Human activities have noticeably reduced microbial diversity in water bodies across the Yunnan-Guizhou plateau region

Abstract Purpose Human activities exert significant impacts on lake microecology. Currently, more attention has been paid to their direct effects on water quality, while the influence on microbial community structures in lake ecosystems remains poorly understood. This study investigates the bacteria, fungi, and protists in three types of typical human-disturbed lake ecosystems, aiming to explore the effects of different anthropogenic disturbances on aquatic microbial communities. Methods We collected water samples from three lakes with distinct anthropogenic disturbance statuses in Zhaotong City, Yunnan-Guizhou Plateau: ML (agricultural production area lake), SGGY (urban park lake), and XCB (nature reserve lake). After filtration through 0.22-μm aqueous filter membranes, we conducted 16S rRNA and 18S rRNA gene amplicon sequencing. Subsequently, differential analyses of bacterial, fungal, and protistan community structures were performed based on the sequencing data. Results Shannon index analysis at the ASV level revealed revealed significantly higher bacterial diversity in XCB compared to SGGY. Functional heatmap analysis based on ASVs demonstrated that cyanobacteria exhibited the highest abundance in SGGY, followed by ML, with the lowest levels in XCB. Fungal Shannon indices were notably higher in XCB than in ML and SGGY. Protist analysis showed markedly elevated abundances of Angulamoeba and Pterocystis in SGGY, while Neobodo and Ichthyobodo were significantly enriched in XCB. Conclusions Anthropogenic disturbance reduces the diversity of bacteria, fungi, and protists in aquatic ecosystems, while increasing the relative abundance of dominant taxa, ultimately driving convergent structural shifts in microbial communities.