Metagenomic Exploration of Plastic Degrading Microbes for Biotechnological Application

Abstract

Since the last few decades, the promiscuous and uncontrolled use of plastics led to the accumulation of millions of tons of plastic waste in the terrestrial and marine environment. It elevated the risk of environmental pollution and climate change. The concern arises more due to the reckless and unscientific disposal of plastics containing high molecular weight polymers, viz., polystyrene, polyamide, polyvinylchloride, polypropylene, polyurethane, and polyethylene, etc. which are very difficult to degrade. Thus, the focus is now paid to search for efficient, eco-friendly, low-cost waste management technology. Of them, degradation of non-degradable synthetic polymer using diverse microbial agents, viz., bacteria, fungi, and other extremophiles become an emerging option. So far, very few microbial agents and their secreted enzymes have been identified and characterized for plastic degradation, but with low efficiency. It might be due to the predominance of uncultured microbial species, which consequently remain unexplored from the respective plastic degrading milieu. To overcome this problem, metagenomic analysis of microbial population engaged in the plastic biodegradation is advisable to decipher the microbial community structure and to predict their biodegradation potential in situ. Advancements in sequencing technologies and bioinformatics analysis allow the rapid metagenome screening that helps in the identification of total microbial community and also opens up the scope for mining genes or enzymes (hydrolases, laccase, etc.) engaged in polymer degradation. Further, the extraction of the core microbial population and their adaptation, fitness, and survivability can also be deciphered through comparative metagenomic study. It will help to engineer the microbial community and their metabolic activity to speed up the degradation process.

Keywords: Metagenomics; genetic engineering; microbial community; microbiome engineering; plastic degrading microbes; prebiotics; probiotics.

Fig. (1)

Mechanism of plastic biodegradation. The physical bio-deterioration by sunlight, UV-radiation predisposes plastic waste for microbial biodegradation that is carried out through enzymatic action. The conversion of complex polymer into monomers or oligomers facilitates their assimilation by cellular ATP binding cassette (ABC), Major facilitator superfamily (MFS) protein, and undergoes β-oxidation by intracellular enzymes to produce Acetyl CoA, Propinoyl CoA, or Succinyl CoA which are used as the substrate for TCA cycle to produce energy (ATP) in the form of Flavin adenine dinucleotide, (FADH₂), Nicotinamide adenine dinucleotide (NADH). (A higher resolution / colour version of this figure is available in the electronic copy of the article).

Fig. (2)

Metagenomics approach to decipher the structure and function of microbial community in plastisphere. The exploration of taxonomic identity of microbial population and the discovery of novel genes and their functional prediction in the complex metabolic pathways could be possible in different spatiotemporal scales.

Fig. (3)

Approaches of microbiome engineering of plastisphere. The metagenomic study of different plastisphere from diverse ecosystem helps to identify the core and specific microbial population along with their ecological preferences. It opens up the scope of manipulating the microbial community composition via prebiotic and probiotic approaches. The discovery of novel genes, metabolic pathways leads the way for engineering microbial genetic constitution through plasmid augmentation, recombinant DNA technology, genome editing, protein engineering, etc. to enhance their metabolic activity and speed up the plastic degradation process. (A higher resolution / colour version of this figure is available in the electronic copy of the article).