Warm‐wet transition restructures arid lake microbiomes and functional potential

Abstract Over the past six decades, northwestern China has undergone a pronounced climatic transition from a “warm‐dry” to a “warm‐wet” regime, driving substantial shifts in lake water level (WL), salinity, and nutrient conditions. However, how this hydroclimatic transition restructures lake microbiomes and their functional potential remains poorly understood. Here, we used Lake Bosten, the largest inland lake in arid northwestern China, as a model ecosystem to examine the long‐term impacts of climate‐driven environmental change on microbial diversity, community assembly, network structure, and functional potential. We combined (1) meteorological and aquatic environmental records from 1958 to 2022, (2) decade‐separated field surveys of microbial communities (2010−2011 vs. 2021−2022) using amplicon sequencing and metagenomics, and (3) mesocosm experiments simulating projected future hydroclimatic conditions. Warm‐wet conditions influenced the Lake Bosten ecosystem through two main pathways: direct temperature effects and indirect WL mediated effects on hydrological connectivity and water chemistry. Field observations showed that the warm‐wet period was characterized by higher WL, lower salinity and total nitrogen, and increased bacterial and eukaryotic diversity. Community assembly shifted toward stronger homogeneous selection and weaker dispersal limitation in both bacterial and eukaryotic communities, consistent with enhanced hydrological connectivity. At the same time, both microbial domains showed reduced community stability, and their co‐occurrence networks exhibited lower complexity and structural stability. In contrast, broad metagenomic functional composition showed no significant shift despite pronounced taxonomic and network reorganization. Nitrogen cycling genes showed pathway‐specific redistribution, with enhanced nitrogen fixation and selected nitrification related genes but reduced nitrate reduction, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA). Taxon‐function linkage further indicated that functional compensation was mainly mediated by replacement within bacterial functional guilds. Overall, our study links warm‐wet hydroclimatic change to altered water level, salinity, nutrient conditions, microbiome restructuring, cross domain network rewiring, and buffered functional potential in an arid lake.