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Microorganisms
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Microbial Biodegradation of Toxic Pollutants
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Microbial Biodegradation of Toxic Pollutants

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 13060

Special Issue Editors

Dr. Miroslav Pátek

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Guest Editor
Institute of Microbiology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
Interests: the studies of gene expression control and enzyme systems in laboratory strains of model bacterial species (Escherichia coli) and on construction and analysis of strains of industrial bacteria that are used in biotechnology-based syntheses of various compounds and environmental applications (e.g., Corynebacterium glutamicum, Rhodococcus erythropolis)
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Tomas Cajthaml

E-Mail Website
Guest Editor
Faculty of Science, Charles University, Prague, Czech Republic
Interests: ligninolytic; filamentous fungi and bacteria

Special Issue Information

Dear Colleagues,

During the last few decades, the rapid development of industry and urbanization resulted in a massive release of toxic organic compounds into the environment and consequent ubiquitous pollution of air, soil, and water. The contaminating compounds include natural substances as well as xenobiotics, which are manmade chemicals that did not occur in nature before the industrial revolution. Microorganisms, which developed the abilities to degrade most naturally existing organic compounds and use them as carbon and energy sources, may also remove xenobiotics with a similar molecular structure or adapt gradually to utilization of these unnatural compounds. Biodegradable compounds include, e.g., aliphatic and aromatic hydrocarbons, halogenated compounds, phenols, polychlorinated biphenyls (PCBs), and even polymers and herbicides. Enzymatic pathways, the respective genes, and regulation of their expression have been intensively studied. In addition to description of enzymatic systems, aspects such as bioavailability and transport of pollutants and chemostress response of microbes should be uncovered before microbial abilities can be efficiently used in bioremediation and other biotechnological processes.

The Editors of this Special Issue of Microorganisms invite you to submit manuscripts concerning all aspects of the biodegradation of pollutants using microorganisms, involved enzymes and regulatory mechanisms, stress response connected to effects of toxic compounds, and biotechnological processes based on the achieved knowledge.

Dr. Miroslav Pátek
Prof. Dr. Tomas Cajthaml
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biodegradation
  • pollutant
  • biotechnological applications
  • stress response
  • omics gene engineering

Published Papers (7 papers)

