The nitrogen cycle is one of the most important nutrient cycles in terrestrial ecosystems. Environmental bacteria maintain the global nitrogen cycle by metabolizing organic as well as inorganic nitrogen compounds. It is thought that most of the microbial taxa cannot be cultured outside of their natural environment, thus, microbial diversity remains poorly described before a decade. But the metagenomic techniques developed recently have therefore greatly extended our knowledge of microbial genetic diversity. The objective of this work was to analyze the taxonomic composition of three metagenome communities from the soil sample mainly rain forest, temperate broadleaf and temperate grassland via MG-RAST. Using the M5NR database, the affinities were tested for the sequences of known metabolic function against both SEED subsystems and KEGG metabolic pathways using a maximum e-value of 1e-5. Although there are a number of metabolic functions that can be tested but we probed particularly for enzymes related to the components of nitrogen cycle. The results explain the potential taxonomic diversity of nitrate reducing bacteria with the dominance of Bradyrhizobium japonicum from soil sample.