The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan–Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes.

Eutrophication threatens vulnerable plateau lakes, yet the gene-level microbial processes behind spatial heterogeneity of sediment carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycling and their environmental driver remain unclear. This study first applies the high-throughput Quantitative Microbial Ecology Chip (QMEC) to quantify 71 functional genes involved in geochemical cycling in sediment of a large Chinese plateau lake, Erhai, aiming to elucidate how environmental factors shape the spatial distribution and coupling patterns of these genes. The results revealed that total functional gene abundance exhibited a pronounced south-to-north decline, with key genes (rbcL, mct, nirS, nosZ, phoD, pqqC and yedZ) being significantly higher in the southern sector (p < 0.05). Lignocellulose-degrading genes (abfA, xylA and mnp) exceeded 10⁶ copies g⁻¹ and were significantly enriched in the south, indicating faster organic-matter turnover. Denitrification dominated the nitrogen cycle, with nirS-type denitrifiers being overwhelmingly prevalent; genes associated with nitrate reduction (napA, narG) were also significantly more abundant in the south. Sediment total phosphorus (TP) was significantly correlated with genes involved in carbon fixation, methane production, nitrogen fixation and sulfur metabolism (Mantel test, p < 0.05), suggesting that TP is a key driver of microbial nutrient cycling in Erhai sediment. Furthermore, co-abundance of these functional genes was observed across all sites (Spearman correlation, p < 0.05), which in turn implies potential coupling of the major elemental cycles. Accordingly, the differentiation of the carbon, nitrogen, phosphorus and sulfur cycling genes and metabolic potential in the different sectors reveals heterogeneous microbial regulation of Erhai’s endogenous nutrient cycling. It highlights precision and differentiated management as a key for large lake restoration.