Chapter 2 - Omics technology to study bioremediation and respective enzymes

Abstract

Nature has its own ways of maintaining a balance in its environment. Microorganisms on Earth are one of the best natural tools that can be used to eradicate toxic pollutants. This phenomenon of using microbes to clean the environment by eliminating pollutants is termed bioremediation. In comparison to other conventional techniques, such as incineration, etc., this method is economically affordable as well as being eco-friendly. In order to successfully implement the various bioremediation techniques, one needs to have a deep knowledge of the factors regulating the growth, development, metabolism, and functions of native microbial communities that are present at the contamination site. Breakthrough innovative discoveries in high-throughput technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, along with the bioinformatics tools, have led to a better understanding of different microbial communities and their role in bioremediation. The use of microbe-assisted bioremediation has great potential in effectively restoring contaminated environments, but there implementation is often restricted due to the absence of adequate information on factors that regulate the growth and metabolism of diverse microbial communities in polluted environments. Advances in the high-throughput technologies have considerably improved the efficacy determination and implementation of microbial bioremediation strategies. Biocatalysis is another method that has improved the existing bioremediation strategies and thereby also increased the cost–benefit ratios. Enzymatic remediation, which is a valuable alternative, is easier to work with than whole organisms, particularly in extreme environments. Moreover, using free enzymes circumvents the release of exotic or genetically modified organisms (GMOs) into the surroundings. Identifying the differentially expressed proteins and screening the entire genome for the proteins that interact with the regulatory factors participating in mineralization would help us to gain a deeper understanding of bioremediation. Furthermore, metabolomics is yet another budding field of science which is in its growing phase, and metabolomic analysis has become very popular lately; the field of bioremediation could gain benefits from advances in this emerging area. Thus, there is a need to explore the potential of various metabolomic approaches to be applied in bioremediation research, such as adopting strategies for understanding biodegradation pathways, assessment of the mineralization process, and improvement of the biodegradation process. This chapter is therefore focused on the application of high-throughput “omics” technologies in gaining insights into the innate microbial community structures and functions at contamination sites and further exploring their potential in bioremediation or pollution containment facilities.