the functional genes underscore the significance of Type II MOB to mitigate greenhouse gas emission and produce PHA.

Keywords: 16S rRNA gene amplicon sequencing; Culture; Methane-oxidizing bacteria; Microbial community transition; Polyhydroxyalkanoate; Quantitative PCR; phaC; pmoA.