| Mining activities result in the formation of a widespread environmental problem known as acid mine drainage (AMD), which results from chemical and biological oxidation of exposed sulfide minerals. AMD have high concentration of sulfate and toxic metals. A surprisingly wide diversity of microorganisms populate AMD environments. These organisms, mostly bacteria and archaea, can form a chemautotrophically-based biosphere in the subsurface and their activity increases the rate of AMD formation and may be responsible for the bulk of AMD generated.The intention of understanding the structure, composition, and adaptive responses of microbial community is to elucidate the factors by examining the interactions of microorganisms and mineral and the biotic and abiotic characteristics of AMD environment. The notable simplicity of AMD environments may permit a more fundamental understanding of biogeochemical interactions and feedbacks and microbial communities structure and function than is possible through study of more complex ecosystems. The composition and proportion of microbes could be influenced by the mineral and the condition of bioleaching systems.Culture-independent methods have provided a detailed understanding of the full diversity and phylogeny of organisms populating AMD and bioleaching systems. However, the detection, characterization, and quantification of microbial population diversity in various environments are formidable tasks. Microarray-based genomic technology provides the opportunity to identify thousands of microbial genes or populations simultaneously and the high-throughput advantages necessary for comprehensive characterization of complex microbial community overcomes the limitations of traditional microbial characterization. However, applications of this technology to the characterization of microbial communities are still limited, mainly because of the inherent unknown and miscellaneous composition of these samples. There are several types of microarrays has been successfully applied to microbial ecology research, such as functional gene array (FGA), community genome array (CGA) and phylogenetic oligonucleotide array (POA).This research have been developed and evaluated a community genome array (CGA) for bacterial detection and microbial community analysis of acid mine drainage and bioleaching systems. Community genome array (CGA) consisting of whole genomic DNA is used as a probe for identifying microorganisms within the context of microbial communities isolated from 51 closely or distantly related representative bacterial strains. This approach is similar to the Reverse Sample Genome Probing (RSGP) methodology but modification. Based on the results of microarray hybridization, specificity tests with representation pure cultures indicated that the probes on the arrays appeared the be specific to their corresponding target genomic DNA. Cross-hybridization occurred between strains of the same species, but little cross-hybridization was observed among different species. The detection limit was estimated to be approximately 0.2 ng with genomic DNA from a single pure culture bacterial and 5 ng with mixed genomic DNA from mixtures of known amounts of different species' genomic DNA. In addition, strong linear relationships were observed between hybridization signal intensity and the target DNA concentrations from 0.2 ng to 2000 ng for pure cultures and a mixture of DNA template (r~2=0.95 to 0.985). Application of this type of the microarray revealed differences in microbial community composition. The results indicate that this technology has potential as a specific, sensitive and quantitative tool for detection and identification of acidophilic microorganism and the microbial community in acid mine drainage and bioleaching systems, although more work is needed to improve.
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