Abstract
Microbial communities are key regulators of ecological processes in aquatic ecosystems and serve as sensitive indicators of environmental change. Here, we investigated the diversity, assembly mechanisms, and spatial differentiation of bacterial and fungal communities across three representative regions of Dianchi Lake-a large, shallow, eutrophic plateau lake in Southwest China characterized by severe nutrient enrichment and organic pollution. The lake was divided into a submerged macrophyte remnant zone (SubmP), the heavily polluted Caohai area (hPollut), and a cyanobacterial bloom zone (HABs). Amplicon sequencing of the 16S rRNA and ITS genes revealed 7862 bacterial and 3141 fungal OTUs, spanning 69 bacterial phyla (1128 genera) and 9 fungal phyla (477 genera). Although 69 dominant bacterial genera (e.g., Flavobacterium) and 9 dominant fungal genera (e.g., Metschnikowia) were shared across regions, pronounced spatial heterogeneity was observed, primarily driven by total nitrogen and dissolved oxygen. Taxonomic richness and abundance were decoupled: rare (RT) and intermediate taxa (IT) accounted for the most richness, whereas abundant taxa (AT) dominated the total abundance but exhibited comparatively low diversity. IT and RT displayed significantly higher Shannon diversity and greater network robustness than AT; bacterial RT showed the highest robustness (0.35-0.45), while fungal IT demonstrated superior resilience. Community assembly was largely governed by stochastic processes (59-99% contribution), yet deterministic selection exerted stronger effects on IT and RT, particularly for bacteria in SubmP, where habitat heterogeneity enhanced environmental filtering. Functional prediction revealed distinct ecological strategies, with enhanced nitrogen cycling in hPollut, phototrophy in HABs, and pollutant degradation in SubmP. Collectively, these findings demonstrate that rare and intermediate taxa, rather than numerically dominant populations, underpin microbial stability and spatial differentiation in eutrophic lakes, highlighting the importance of nitrogen management and habitat heterogeneity in lake restoration.