Soil microbes play important roles in regulating soil health. The addition of organic materials to the soils can improve the activities of the microbes. Specifically, soil microbes utilize carbon (C) from the applied organic materials to increase their abundance and activities. Contrastingly, soil microbes decompose the added materials and emit the C to the atmosphere as carbon dioxide (CO2). Studies have shown that charred organic materials like biochar can store C in the soil and improve the microbial activities. However, research to verify the impact of biochar on microbial communities under different biochar applications is needed. Also, compared to biochar, manure can support microbial activities but the factors regulating the variabilities in manure decomposition are underexplored. The first study investigated the effects of different biochar materials on the bacterial community. The second study examined the microbial community using network analysis. The third experiment examined the decomposition of cow dung and gas emissions. A pot experiment was conducted to investigate the effects of different materials (chicken manure CM, rice straw RS, and rice husk RH) used to produce biochar on soil microbiome. The biochar was applied as a single (CM, RS, and RH), combined from CM+RS, or CM+RH as mixed or surface under a dent corn. In results, surface applications increased the microbial diversity in the soil. This increase was attributed to the increased numbers of OTU such as Actinobacteria and Proteobacteria at the phylum level. Also, RS treatments impacted the microbial richness, and evenness under surface application. Thus, the effect on microbial diversities found in this study depends on the feedstock biochar, therefore biochar materials and application methods should be considered when interpreting its impact on the microbial community. The second study was aimed at investigating the microbial community interactions among different biochar materials using network analysis. Statistical analysis investigating the co-occurrence of microbial taxa were evaluated. The analysis was performed in R software and the network visualizations and correlation statistics were carried out in Gephi software. The results showed dominant phyla to be Proteobacteria, Actinobacteria, and Chloroflexi within the biochar materials. Further, rice husk biochar increased Euryarchaeota, while chicken manure biochar increased Planctomycetes in the soil. Therefore, variabilities of biochar feedstocks should be considered when choosing biochar type for soil amendment because different biochar materials have different impact on the microbial community structure. The third experiment was carried out to investigate the soil and dung properties influencing the decomposition of cow dung and gas emissions. An incubation study was set-up with the dung and soil sampled from 15 different farms within Hokkaido, Japan. Gas emissions was also measured. During the incubation, samples were taken at three different timings (before, middle, and final incubation) for microbial analysis. Results showed that Firmicutes and Bacteroidetes were significantly decreased while Proteobacteria and Actinobacteria increased during dung decomposition. Also, in each location, there are differences in CO2 emissions patterns which were categorized as high and low CO2 emissions. Following this trend, higher numbers of OTUs were found in low CO2 (3750) compared to high CO2 (3438). Further insight revealed that soil properties strongly influenced the emissions pattern based on the positive Pearson correlation coefficient between high CO2 emissions and soil properties such as soil C, nitrogen, and CEC. These results indicate that soil properties were the strong determinant of dung decomposition and gas emissions.