Synergistic regulation of aquatic microbiome assembly and function by carbon resource availability and a bivalve bioengineer.

While resource subsidies and biotic manipulation are prevalent in managed ecosystems, their interactive effects on microbial community assembly and function remain elusive. Here, we investigated how external carbon (molasses) and a filter-feeding ecosystem engineer (Anodonta woodiana) interactively shape bacterial communities in aquaculture systems using a factorial mesocosm experiment (n = 3 replicate tanks per treatment, sampled at three time points). Integrating 16 S rRNA sequencing, community-level physiological profiling, and null model analyses, we found that combined treatment was associated with shifts in inferred assembly process proportions including an increase in the relative contribution of dispersal limitation. Molasses dose-dependently increased co-occurrence network connectivity and topological robustness metrics, whereas mussel presence was associated with local clustering and elevated betweenness centrality. Their combined application, particularly under high-dose molasses, yielded structurally distinct co-occurrence network configurations. Notably, a core subset comprising 10% of identified taxa showed Procrustes congruence with carbon utilization patterns comparable to the full community, although this reflects statistical association rather than mechanistic causation. These findings offer descriptive insights into how resource addition and biotic manipulation may influence microbial co-occurrence structure and potential substrate utilization, while highlighting the inferential limitations of correlation-based and compositional data approaches.