Chapter 8 - Application of metagenomics in remediation of contaminated sites and environmental restoration

Abstract

Rapid industrialization, urbanization, and agricultural practices have led to the generation and release of various toxic organic and inorganic contaminants into the environment. These toxic contaminants can accumulate and persist for long periods of time and deteriorate the surrounding environment. Thus remediation of contaminated sites using microbial process (bioremediation) has proven an ecofriendly, reliable technology, promising technology due to its overall high efficiency and cost-effectiveness. However, bioremediation of contaminated sites has been hampered by the lack of a holistic system-wide understanding of the complex interactions between degrading organisms and genes, the wider metabolic network of the microbial community, and the environmental variability in each specific habitat. Although conventional or culture-dependent methods are currently being applied to characterize the potential pollutants degrading/detoxifying microorganisms, these techniques are often biased and of limited value owing to the inability to cultivate many naturally occurring species. Many molecular culture-independent methods have been widely used to investigate the microbial community structure and their function in a contaminated environment. However, these low-throughput approaches are not able to completely explore the detailed microbial community structure due to the extremely complex communities and overwhelming genetic diversities in contaminated sites. Recently, advanced metagenomics approaches based on high-throughput sequencing, which can be used to directly sequence genomic DNA, have been widely used in studies to explore the structures and functions of microbial communities in the biogeochemical cycles and degradation and detoxification of environmental pollutants. In this chapter we seek to provide key background on metagenomics approaches and summarize how these tools have been employed to understand contaminated environments in an effort to inform the best practices for environmental cleanup. We also discuss the potential of metagenomics to boost the development of improved metagenomics strategies for cleaning up contaminated environments with the help of recent multiple case studies and highlight how this approach has allowed the recent discovery of new biodegradation genes/pathways and microbial adaptation and synergistic.