Gene-targeted Metagenomic analysis of four NEON ecological sites in four different ecoclimatic zones using pyrosequencing targeting nitrogenase reductase (nifH) functional gene

Biological nitrogen fixation is an important driver of soil fertility and is carried out exclusively by nitrogen fixing Bacteria and Archaea. The nifH gene, coding for nitrogenase reductase, is commonly used as a marker for the nitrogen fixation pathway and is one of the best-studied ecofunctional genes. In this study, we applied nifH gene-targeted metagenomic analysis to examine the nitrogen-fixing microbial communities in 222 soil samples collected from four ecological sites in four different ecoclimatic zones. The taxonomic groups and ecological pattern were analyzed using RDP FrameBot, a frameshift-correction and nearest neighbor assignment tool. The nifH sequences related to the Proteobacteria phylum were the most abundant, followed by those for Cyanobacteria in the Alaska and Utah sites. Predominant genera with similar nifH sequences included Azospirillum, Bradyrhizobium and Rhizobium, the latter two without obvious plant hosts at the sites. The soil samples were grouped by site and correlated with soil environmental factors such as water content, organic matter, biomass, total carbon and nitrogen content. Indicator species were mostly Proteobacteria, but include diverse bacterial phyla and Archaea, most notably several Cyanobacterial indicators for the AK and UT sites.