Methane-fed microbial communities enriched from field-grown rice support diverse heterotrophic bacteria

Rice paddies naturally host methane-oxidizing bacteria known as methanotrophs, due to the production of methane in flooded soils. Enhancing the activity of native methanotrophs could improve the sustainability of rice cultivation, but knowledge of how this could impact other members of the rice microbiome remains incomplete. To gain insight into which members of the rice microbiome might benefit from increased methanotrophic activity, we passaged 51 aerobic microbial enrichment cultures from rice rhizosphere and tissue samples in a chemically defined medium with methane as the primary carbon source and electron donor. We profiled the cultures over time by 16S rRNA gene amplicon sequencing and sequenced the genomes of 44 isolates to gain functional insights. Taxa whose relative abundance increased during community growth on methane represented more than a dozen families, many of which are not known to utilize one-carbon substrates. Several of the enriched genera have not previously been linked to methane cycling in rice fields, and genomic analysis of the sequenced isolates revealed considerable variation in predicted carbon source utilization and nitrogen cycling capabilities. Together, these findings broaden the understanding of how aerobic methanotrophs may impact microbiome assembly and nutrient cycling in rice paddies.