Abstract Rice paddies naturally host significant populations of methanotrophs, due to the production of methane in flooded soils. However, relatively little is known about how the activity of these bacteria impacts the structure of the broader microbial community in this important agricultural environment. To address this question, we passaged 51 microbial aerobic enrichment cultures from rice rhizosphere, root, and stem samples in a chemically-defined medium with methane as sole electron donor.