Microbial metabolism of aromatic pollutants: High-throughput OMICS and metabolic engineering for efficient bioremediation

Multifaceted catabolic interaction among key microbial populations is the most crucial factor for biodegradation and elimination of toxic and xenobiotic aromatic pollutants. With genomic plasticity conferring adaptation and evolution of functional traits, bacteria use arrays of biochemical routes to mineralize these anthropogenic and synthetic organics. However, lack of suitable microbes with desired robust degradation metabolic pathways, appropriate regulatory features together with survivability to environmental/physicochemical extremities have led to unsuccessful in-situ biodegradation attempts. In the last few decades, elucidation of biochemical pathways, enzyme systems, genetic organization, and its regulation for degradation of aromatic pollutants have been studied in depth. Though some metabolic patchwork-based engineering of degrading microbes has shown promising results under laboratory in-vitro conditions, these approaches have disappointed at the field-scale. The paucity of knowledge on the process complexity and genetic/metabolic/regulatory/enzymatic features, thermodynamic feasibility of assembled catabolic networks, expression levels of pathway modules, cross-talk between metabolic routes/fluxes, and overall cellular responses/physiology have resulted in such failures. In the postgenomics era, recent advancement of high-throughput OMICS such as (meta)genomics, (meta)transcriptomics, (meta)metabolomics, and (meta)proteomics in combination with system biology and metabolic engineering allows to reveal newer insights of molecular and genetic (interactomic) details of microbes. Such knowledge is of prime importance to get detailed understanding of metabolism and interaction of microorganisms with pollutants at the level of both single species and microbial communities. This paves the way for the selection of microbial host(s) to design new, efficient, and environmental-friendly remediation strategies and minimize uncertainties of successful on-site clean-up plans. In this chapter, we focus on deciphering multi-OMICS (genomic, proteomic, transcriptomic, and metabolomics)-based insights on metabolism, regulatory features, and interaction among aromatic degraders. Such understanding aids in designing new catabolic pathways for achieving eco-friendly and trash-to-treasure conversions by potential microbes.