Background and aims: Human health is intimately related to environmental quality. The underlying microbial activity and its complex relationship with environments are significant to better understand the interaction between human and environments. With the development of molecular technologies, high-throughput qPCR based chips have become a rapid and practical molecular tool for the large-scale detection and quantification of genes in environments to investigate various microbial processes. Up to now, contaminants such as arsenic and antibiotic resistance genes have attracted much attention since their deleterious impacts on public health. The aims of this thesis are to enhance our understanding of arsenic biotransformation genes and antibiotic resistance genes in environments, and the role of contaminants played in developing and promoting them in contaminated environments. Methods: In Paper 1, I developed a high-throughput qPCR based AsChip for comprehensive profiling of arsenic biotransformation genes in environments. In Paper 2, feed additives, gut microbiota and antibiotic resistance genes in pig gut were studied to elucidate the effect of infeed antibiotics and metals on gut microbial community and antibiotic resistance genes in guts with the application of the ARG chip. In Paper 3, antibiotic resistance genes were profiled in metal-contaminated urban soils by the ARG chip and linked to metals contaminations to investigate the role of metals in the environmental dimension of antibiotic resistance genes. Results and discussion: AsChip containing 81 primers sets for 19 arsenic biotransformation genes and a 16S rRNA gene as a reference gene was developed and validated to be an effective tool with high coverage, sensitivity, specificity and efficiency (Paper 1). Diverse and abundant ARGs were identified in pig manure samples from large-scale Chinese pig farms. Total abundance of ARGs was positively correlated to in-feed antibiotics, microbial biomass and mobile genetic elements (P < 0.05). Partial redundancy analysis revealed that the variance in ARGs profiles was primarily attributed to antibiotics and metals in the feed (31.8%) andmicrobial community (23.3%) (Paper 2). High diversity and abundance of ARGs were detected in metal-polluted urban soils. Network analysis and path analysis revealed the strong association between metal contaminants and ARGs, indicating the role of soil metals in co-selection of ARGs and MGEs in urban soils and potential horizontal gene transfer (Paper 3). Conclusions: Overall, this thesis provides tools and studies to elevate our knowledge of arsenic biotransformation and antibiotic resistance in environments and their underlying genetic basis by developing and applying corresponding HT-qPCR based chips. AsChip was proven a robust, rapid molecular tool for comprehensive detection and quantification of arsenic biotransformation genes (Paper 1). Antibiotics and metals as feed additives could shift pig gut microbiota and enrich antibiotic resistance genes in pig guts (Paper 2). Metal contaminants may release a persistent selection pressure on antibiotic resistance genes and mobile genetic elements in urban soils (Paper 3).