Quantifying the functional genes of C, N, P, and S cycling in a deep lake: Depth patterns and drivers

Microbial functional composition is important for biogeochemical cycles, and is usually constrained by taxonomic species pool and natural environmental gradients. However, the distribution of functional genes in deep lakes and the driving factors remains elusive. Here, we quantified the abundance of 71 functional genes relevant to carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus cycling, and sulfur cycling in 38 sediments along the water depth ranging from 0 to 90 m in Lugu Lake, China, using Quantitative Microbial Ecology Chip (QMEC) and then explored their water-depth diversity pattern and abiotic and biotic drivers. Functional gene diversity showed a hump-shaped pattern along the depth and peaked at around 50 m which is the low boundary of thermocline layer. There were specific environmental preferences among functional gene subgroups such as nitrogen and sulfur cycling genes preferring to deeper and shallow waters, respectively. The dissimilarity of total functional genes increased with water depth distance indicating a distance-decay relationship. There was a congruence between functional and taxonomic composition by showing the positive correlations between the compositions of functional genes and bacteria or archaea. This phenomenon is consistently observed for the six functional gene subgroups, and the congruence strength was highest for nitrogen cycling while lowest for sulfur cycling. Compared to abiotic factors, biotic factors were more relevant to the functional gene diversity and composition. Biotic factors explained 28.5 % of the variance of functional gene diversity, while water depth and other environmental factors such as water total phosphorus and sediment carbon explained 4.2 % and 3.8 %, respectively. For functional gene composition, biotic factors accounted for 25.2 % of the variance, whereas water depth and other environmental factors contributed to 0.7 % and 4.4 %, respectively. Among all explanatory variables for function genes, bacterial composition had the highest contribution, which was further supported by showing its direct effects of 1.45 and 0.86 on functional diversity and composition, respectively. This study for the first time quantified the microbial functional genes along water depth in deep lakes and provided a more comprehensive understanding of the functional dynamics in microbial communities within aquatic ecosystems.