Rhizosphere microbial community dynamics in rice under alternate wetting and drying irrigation management

Abstract

What lives in the thin film of soil clinging to a rice root—and how does drying that soil change the community? This research tracked rhizosphere microbial diversity in lowland rice under alternate wetting and drying (AWD) versus continuous flooding (CF) at Makerere University Agricultural Research Institute, Kabanyolo, Uganda, during the 2022 wet season. Rhizosphere soil was sampled biweekly from transplanting to harvest and profiled with 16S rRNA amplicon sequencing. Shannon diversity rose from 2.41 to 2.87 under AWD but declined from 2.43 to 2.31 under CF by 12 weeks. AWD enriched aerobic genera (Bacillus, Burkholderia) while CF favoured methanogens (Methanobacterium). Grain yield didn’t differ significantly between treatments (4.72 vs. 4.84 t ha⁻¹), suggesting AWD maintains productivity while shifting microbial function toward lower methane emission potential.