Rare bacteria with low absolute abundance as sensitive bioindicators of riverine pollution: A comparative study across river water, sediment, and riparian soils

Microorganisms underpin nutrient cycling and ecosystem functioning in riverine systems and, due to their high sensitivity to pollution and hydrological stress, their taxon-specific responses serve as valuable indicators for assessing river health and restoration effectiveness. This study investigated a Yangtze River tributary with a strong pollution gradient and, for the first time, applied an absolute abundance framework to assess the response patterns of rare and abundant bacterial subcommunities in water, sediment, and riparian soils under environmental stress. Bacterial community compositions significantly differed among the three habitats, and the α diversity of rare taxa was consistently higher than that of abundant taxa. Moreover, rare taxa were more sensitive to changes in the Composite Quality Index, with TN and NH4+-N identified as the main drivers of rare community diversity in the water samples. Environmental stress enhanced cooperative interactions within the bacterial co-occurrence network but may concurrently reduce the connectivity between rare taxa and other groups, thereby weakening structural redundancy and compromising network stability. Moreover, bacterial community assembly was primarily governed by stochastic processes, as supported by Sloan's neutral model (R2 = 0.63–0.69) and NST values exceeding 0.5. Abundant taxa exhibited higher stochasticity, while rare taxa displayed greater β-diversity, indicating more frequent species turnover under changing environmental conditions. This study provides insights into microbial community assembly and stability under environmental disturbances and highlights the role of low-abundance rare taxa as sensitive indicators of river health and restoration.