This dataset is divided in to three parts:<br><b>part 1:</b> Chapter 3 and 4: include the functional genes of N cycle (amoA-B, amoA-arch and ureCgenes ), C cycle ( mcrA pmoA genes), and S cycle (aprA gene). These data were obtained by qPCR. Additional to the total DNA and 16SrRNA and the physiological parameter of soil ( OC, P,Fe, Cu, Mn, Zn ,NH4 and NO3). there is a sheet for all graphs of genes.<br><b>part 2:</b> chapter 5: include the row data of Biology Eco plate and NGS. For Biology Eco plate, I include Richness, Eveness, SAWCD, AWCD, and row data of farm B, C, P3, Q and T at 72hr. It is also include the the five guilds of Biolog eco-plate (carbohydrates, polymers, amino acid, carboxylic and acetic acid and amines/amides). For NGS, I include OTU graph, faith-pd, PcoA plot, phylogenetic bars, weight-Unifrac and unweight-Unifrac.<br><b>part 3:</b> include the data that were performed in the glasshouse, which include the functional genes that amplified by qPCR (amoA-B, amoA-arch, ureC,nirK,nosZ,nirS pmoA, mcrA and aprA genes. the other data belong to this chapter is a table of physicochemical parameter of soil.