Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Abstract

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Keywords: bioremediation; environmental pollution; fluxomics; metabolomics; metagenomics; metatranscriptomics; proteomics.

Figure 1

Different sources of environmental contamination.

Figure 2

Microbial-based bioremediation mechanism.

Figure 3

Genome-based approaches that contribute toward the development of models of how microbes function in the polluted environments (a) Cells: the isolated cells from the environmental samples gives an opportunity to furnish/obtain information on the gene composition as well as in-depth physiological analysis (b) DNA: Genomic DNA extracted from the environmental samples provides information and knowledge regarding the genetic potential of the yet-unculturable microorganisms (c) mRNA and Proteins: mRNA and proteins extracted from the environments furnishes information about the gene expression under varied environmental conditions.

Figure 4

Novel processes in order to improve bioremediation of polluted environments.