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Special Issue: Microbial Degradation of Xenobiotics

Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
Microorganisms 2020, 8(4), 487;
Submission received: 20 March 2020 / Accepted: 26 March 2020 / Published: 30 March 2020
(This article belongs to the Special Issue Microbial Degradation of Xenobiotics)
Xenobiotics are released into the environment by human activities, and they often cause problems such as environmental pollution, since most such compounds cannot be readily degraded, and have harmful effects on human beings and the natural ecosystem. However, some microorganisms that degrade man-made xenobiotics have been isolated. Most of these aerobic xenobiotics-degrading bacterial strains use xenobiotics as their sole source of carbon and energy, and thus they are excellent models for studying the adaptation and evolution of bacteria in the environment.
Recent genome analyses of bacterial strains that degrade xenobiotics have strongly suggested that they indeed emerged relatively recently by gathering genes for the degradation of xenobiotics, and mobile genetic elements played important roles in the recruitment of the genes [1]. However, the origin of the genes and the evolutionary processes of such bacterial strains remain largely unknown. Ongoing comprehensive genome and metagenome analyses may provide some insights into these mysteries, and the genes for the degradation of xenobiotics can be used as probes to reveal novel mechanisms for the evolution of microorganisms. In addition, enzymes for the degradation of xenobiotics are good materials for studies on protein evolution, since generally they have promiscuous activities, and their properties change dramatically with a small number of mutations [2]. On the other hand, the importance of microbial consortia and symbiosis for the degradation of xenobiotics in the environment has also been suggested [3], and thus studies on xenobiotics degradation may provide some novel concepts in the field of microbial ecology.
This issue gathers 13 articles dealing with various aspects of the microbial degradation of xenobiotics. Four of them deal with the bacterial strains that degrade monocyclic phenolic compounds [4], polylactic acid [5], and naphthalene [6], and those that accumulate perfluorohexane sulfonate [7]. Two are dedicated to bacterial consortia degrading diesel [8] and dioxane [9]. Two focus on the enzymes for degradation of haloalkanes [10] and bisphenols [11]. Three articles are related to “indirect” factors that are necessary or important for the microbial degradation of xenobiotics, i.e., transcriptional regulation [12], transporters that are involved in the transport of xenobiotic compounds across the outer membrane [13], and mobile genetic elements [14]. The last two articles address metabolic engineering [15] and the bioreactors [16] necessary for practical application.


I would like to thank all authors who contributed their excellent papers to this Special Issue. I thank the reviewers for their help in improving the papers to the highest standard of quality. I am also grateful to all members of the Microorganisms Editorial Office for giving me this opportunity, and for their continuous support in managing and organizing this Special Issue.

Conflicts of Interest

The author declares no conflict of interest.


  1. Nagata, Y.; Kato, H.; Ohtsubo, Y.; Tsuda, M. Lessons from the genomes of lindane-degrading sphingomonads. Environ. Microbiol. Rep. 2019, 11, 630–644. [Google Scholar] [CrossRef] [PubMed]
  2. Nagata, Y.; Ohtsubo, Y.; Tsuda, M. Properties and biotechnological applications of natural and engineered haloalkane dehalogenases. Appl. Microbiol. Biotechnol. 2015, 99, 9865–9881. [Google Scholar] [CrossRef] [PubMed]
  3. Ogawa, N.; Kato, H.; Kishida, K.; Ichihashi, E.; Ishige, T.; Yoshikawa, H.; Nagata, Y.; Ohtsubo, Y.; Tsuda, M. Suppression of substrate inhibition in phenanthrene-degrading Mycobacterium by co-cultivation with a non-degrading Burkholderia strain. Microbiology 2019, 165, 625–637. [Google Scholar] [CrossRef] [PubMed]
  4. Mpofu, E.; Chakraborty, J.; Suzuki-Minakuchi, C.; Okada, K.; Kimura, T.; Nojiri, H. Biotransformation of Monocyclic Phenolic Compounds by Bacillus licheniformis TAB7. Microorganisms 2020, 8, 26. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  5. Decorosi, F.; Exana, M.L.; Pini, F.; Adessi, A.; Messini, A.; Giovannetti, L.; Viti, C. The Degradative Capabilities of New Amycolatopsis Isolates on Polylactic Acid. Microorganisms 2019, 7, 590. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  6. Miyazawa, D.; Thanh, L.T.H.; Tani, A.; Shintani, M.; Loc, N.H.; Hatta, T.; Kimbara, K. Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8. Microorganisms 2020, 8, 44. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  7. Presentato, A.; Lampis, S.; Vantini, A.; Manea, F.; Daprà, F.; Zuccoli, S.; Vallini, G. On the Ability of Perfluorohexane Sulfonate (PFHxS) Bioaccumulation by Two Pseudomonas sp. Strains Isolated from PFAS-Contaminated Environmental Matrices. Microorganisms 2020, 8, 92. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  8. Farber, R.; Rosenberg, A.; Rozenfeld, S.; Banet, G.; Cahan, R. Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste. Microorganisms 2019, 7, 497. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  9. Tusher, T.R.; Shimizu, T.; Inoue, C.; Chien, M.-F. Enrichment and Analysis of Stable 1,4-dioxane-Degrading Microbial Consortia Consisting of Novel Dioxane-Degraders. Microorganisms 2020, 8, 50. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  10. Chrast, L.; Tratsiak, K.; Planas-Iglesias, J.; Daniel, L.; Prudnikova, T.; Brezovsky, J.; Bednar, D.; Kuta Smatanova, I.; Chaloupkova, R.; Damborsky, J. Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. Microorganisms 2019, 7, 498. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  11. Takeo, M.; Akizuki, J.; Kawasaki, A.; Negoro, S. Degradation Potential of the Nonylphenol Monooxygenase of Sphingomonas sp. NP5 for Bisphenols and Their Structural Analogs. Microorganisms 2020, 8, 284. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  12. Gibu, N.; Kasai, D.; Ikawa, T.; Akiyama, E.; Fukuda, M. Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1. Microorganisms 2019, 7, 479. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  13. Samantarrai, D.; Lakshman Sagar, A.; Gudla, R.; Siddavattam, D. TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation. Microorganisms 2020, 8, 359. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  14. Chien, M.-F.; Ho, Y.-N.; Yang, H.-E.; Narita, M.; Miyauchi, K.; Endo, G.; Huang, C.-C. Identification of A Novel Arsenic Resistance Transposon Nested in A Mercury Resistance Transposon of Bacillus sp. MB24. Microorganisms 2019, 7, 566. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  15. Demko, M.; Chrást, L.; Dvořák, P.; Damborský, J.; Šafránek, D. Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms 2019, 7, 553. [Google Scholar] [CrossRef] [Green Version]
  16. Miyoshi, Y.; Okada, J.; Urata, T.; Shintani, M.; Kimbara, K. A Rotational Slurry Bioreactor Accelerates Biodegradation of A-Fuel in Oil-Contaminated Soil Even under Low Temperature Conditions. Microorganisms 2020, 8, 291. [Google Scholar] [CrossRef] [PubMed] [Green Version]

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Nagata, Y. Special Issue: Microbial Degradation of Xenobiotics. Microorganisms 2020, 8, 487.

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Nagata Y. Special Issue: Microbial Degradation of Xenobiotics. Microorganisms. 2020; 8(4):487.

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Nagata, Yuji. 2020. "Special Issue: Microbial Degradation of Xenobiotics" Microorganisms 8, no. 4: 487.

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