Abstract:[Objective] To explore the organic carbon composition in lake sediments and the influence on the composition of lake microbial communities. [Methods] We collected 81 sediment samples from 29 lakes on the Qinghai-Tibet Plateau. The concentration of labile and recalcitrant organic carbon in the studied lake sediments was determined after sulfuric acid hydrolysis, and the correlation with environmental variables was analyzed. Meanwhile, the diversity and composition of prokaryotic and fungal communities in the sediments and their correlation with the concentration of labile and recalcitrant organic carbon were investigated by Illumina sequencing and ecological statistics. [Results] The concentration of labile organic carbon I (LOC Ⅰ), labile organic carbon Ⅱ (LOC Ⅱ), and recalcitrant organic carbon (ROC) in the studied lake sediments was 0.03-29.62 mg/g, 0.02-23.38 mg/g, and 0.64-75.72 mg/g, respectively. ROC was the major component of organic carbon in the studied lake sediments, accounting for 54.97%±19.50%. Concentration of LOC Ⅰ was significantly correlated with elevation, and concentration of total nitrogen, total phosphorus, calcium ion, active calcium, and iron (P<0.05). Concentration of LOC Ⅱ was significantly correlated with concentration of total nitrogen, calcium ion, and active calcium. ROC concentration was significantly correlated with elevation, concentration of total nitrogen, total phosphorus, calcium ion, and active calcium. Among them, the concentration of calcium ion and active calcium was positively correlated with the concentration of LOC Ⅰ, LOC Ⅱ, and ROC, suggesting that organic matter binding with calcium may be an important mechanism for the preservation of organic carbon in lake sediments on the Qinghai-Tibet Plateau. The alpha diversity of prokaryotic community was positively correlated with the concentration of LOC Ⅰ, LOC Ⅱ, and ROC, while the α diversity of fungal community was only positively correlated with ROC concentration. The relative abundance of Alphaproteobacteria, Actinobacteria, Anaerolineae, Phycisphaerae, and Rhodothermes was significantly correlated with LOC Ⅰ concentration. The relative abundance of Anaerolineae, Gammaproteobacteria, and Phycisphaerae was significantly correlated with the concentration of LOC Ⅱ. The relative abundance of Actinobacteria and Anaerolineae was significantly correlated with ROC concentration. The concentration of LOC Ⅰ significantly affected both prokaryotic and fungal community composition in the studied lake sediments with the variance explained of 1.1% and 0.3%, respectively. Environmental factors explained 7.2% and 3.9% of the variation in prokaryotic and fungal community composition among samples, respectively, while spatial factors explained 14.6% and 6.4%, separately. The contributions of stochastic process to prokaryotic and fungal community assembly were 50% and 47%, respectively. [Conclusion] Organic carbon preservation in the studied lake sediments was controlled by the chemical protection of iron and calcium. Organic carbon components significantly affected the diversity and composition of prokaryotic and fungal community, but the variance explained was low. Physicochemical variables, spatial factors, and stochastic processes exhibited important influence on prokaryotic and fungal community composition in the studied lake sediments. This study advances our understanding of organic carbon components in sediments and their impact on microbial community composition in lakes.