Genomic and transcriptomic perspectives on mycoremediation of polycyclic aromatic hydrocarbons

Abstract

Mycoremediation holds great potential in remedying toxic environments contaminated with polyaromatic organic pollutants. To harness the natural process for practical applications, understanding the genetic and molecular basis of the remediation process is prerequisite. Compared to known bacterial degradation pathways of aromatic pollutants, however, the fungal degradation system is less studied and understanding of the genetic basis for biochemical activity is still incomplete. In this review, we surveyed recent findings from genomic and transcriptomic approaches to mycoremediation of aromatic pollutants, in company with the genomic basis of polycyclic aromatic hydrocarbon (PAH) degradation by basidiomycete fungi, Dentipellis sp. KUC8613. Unique features in the fungal degradation of PAHs were outlined by multiple cellular processes: (i) the initial oxidation of recalcitrant contaminants by various oxidoreductases including mono- and dioxygenases, (ii) the following detoxification, and (iii) the mineralization of activated pollutants that are common metabolism in many fungi. Along with the genomic data, the transcriptomic analysis not only posits a full repertoire of inducible genes that are common or specific to metabolize different PAHs but also leads to the discovery of uncharacterized genes with potential functions for bioremediation processes. In addition, the metagenomic study accesses community level of mycoremediation process to seek for the potential species or a microbial consortium in the natural environments. The comprehensive understanding of fungal degradation in multiple levels will accelerate practical application of mycoremediation.

Key points
• Mycoremediation of polyaromatic pollutants exploits a potent fungal degrader.
• Fungal genomics provides a full repository of potential genes and enzymes.
• Mycoremediation is a concerted cellular process involved with many novel genes.
• Multi-omics approach enables the genome-scale reconstruction of remedying pathways.

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Funding

This work is supported by the Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01337602) and Rural Development Administration and New and Renewable Energy Core Technology Program of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grants from the Ministry of Trade, Industry, and Energy (No. 20173010092460), Republic of Korea.

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HP and I-GC conceived and designed research. HP conducted experiments. HG and I-GC analyzed data. HP and I-GC wrote and approved the manuscript.

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Correspondence to In-Geol Choi.

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Park, H., Choi, I. Genomic and transcriptomic perspectives on mycoremediation of polycyclic aromatic hydrocarbons. Appl Microbiol Biotechnol (2020). https://doi.org/10.1007/s00253-020-10746-1

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Keywords

  • Polycyclic aromatic hydrocarbons
  • Mycoremediation
  • Dentipellis sp. KUC8613
  • Transcriptomics
  • Metagenomics