Bacterial community adaptation after brackish and freshwater coalescence

Microbial community coalescence, the merging of entire microbial communities, is common in estuaries, yet the ecological processes governing community assembly after coalescence remain unclear. To uncover these mechanisms, we conducted controlled microcosm experiments simulating coalescence between freshwater and brackish water bacterial communities across five mixing ratios and incubated them in either freshwater or brackish water. We tracked 40 mixed communities over six passages using Nanopore full-length 16S rRNA gene sequencing. Laboratory incubation reduced diversity and increased taxonomic overlap, but preserved habitat-associated compositional signatures. Coalescence outcomes were asymmetric and strongly shaped by the incubation water. In both environments, coalesced communities remained compositionally closer to the native than to the introduced community. However, the relative influence of environmental filtering differed between habitats. In freshwater, strong filtering drove communities to closely resemble the freshwater source, even when the freshwater inoculum was small. In brackish water, weaker filtering made coalescence outcomes more dependent on initial mixing ratios and propagule pressure. Neutral model analyses confirmed a greater contribution of stochastic processes in brackish water. Co-occurrence network analysis revealed predominantly positive associations within the same source community and fewer but negative associations across sources. These within-source associations may reinforce propagule pressure by facilitating the establishment of co-adapted species. Overall, our results demonstrate that environmental filtering primarily governs coalescence outcomes, modulated by source composition, stochasticity, and species co-adaptation, offering new insights into microbial assembly in dynamic estuarine systems.