Bacterial assembly and yield associations across abundance classes at the soil–water interface under long-term rice–crab co-culture

How long-term rice–crab co-culture changes bacterial organization across the soil–water interface and how these changes relate to crop productivity remain unclear. We compared abundant, intermediate, and rare bacterial subcommunities in paired overlying water and interface soil from six rice monoculture and six rice–crab co-culture plots, each managed for more than 20 years. Co-culture increased grain yield by 14.07%. Alpha diversity remained unchanged in overlying water, whereas the richness of intermediate and rare taxa declined in interface soil, together with the Shannon diversity of rare taxa. Community composition changed across all abundance classes in both habitats. Dispersal limitation predominated in abundant taxa, while homogeneous selection was more important for rare taxa. Co-culture increased variable selection among intermediate taxa, particularly in interface soil. Networks became larger and more connected in overlying water but smaller and more modular in interface soil. Urease, alkaline phosphatase, and β-glucosidase activities increased significantly under co-culture only in interface soil. Yield was associated with the composition of all three abundance classes, and rare community composition accounted for a significant unique fraction of yield variation in interface soil (19.62%). Yield-associated potential keystones occurred mainly among intermediate taxa in overlying water and abundant taxa in interface soil, including a Rhodocyclaceae-affiliated taxon and Luteolibacter , respectively. Together, higher productivity under rice–crab co-culture coincided with changes in bacterial composition, assembly, and network organization that differed between habitats and abundance classes. Interface soil emerged as the principal habitat in which microbial reorganization, enzyme activity, nutrient transformation potential, and rice yield converged.