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Research

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13 pages, 4861 KiB  
Article
Multi-Approach Characterization of Novel Pyrene-Degrading Mycolicibacterium austroafricanum Isolates Lacking nid Genes
by Natalia Maria Silva, Camila Lopes Romagnoli, Caio Rafael do Nascimento Santiago, João Paulo Amorim de Lacerda, Sylvia Cardoso Leão, Luciano Antonio Digiampietri and Cristina Viana-Niero
Microorganisms 2023, 11(6), 1413; https://doi.org/10.3390/microorganisms11061413 - 27 May 2023
Cited by 2 | Viewed by 1357
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are chemical compounds that are widespread in the environment, arising from the incomplete combustion of organic material, as well as from human activities involving petrol exploitation, petrochemical industrial waste, gas stations, and environmental disasters. PAHs of high molecular weight, [...] Read more.
Polycyclic aromatic hydrocarbons (PAHs) are chemical compounds that are widespread in the environment, arising from the incomplete combustion of organic material, as well as from human activities involving petrol exploitation, petrochemical industrial waste, gas stations, and environmental disasters. PAHs of high molecular weight, such as pyrene, have carcinogenic and mutagenic effects and are considered pollutants. The microbial degradation of PAHs occurs through the action of multiple dioxygenase genes (nid), which are localized in genomic island denominate region A, and cytochrome P450 monooxygenases genes (cyp) dispersed in the bacterial genome. This study evaluated pyrene degradation by five isolates of Mycolicibacterium austroafricanum using 2,6-dichlorophenol indophenol (DCPIP assay), gas chromatography/mass spectrometry (CG/MS), and genomic analyses. Two isolates (MYC038 and MYC040) exhibited pyrene degradation indexes of 96% and 88%, respectively, over a seven-day incubation period. Interestingly, the genomic analyses showed that the isolates do not have nid genes, which are involved in PAH biodegradation, despite their ability to degrade pyrene, suggesting that degradation may occur due to the presence of cyp150 genes, or even genes that have not yet been described. To the best of our knowledge, this is the first report of isolates without nid genes demonstrating the ability to degrade pyrene. Full article
(This article belongs to the Special Issue Microbial Biodegradation of Toxic Pollutants)
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14 pages, 9756 KiB  
Article
Characterization and Genomic Analysis of the Naphthalene-Degrading Delftia tsuruhatensis ULwDis3 Isolated from Seawater
by Olesya I. Sazonova, Anastasia A. Ivanova, Yanina A. Delegan, Rostislav A. Streletskii, Diana D. Vershinina, Sergei L. Sokolov and Anna A. Vetrova
Microorganisms 2023, 11(4), 1092; https://doi.org/10.3390/microorganisms11041092 - 21 Apr 2023
Cited by 1 | Viewed by 1582
Abstract
Strains of the genus Delftia are poorly studied microorganisms. In this work, the complete genome of the naphthalene-degrading Delftia tsuruhatensis strain ULwDis3 isolated from seawater of the Gulf of Finland of the Baltic Sea was assembled. For the first time, genes encoding naphthalene [...] Read more.
Strains of the genus Delftia are poorly studied microorganisms. In this work, the complete genome of the naphthalene-degrading Delftia tsuruhatensis strain ULwDis3 isolated from seawater of the Gulf of Finland of the Baltic Sea was assembled. For the first time, genes encoding naphthalene cleavage pathways via salicylate and gentisate were identified in a strain of the genus Delftia. The genes are part of one operon (nag genes). Three open reading frames (ORFs) were found in the genome of D. tsuruhatensis strain ULwDis3 that encode gentisate 1.2-dioxygenase. One of the ORFs is part of the nag operon. The physiological and biochemical characteristics of the strain ULwDis3 when cultured in mineral medium with naphthalene as the sole source of carbon and energy were also studied. It was found that after 22 h of growth, the strain stopped consuming naphthalene, and at the same time, naphthalene 1.2-dioxygenase and salicylate 5-hydroxylase activities were not detected. Later, a decrease in the number of living cells and the death of the culture were observed. Gentisate 1.2-dioxygenase activity was detected from the time of gentisate formation until culture death. Full article
(This article belongs to the Special Issue Microbial Biodegradation of Toxic Pollutants)
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17 pages, 3555 KiB  
Article
Characterization of a New Pseudomonas Putida Strain Ch2, a Degrader of Toxic Anthropogenic Compounds Epsilon-Caprolactam and Glyphosate
by Tatiana Z. Esikova, Tatiana O. Anokhina, Nataliya E. Suzina, Tatiana V. Shushkova, Yonghong Wu and Inna P. Solyanikova
Microorganisms 2023, 11(3), 650; https://doi.org/10.3390/microorganisms11030650 - 03 Mar 2023
Cited by 3 | Viewed by 2009
Abstract
In this work, a new Ch2 strain was isolated from soils polluted by agrochemical production wastes. This strain has a unique ability to utilize toxic synthetic compounds such as epsilon-caprolactam (CAP) as a sole carbon and energy source and the herbicide glyphosate [...] Read more.
In this work, a new Ch2 strain was isolated from soils polluted by agrochemical production wastes. This strain has a unique ability to utilize toxic synthetic compounds such as epsilon-caprolactam (CAP) as a sole carbon and energy source and the herbicide glyphosate (GP) as a sole source of phosphorus. Analysis of the nucleotide sequence of the 16S rRNA gene of Ch2 revealed that the strain belongs to the species Pseudomonas putida. This strain grew in the mineral medium containing CAP in a concentration range of 0.5 to 5.0 g/L and utilized 6-aminohexanoic acid and adipic acid, which are the intermediate products of CAP catabolism. The ability of strain Ch2 to degrade CAP is determined by a conjugative megaplasmid that is 550 kb in size. When strain Ch2 is cultured in a mineral medium containing GP (500 mg/L), more intensive utilization of the herbicide occurs in the phase of active growth. In the phase of declining growth, there is an accumulation of aminomethylphosphonic acid, which indicates that the C-N bond is the first site cleaved during GP degradation (glyphosate oxidoreductase pathway). Culture growth in the presence of GP during the early step of its degradation is accompanied by unique substrate-dependent changes in the cytoplasm, including the formation of vesicles of cytoplasmic membrane consisting of specific electron-dense content. There is a debate about whether these membrane formations are analogous to metabolosomes, where the primary degradation of the herbicide can take place. The studied strain is notable for its ability to produce polyhydroxyalkanoates (PHAs) when grown in mineral medium containing GP. At the beginning of the stationary growth phase, it was shown that, the amount and size of PHA inclusions in the cells drastically increased; they filled almost the entire volume of cell cytoplasm. The obtained results show that the strain P. putida Ch2 can be successfully used for the PHAs’ production. Moreover, the ability of P. putida Ch2 to degrade CAP and GP determines the prospects of its application for the biological cleanup of CAP production wastes and in situ bioremediation of soil polluted with GP. Full article
(This article belongs to the Special Issue Microbial Biodegradation of Toxic Pollutants)
