Functional genes involved in the nitrogen cycling A total of 3763 gene probes belonging to different key gene categories involved in nitrogen fixation, denitrification, nitrification, dissimilatory GSI-IX N reduction, assimilatory N reduction and anaerobic ammonium oxidation are present in Geochip 3.0 [14]. Among

them, 754 gene probes were detected in all six soil samples (Table 3). 224, 372, 17, 51, 27 and 63 genes involved in nitrogen fixation, denitrification, nitrification, dissimilatory N reduction, assimilatory N reduction and anaerobic ammonium oxidation were detected in all samples, respectively (Table 3). Sample SJY-GH and SJY-CD have the most and least detected gene number, respectively. Microbe-mediated nitrogen fixation and denitrification are the most important processes in nitrogen cycling. Microbe-mediated nitrogen fixation is the most important source of nitrogen in natural ecosystems, and occurs

across a wide range of bacteria phyla, from Archaebacteria to Eubacteria [28]. The majority of nifH genes (155/224) were derived from unidentified or uncultured organisms retrieved from different environments. Among nifH genes, 19 were shared by all samples. The shared gene 44829093 derived from an uncultured bacterium was dominant in samples SJY-GH and SJY-YS, and 780709 from an unidentified marine eubacterium was the most dominant gene in sample SJY-CD. These samples had a relatively high abundance of BKM120 genes involved in nitrogen cAMP fixation. Denitrification is a dissimilatory process of denitrifying bacteria where oxidized nitrogen compounds are used as alternative electron acceptors and nitrogen is transferred into the atmosphere in form of N2. Most of the detected genes involved in denitrification (320/372) were derived from the unidentified or uncultured organisms retrieved from different environments. These samples had a relatively high abundance of

genes involved in denitrification (Table 3). 67 nosZ genes which encoding nitrous oxide reductase and it is considered a key enzyme in the denitrification process were detected. Few genes (13/67) were derived from the isolated bacteria. Four genes were shared and derived from the uncultured bacteria by all six soil samples (Additional file 1: Figure S3). Together, these results indicated that all the processes involved in nitrogen cycling existed, and there were high gene diversity as well as high potential metabolic ability in nitrogen fixation and denitrification in all these samples. Relationships between microbial community structure and environmental variables To assess the relationships between microbial community structure and soil environmental variables, Mantel test and canonical correspondence analysis (CCA) were used. Mantel tests of all six soil samples were performed with 12 individual environmental variables.