Bacterial abundance and diversity in rhizosphere and bulk soils of organic and conventional rice cultivation fields

The rhizosphere microbiome plays a critical role in plant growth, particularly under organic cultivation. However, the combined effects of rice agroecosystem (upland vs. lowland) and cultivation systems (organic vs. conventional) on rhizosphere bacterial communities remain poorly understood. In this study, we investigated bacterial abundance and diversity in rhizosphere and bulk soils under six treatments combining water regime and fertilizer input: organic lowland, organic upland, organic bulk soil, conventional lowland, conventional upland, and conventional bulk soil. Rice (Oryza sativa L.) was grown under controlled upland and lowland conditions using soils collected from organic and conventional fields. Amplicon sequencing of 16S rRNA genes revealed that organic upland significantly increased bacterial abundance, richness, and Shannon diversity at both phylum and genus levels compared to conventional upland. Similarly, organic lowland and organic bulk soil supported greater bacterial richness and diversity than their conventional counterparts (conventional lowland and conventional bulk soil, respectively). A total of 57 microbial phyla and 819 genera were identified, with Pseudomonadota and Actinomycetota dominating across samples. Notably, organic upland exhibited the highest genus-level bacterial richness and the largest number of unique operational taxonomic units, suggesting enhanced microbial niche differentiation. Principal component analysis further confirmed distinct community structuring between organic and conventional systems. These results demonstrate that organic cultivation fosters a more diverse and abundant rhizosphere bacterial community, highlighting its potential to increase microbial-driven soil health and ecosystem functioning in rice agroecosystems. © 2025 Elsevier Inc.