Bacterial Community Assembly Patterns Across Distinct Freshwater Habitats

Understanding microbial community assembly mechanisms in aquatic habitats is fundamental to predicting ecosystem responses to environmental change, yet systematic comparisons of deterministic versus stochastic process contributions among different water types remain limited. We conducted monthly sampling over one year from four freshwater habitats, including two aquaculture ponds (WC01, WC02), an enclosed urban lake (TZ), and a flowing river (XJ), and applied a phylogenetic-bin-based null model framework to uncover how bacterial community assembly processes change among habitats and time/season. The results indicated that homogeneous selection (33.5%), dispersal limitation (31.0%), and drift (26.5%) jointly governed community assembly across all samples. Among the four investigated systems, water type, rather than season or their interactions, emerged as the primary factor regulating assembly process differentiation. Specifically, homogeneous selection was significantly stronger in the two aquaculture ponds (WC01, WC02) than in the natural water bodies (TZ and XJ), while the flowing river XJ exhibited the highest dispersal limitation and the lowest drift. At the phylogenetic bin level, over 98% of bins switched their dominant assembly strategies across the four water bodies, especially between the two aquaculture ponds and the two natural water bodies. Environmental factor analyses also revealed habitat-specific driving patterns: nitrogen and phosphorus nutrients dominated homogeneous selection in the aquaculture ponds, whereas dissolved oxygen, turbidity and oxidation reduction potential mainly regulated dispersal limitation in the natural waters. Collectively, these findings reveal a hierarchical pattern of freshwater bacterial assembly with multi-process coordination, habitat dominance, and lineage-level differentiation, and underscore that lineage-level analyses are essential for uncovering assembly patterns hidden at the community level, offering practical guidance for microbial management under diverse hydrological conditions.