Bioprospecting culturable and unculturable microbial consortia through metagenomics for bioremediation

Abstract

With the enormous increase in population and industrial network, the harmful pollutants affecting biota have also escalated. The pollutants are consumed by living organisms directly or indirectly reducing animal and economic wellbeing. The degradation of contaminants is imperative owing to the prolonged persistence of contaminants like plastics, heavy metals, pesticides, dyes, pharmaceuticals, and hydrocarbons. Remediation of such pollutants requires efficient methods to prevent mobilizing-contaminants leaching into soil and finally to human beings. In this regard, metagenomics (MGs), a non-culturable technique, involving the direct recovery of the genetic material from environmental samples is an effective tool for understanding the remediation process mediated by microorganisms and their gene products like enzymes. MGs offers a gateway to previously hidden microbial communities grown in the normal and extreme environment through sequence-based or function-based approaches. The culture-independent MGs approach in combination with other meta-omics approaches involves an easy and rapid method for the selection of remediation-efficient microbes. This paper elucidates the negative implications of several contaminants on terrestrial and aquatic biota besides highlighting the role of MGs and associated meta-omics approaches in characterizing contaminant degrading microbes. The MGs research related to bioremediation can help to generate information that will improve the bioremediation process and aid in deciphering the complete microbe-mediated bioremediation mechanism pathways. In future MGs can be helpful to comprehensively understand the mechanisms involved in efficient bioremediation, develop new strategies and models for application in rapid, accurate and efficient bioremediation process and optimize the bioremediation technique. Furthermore, the application of metagenomics to determine microbial diversity and specific genes can act as pollution biomarkers.