Vertical Zonation and Functional Characteristics of Sediments Bacteria in Rural Black-Odorous Waterbodies: A Microbiological Perspective for Sustainable Management

Rural black-odorous waterbodies (RBOWBs) represent a critical environmental challenge in China, yet the vertical stratification of sedimentary bacterial communities and its underlying drivers remain poorly understood. This study combined 16S rRNA gene amplicon sequencing across five sediment depths (0–125 cm) with shotgun metagenomic analysis of surface sediments to investigate bacterial diversity, composition, and functional potential in typical rural black-odorous systems of Dongming County, Shandong Province. Results showed a clear decline in bacterial richness with increasing sediment depth, with the surface layer (0–25 cm) exhibiting 1.2–1.9 times higher diversity than deeper strata. Community composition displayed distinct vertical zonation: Chloroflexi and Thiobacillus dominated surface layers and were linked to carbon hydrolysis and desulfurization, whereas Bacillus and nitrifying bacteria prevailed in deeper anoxic layers. Metagenomic analysis revealed high genetic potential for carbohydrate metabolism, amino acid biosynthesis, and sulfur-nitrogen cycling, with glycoside hydrolases (GHs) and glycosyl transferases (GTs) being particularly abundant. Statistical correlations identified total phosphorus (TP1), dissolved oxygen (DO), and pH of the overlying water—rather than sediment intrinsic nutrients—as the primary environmental factors associated with microbial functional stratification. These findings provide a mechanistic understanding of vertical microbial zonation in rural black-odorous sediment and offer a microbiological basis for developing depth-resolved sustainable remediation strategies.