Soil pH and nutrients shape the vertical distribution of microbial communities in an alpine wetland

Soil microbial communities are vital for maintaining functions of alpine wetland ecosystems, which have been shown to be sensitive to climate change and anthropogenic disturbances in recent decades. The diversity and community structure of soil bacteria and fungi are often highly heterogeneous across vegetation types and soil layers. However, the relative contributions of vegetation, soil properties, and spatial structure to variation in the microbial community remain unclear. Here, we studied the linkage between plant functional groups, soil water content, pH as well as nutrient contents and soil microbial diversity and communities in different soil layers (0–20 cm and 20–40 cm) in Lalu Wetland on the Tibetan Plateau. Plant and soil samples from eighteen plots of six sites were collected to determine the community structure of bacteria and fungi, plant functional groups, and soil characteristics. Our results showed that bacterial and fungal diversity at the 0–20 cm soil depth were significantly negatively (Shannon index, r = −0.65, P < 0.01) and positively (phylogenetic diversity, r = 0.72, P < 0.001) related to pH, respectively. Soil ammonium content was positively correlated with bacterial diversity at the 20–40 cm soil layer (Shannon index: r = 0.55, P < 0.05). Bacterial community structure was most significantly related to soil organic carbon. Fungal diversity and community structure were significantly related to soil organic carbon, available phosphorus, and available potassium. Spatial structure explained 30–50% of the variation in bacterial and fungal community structures in different soil layers in Lalu wetland. In conclusion, pH and soil nutrients were the main factors driving variation in microbial diversity and community structure in the upper and deeper soil layers, respectively. Spatial structure contributed more than vegetation and soil characteristics to explaining variation in bacterial and fungal community structures in both upper and deeper soil layers.