Intensive rice cropping drives shifts in abundance, activity, and assembly of root-associated methanotrophic community

Rice is a staple crop relevant to present and future human feeding. However, these agroecosystems significantly contribute to greenhouse gas methane emissions. In Uruguay, a traditional low-intensity, reduced-tillage rice system alternates annual rice crops with pastures for livestock. We hypothesize that rice crop intensification impacts aerobic methanotrophic communities associated with rice roots, which are crucial in mitigating methane emissions. The pmoA gene abundance, methane oxidation potential (MOP), and methanotrophic community composition by 16S rRNA gene Illumina MiSeq (V4 region) allowed us to determine the dynamics of these communities in bulk and rhizospheric soils from continuous rice (CR) and rice-pastures (RP) rotations throughout the crop cycle. Results showed that rice crop intensification significantly affected MOP and pmoA abundance in both compartments. The tillering stage showed the greatest pmoA abundance and MOP. Rhizospheric methanotrophic communities from the CR and RP systems at flowering differed greatly. While Methylocystis dominated rhizospheric CR soil, Methylocella predominated in those from RP rotation. Active rhizospheric methanotrophic communities at flowering detected by 13CH4 DNA-SIP were dominated by distinct Methylocystis-affiliated ASVs in both cropping systems. However, other active genera were differentially enriched in the two contrasting cropping systems. These results suggest aerobic methanotrophs could be a microbial guild sensitive to crop intensification.