Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology

Abstract

Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

“…However, effective implementation of microbial remediation strategies needs advanced technical approaches, which provide an in-depth understanding about the dynamics aspects of microbial activity and survival under stressed environment (Rastogi and Sani, 2011 ; Lima-Morales et al, 2016 ; Mao et al, 2019 ). The development in molecular, biotechnological, bioinformatics and system biology tools pertaining to bio-remedial problems have provided gene level mechanisms of bioremediation (Ahmad and Ahmad, 2014 ; Aora and Bar, 2014 ; Singh D. P. et al, 2018 ; Jaiswal and Shukla, 2020 ; Nkongolo and Kotha, 2020 ; Wolf et al, 2020 ). Moreover, the direct study of microorganisms in a contaminated environment including the whole microbial population granted a new frontier of the scientific community to share the knowledge of the uncultured microbial world (Zepeda et al, 2015 ; Zhao Q. et al, 2017 ; Panigrahi et al, 2019 ; Yan et al, 2020 ).…”

Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

“…Metagenomics, together with other tools (transcriptomics, proteomics, and metabolomics) can lead to the identification of genes and pathways involved in the biodegradation of different recalcitrant pollutants. The possibility of understanding the degradation potential of each microorganism lays the foundations for the engineering of synthetic microbial consortia optimized for the complete breakdown of specific pollutants, which often require multiple enzymes, hardly possessed by a single microbial strain [ 187 , 188 ].…”

Synthetic Organic Compounds From Paper Industry Wastes: Integrated Biotechnological Interventions

“…Degradation of these compounds depends upon the secretion of enzymes by microorganisms that participate in the metabolic pathways. The traditional physicochemical bioremediation methods ( in situ and ex situ ) ( Jaiswal et al, 2020 ) are inefficient for degradation and removal of new emerged compounds ( Jaiswal and Shukla, 2020 ). With the development of genetic engineering and Recombinant DNA technology many genetically modified microorganisms were constructed by using various techniques for the remediation of synthetic organic compounds ( Liu et al, 2019 ).…”

“…With the help of gene-editing techniques, modified microorganisms with maximum quality can be produced by making targeted modifications in the genome using molecular scissors involving engineered nucleases. Clustered regularly interspaced short palindromic repeat (CRISPR-Cas), zinc finger nucleases (ZFNs) and Transcription-activators like effector nucleases (TALENs) are the main gene-editing tools that have the dynamic capacity to boost bioremediation of synthetic pesticides ( Jaiswal and Shukla, 2020 ; Kumari and Chaudhary, 2020 ). The gene editing process involves self-designed guide sequences that are inserted complementary to the sequence of the gene of interest assisting break at a site, repaired by homologous recombination, insertion, or deletion of desired sequence fragments.…”