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16 pages, 1754 KiB  
Article
Microcystin-Detoxifying Recombinant Saccharomyces cerevisiae Expressing the mlrA Gene from Sphingosinicella microcystinivorans B9
by Fernando de Godoi Silva, Daiane Dias Lopes, Ronald E. Hector, Maikon Thiago do Nascimento, Tatiana de Ávila Miguel, Emília Kiyomi Kuroda, Gisele Maria de Andrade de Nóbrega, Ken-Ichi Harada and Elisa Yoko Hirooka
Microorganisms 2023, 11(3), 575; https://doi.org/10.3390/microorganisms11030575 - 24 Feb 2023
Cited by 2 | Viewed by 1308
Abstract
Contamination of water by microcystins is a global problem. These potent hepatotoxins demand constant monitoring and control methods in potable water. Promising approaches to reduce contamination risks have focused on natural microcystin biodegradation led by enzymes encoded by the mlrABCD genes. The first [...] Read more.
Contamination of water by microcystins is a global problem. These potent hepatotoxins demand constant monitoring and control methods in potable water. Promising approaches to reduce contamination risks have focused on natural microcystin biodegradation led by enzymes encoded by the mlrABCD genes. The first enzyme of this system (mlrA) linearizes microcystin structure, reducing toxicity and stability. Heterologous expression of mlrA in different microorganisms may enhance its production and activity, promote additional knowledge on the enzyme, and support feasible applications. In this context, we intended to express the mlrA gene from Sphingosinicella microcystinivorans B9 in an industrial Saccharomyces cerevisiae strain as an innovative biological alternative to degrade microcystins. The mlrA gene was codon-optimized for expression in yeast, and either expressed from a plasmid or through chromosomal integration at the URA3 locus. Recombinant and wild yeasts were cultivated in medium contaminated with microcystins, and the toxin content was analyzed during growth. Whereas no difference in microcystins content was observed in cultivation with the chromosomally integrated strain, the yeast strain hosting the mlrA expression plasmid reduced 83% of toxins within 120 h of cultivation. Our results show microcystinase A expressed by industrial yeast strains as a viable option for practical applications in water treatment. Full article
(This article belongs to the Special Issue Microbial Biodegradation of Toxic Pollutants)
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17 pages, 2374 KiB  
Article
Biodegradation of Iprodione and Chlorpyrifos Using an Immobilized Bacterial Consortium in a Packed-Bed Bioreactor
by Marcela Levío-Raimán, Cristian Bornhardt and M. Cristina Diez
Microorganisms 2023, 11(1), 220; https://doi.org/10.3390/microorganisms11010220 - 15 Jan 2023
Cited by 4 | Viewed by 1631
Abstract
This work provides the basis for implementing a continuous treatment system using a bacterial consortium for wastewater containing a pesticide mixture of iprodione (IPR) and chlorpyrifos (CHL). Two bacterial strains (Achromobacter spanius C1 and Pseudomonas rhodesiae C4) isolated from the biomixture of [...] Read more.
This work provides the basis for implementing a continuous treatment system using a bacterial consortium for wastewater containing a pesticide mixture of iprodione (IPR) and chlorpyrifos (CHL). Two bacterial strains (Achromobacter spanius C1 and Pseudomonas rhodesiae C4) isolated from the biomixture of a biopurification system were able to efficiently remove pesticides IPR and CHL at different concentrations (10 to 100 mg L−1) from the liquid medium as individual strains and free consortium. The half-life time (T1/2) for IPR and CHL was determined for individual strains and a free bacterial consortium. However, when the free bacterial consortium was used, a lower T1/2 was obtained, especially for CHL. Based on these results, an immobilized bacterial consortium was formulated with each bacterial strain encapsulated individually in alginate beads. Then, different inoculum concentrations (5, 10, and 15% w/v) of the immobilized consortium were evaluated in batch experiments for IPR and CHL removal. The inoculum concentration of 15% w/v demonstrated the highest pesticide removal. Using this inoculum concentration, the packed-bed bioreactor with an immobilized bacterial consortium was operated in continuous mode at different flow rates (30, 60, and 90 mL h−1) at a pesticide concentration of 50 mg L−1 each. The performance in the bioreactor demonstrated that it is possible to efficiently remove a pesticide mixture of IPR and CHL in a continuous system. The metabolites 3,5-dichloroaniline (3,5-DCA) and 3,5,6-trichloro-2-pyridinol (TCP) were produced, and a slight accumulation of TCP was observed. The bioreactor was influenced by TCP accumulation but was able to recover performance quickly. Finally, after 60 days of operation, the removal efficiency was 96% for IPR and 82% for CHL. The findings of this study demonstrate that it is possible to remove IPR and CHL from pesticide-containing wastewater in a continuous system. Full article
(This article belongs to the Special Issue Microbial Biodegradation of Toxic Pollutants)
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25 pages, 2657 KiB  
Article
Polycyclic Aromatic Hydrocarbon-Degrading Bacteria in Three Different Functional Zones of the Cities of Moscow and Murmansk
by Olesya I. Sazonova, Olga Gavrichkova, Anastasia A. Ivanova, Kirill V. Petrikov, Rostislav A. Streletskii, Dmitriy A. Sarzhanov, Maria V. Korneykova, Andrey I. Novikov, Viacheslav I. Vasenev, Kristina V. Ivashchenko, Marina V. Slukovskaya and Anna A. Vetrova
Microorganisms 2022, 10(10), 1979; https://doi.org/10.3390/microorganisms10101979 - 06 Oct 2022
Cited by 2 | Viewed by 1808
Abstract
We performed a comparative study of the total bacterial communities and communities of cultivable polycyclic aromatic hydrocarbons (PAH)-degrading bacteria in different functional zones of Moscow and Murmansk that were formed under the influence of the PAH composition in road and leaf dust. The [...] Read more.
We performed a comparative study of the total bacterial communities and communities of cultivable polycyclic aromatic hydrocarbons (PAH)-degrading bacteria in different functional zones of Moscow and Murmansk that were formed under the influence of the PAH composition in road and leaf dust. The PAHs were determined by high-performance liquid chromatography (HPLC); the bacterial communities’ diversity was assessed by metabarcoding. The degraders were isolated by their direct plating on a medium with the PAHs. The PAH total quantity declined in the leaf dust from the traffic to the recreational zone. For the road dust, a negative gradient with pollution was observed for Rhodococcus and Acinetobacter degraders and for their relative abundance in the microbiome for the functional zones of Moscow. The opposite effect was observed in the Murmansk leaf dust for the Rothia and Pseudomonas degraders and in the Moscow road dust for Microbacterium. The PCA and linear regression analyses showed that the Micrococcus degraders in the dust were sensitive to anthropogenic pollution, so they can be used as a tool for monitoring anthropogenic changes in the biosphere. The data on the degraders’ and microbial communities’ diversity suggest that minor degrading strains can play a key role in PAH degradation. Full article
(This article belongs to the Special Issue Microbial Biodegradation of Toxic Pollutants)
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Review

