Metagenomic and network analysis of soil fungal and bacterial communities along a soil pH gradient

Increased atmospheric nitrogen (N) deposition into terrestrial ecosystems has become an environmental challenge affecting soil health and biodiversity. It is believed that the increased soil acidity caused by N deposition is the main driver of biodiversity loss but little is known about how increased N content affects the soil functional capacity for carbon (C) and nutrient cycling. Bacterial and fungal communities play a crucial role in important biogeochemical cycles such as C, N and phosphorus (P). Therefore, it is necessary to understand and predict the effects of environmental variables such as soil N content and pH on their diversity, composition and functional capacities. Here we utilized metabarcoding, metagenomics, advanced modeling and network analysis to investigate the responses of microbial communities, functional categories of clusters of orthologous genes (COG), and functional gene modules related to C, N, and P cycling to N deposition along a natural soil pH gradient in pine forests in northern Estonia. The study sites included areas with elevated soil N content caused by anthropogenic pollutants and uncorrelated to soil pH which allowed us to account for their effects on microbial communities independently. Our results indicated that both bacterial and fungal communities were significantly affected by soil pH followed by C:N ratio and N deposition only became a determining factor at the higher values. Most of the COG functional categories were associated with bacterial and fungal richness and diversity and were significantly affected by soil pH, C:N ratio, woody plants composition, and other edaphic parameters such as Ca concentration, N:P ratio and delta-N-15. We observed a significant link between bacterial richness and diversity and fungal richness with functional diversity and richness while they were also significantly affected by soil pH and C:N ratio. Our results also showed a significant effect of soil pH on composition of functional genes related to different cycles followed by bacterial diversity, delta-N-15, and C:N ratio. Our results showed that clustering of functional gene co-occurrence networks of P cycle was linked to soil pH, C:N ratio, and bacterial richness, while for C cycle it was linked to C:N and for N cycle didn't show any significant clustering. The relative abundances of functional gene modules related to different parts of the studied cycles responded strongly and differently to pH and C:N. Our results indicated a stronger role of bacterial communities compared to fungal communities in most biogeochemical processes except nitrification, phosphonate degradation, inorganic phosphate solubilization and response to P starvation which were mostly correlated to fungi.Our findings have brought to light the basis for understanding the effects of N deposition on the microbial component of important biogeochemical cycles.