Impacts of conventional and organic farming practices on soil and aquatic microbial communities in rice (Oryza sativa) agricultural fields in southern Brazil

Microbial communities play essential roles in agroecosystem functioning, yet the effects of different rice farming practices on their structure and dynamics remain underexplored, particularly across soil and water compartments. This study compared microbial assemblages in organic and conventional rice fields in southern Brazil over a single growing season, based on ten samples collected from two fields. High-throughput sequencing of 16S region V3V4 and 18S region V4 rRNA genes was used to profile bacteria, unicellular eukaryotes, fungi, and metazoa at three time points during rice cultivation. Community composition and diversity differed between farming systems and over time. In soil, bacterial richness was higher in conventional systems at specific time points but showed greater temporal variability. In water, microbial communities in organic systems were generally more diverse and stable, with significantly lower bacterial richness in conventional systems at the initial sampling point (p < 0.01). Unicellular eukaryotes and metazoa showed strong farming-system responses, particularly in water, where organic fields supported more diverse assemblages. These findings highlight the influence of farming practices on microbial biodiversity and emphasize the importance of integrated, multi-group approaches for understanding agroecosystem functioning.