Distinct vertical profiles of microbial communities and functional genes between different lake sediment layers mediated by nutrients in the sediments and pore waters.

Lakes, as vital wetland ecosystems, face increasing anthropogenic pressures, including nutrient pollution, which significantly exacerbates the threat of eutrophication. Microorganisms inhabiting lake sediments are key drivers of biogeochemical cycles of essential elements in aquatic ecosystems. While their roles in eutrophic lakes have been explored, their vertical profiles of community compositions and functional genes in the sediments of eutrophic lakes remain poorly resolved. This study aimed to investigate the spatial distribution patterns of and correlations between nutrient concentrations, microbial communities, and element-cycling-related functional genes in the sediment of Honghu Lake, a representative of shallow lakes located in China's Hubei province. 16S rRNA sequencing was used to explore the microbial community structure, and a high-throughput quantitative-PCR-based gene chip, quantitative microbial element cycling (QMEC), was employed to assess the abundance of functional genes for C, N, P, and S metabolisms. A series of bioinformatic analyses were orchestrated to explore the functional differences between sediment layers. The results indicate that nutrient concentrations, functional gene abundance, and alpha diversity of microbial communities generally decrease with depth from the surface sediment to deeper layers. The main environmental variables correlating with the microbial communities included total phosphorus and total nitrogen in the sediments, and NH-N in the pore waters. In the co-occurrence networks, different highly connected species were identified as key members in different sediment layers. Some functional genes were exclusively detected in specific locations and layers, increasing the heterogeneity of the biogeochemical functions, and weakening the functional redundancy of microbial communities. This study showed the connections between environmental variables, microbial community compositions, and element cycling functions in a typical shallow lake, and emphasized the heterogeneity of nutrients, microbial communities, and functional genes in lake sediments and other aquatic ecosystems.