Analysis of the differences and driving factors of bacterial community structure and diversity in multiple habitats of the Qingshui River ecosystem in Ningxia, China

This study investigated bacterial community structure in surface water, sediment, and riparian soil habitats within the Qingshui River Basin in Ningxia, China, across normal, wet, and dry periods using 16S rDNA sequencing. Our findings revealed habitat-specific microbial dynamics, with surface water exhibiting significantly lower α-diversity compared to sediments and riparian soils (e.g., wet period Chao1: 1255.69 vs. 2319.93 and 2377.64, respectively; P < 0.001). Despite this difference, core taxa such as Pseudomonas (average relative abundance: 2.85 % in surface water, 2.05 % in sediments, and 3.53 % in riparian soils) were shared across habitats, suggesting cross-habitat connectivityand thereby reconciling high β-diversity with broad-scale functional stability. Distinct environmental drivers were identified: fluoride (including water-soluble fluoride in sediments and F⁻ in interstitial water) was a key driver of phylum-level community structure in sediments (Mantel test r = 0.189 or 0.116, P < 0.01), enriching fluoride-tolerant Campilobacterota, while ASV/genus-level structure was modulated by pH/EC; TN/TP primarily influenced riparian soils (P < 0.05); and surface water communities were shaped by ionic stress (e.g., Na⁺ up to 1266.68 mg·L⁻¹) and hydrological variability. Hydrological-period-dependent interactions revealed that dry-period surface water formed low-modularity (0.315), high-connectivity networks (1569 edges), favoring functional redundancy. In contrast, sediments maintained stability through high modularity (0.761), while riparian soils exhibited 70.62 % node reduction but increased modularity (0.801) under drought, indicating niche conservatism. These results demonstrate how geochemical gradients (e.g., F⁻, TN/TP) and hydrological variability collectively structure microbial communities in arid watersheds. Our findings provide a framework for managing fluoride and nutrient impacts in the Yellow River Basin and similar ecosystems globally, emphasizing the need for habitat-specific conservation strategies.