Archaeal and Bacterial Communities and Their Relations with Hydrochemistry in Gongzhu Co, a Carbon-Poor, Nutrient-Rich Basin Lake of the Qinghai-Xizang Plateau.

Gongzhu Co (Gz) is in a fault-bounded basin in the Ali region of the western Qinghai–Xizang Plateau (QXP), and its carbonate-rich waters classify the lake as a carbonate-type saline system. However, the Gz archaeal and bacterial communities and their links to environmental factors had not been assessed. We used high-throughput sequencing of the 16 S rRNA gene to profile lake microbial diversity and analyzed water chemistry. The archaeal communities comprised 5 phyla, 6 classes, and 35 genera, with 2,693 operational taxonomic units (OTUs) and Shannon diversity values of 3.77 − 4.14. The dominant archaeal phylum was Woesearchaeota (63.17% to 91.24%), and Woesearchaeota subgroups AR16, AR15, and AR18 accounted for 34.73% to 53.25%, 9.29% to 13.66%, and 4.5% to 13.38%, respectively, of total abundance. Bacterial communities comprised 33 phyla, 52 classes, and 431 genera, with 7,818 OTUs and Shannon values of 5.27 − 5.38. Dominant phyla were Proteobacteria (33.76% to 40.52%), Bacteroidetes (24.96% to 30.79%), and Firmicutes (13.63% to 19.81%), with Azonexus (5.79% to 11.23%) and Arcobacter (1.49% to 8.48%) dominant genera. Redundancy analysis (RDA) suggested that community composition broadly followed salinity- and nutrient-related gradients (Na+, HCO3−, TN, TP) and identified temperature as the only variable significantly associated with bacterial community structure in permutation tests. Using Gz as a case lake, we characterized microbial communities in this high-altitude, carbon-poor but nutrient-rich carbonate-type soda system and provided an exploratory view of hydrochemical controls on community composition. Our findings advanced understanding of microbial ecological processes in extreme lakes on the Qinghai–Xizang Plateau and provided baseline data for microbial resource exploration and lake ecosystem management.