Interaction characteristics of bacterial communities in water and sediment in the Yellow River based on high-throughput absolute quantification.

Bacterial communities are crucial for connecting aquatic and sediment ecosystems. Water and sediment samples were collected from the Jinan section of the lower Yellow River, and absolute abundances of bacterial taxa were obtained via high-throughput absolute quantification. Integrating physicochemical properties, the water-sediment bacterial communities exhibited interactive characteristics of "high connectivity and strong heterogeneity". High connectivity was manifested in similar community and functional compositions and assembly mechanisms, along with shared core genera, in which high-concentration suspended particulates played a key role. Strong heterogeneity was reflected in distinct taxa abundances, diversity, co-occurrence network topologies, and functional specializations, all regulated by environmental factors. Sediments harbored total bacterial abundances and abundances of dominant phyla 1-2 orders of magnitude higher than those in water. Water community showed higher α-diversity and co-occurrence network complexity (edges, average degree, graph density). Eighteen shared genera (belonging to Pseudomonadota and Bacteroidota etc.) with cross-medium survival adaptability were identified. Functional connectivity was supported by 99.1% shared KOs, despite sediments had greater carbon/nitrogen cycling potential than that in water. Stochastic processes, mainly drift, dominated community assembly, contributing more in water (93.6%) than in sediment (75.5%). This study provides microbiological quantitative indicators for Yellow River ecological assessment, identifies cross-medium adaptive genera as potential bioremediation resources, and offers a microbiological perspective on ecosystem maintenance in adjacent river habitats.