The nitrogen cycle and the associated microbes play an important role in natural ecosystems, including terrestrial habitats; they also have a major effect on climate change. The aim of this study was to explore microbial communities in rice paddy soil by detecting and quantifying some key functional genes involved in the nitrogen cycle using molecular techniques such as conventional polymerase chain reaction (PCR), clone library construction, sequencing, phylogenetic analysis, and real-time

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... The genes analyzed were as follows: nitrogenase reductase gene (nifH), hydrazine synthase gene (hzsA), nitrous oxide reductase gene (nosZ), copper-containing (nirK) and cytochrome cd1-containing (nirS) nitrite reductase genes, nitrite oxidoreductase gene (nxrB), and ammonium monooxygenase gene (amoA). The sequence assessment using the clone library targeting these genes revealed high diversity and dominance of bacterial communities. Furthermore, real-time PCR using SYBR green dye and some primers specific for each gene revealed the high abundance of nxrB (4.1 × 10 9 ± 0.4 × 10 9 copies g −1 soil) and low abundance of hzsA (4.0 × 10 5 ± 1.1 × 10 5 copies g −1 soil). The findings of our study will be useful to explore microbial communities in terrestrial habitats, such as agricultural paddy fields. Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.