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15 pages, 2155 KiB  
Review
Investigating Bio-Inspired Degradation of Toxic Dyes Using Potential Multi-Enzyme Producing Extremophiles
by Van Hong Thi Pham, Jaisoo Kim, Soonwoong Chang and Donggyu Bang
Microorganisms 2023, 11(5), 1273; https://doi.org/10.3390/microorganisms11051273 - 12 May 2023
Cited by 11 | Viewed by 2333
Abstract
Biological treatment methods overcome many of the drawbacks of physicochemical strategies and play a significant role in removing dye contamination for environmental sustainability. Numerous microorganisms have been investigated as promising dye-degrading candidates because of their high metabolic potential. However, few can be applied [...] Read more.
Biological treatment methods overcome many of the drawbacks of physicochemical strategies and play a significant role in removing dye contamination for environmental sustainability. Numerous microorganisms have been investigated as promising dye-degrading candidates because of their high metabolic potential. However, few can be applied on a large scale because of the extremely harsh conditions in effluents polluted with multiple dyes, such as alkaline pH, high salinity/heavy metals/dye concentration, high temperature, and oxidative stress. Therefore, extremophilic microorganisms offer enormous opportunities for practical biodegradation processes as they are naturally adapted to multi-stress conditions due to the special structure of their cell wall, capsule, S-layer proteins, extracellular polymer substances (EPS), and siderophores structural and functional properties such as poly-enzymes produced. This review provides scientific information for a broader understanding of general dyes, their toxicity, and their harmful effects. The advantages and disadvantages of physicochemical methods are also highlighted and compared to those of microbial strategies. New techniques and methodologies used in recent studies are briefly summarized and discussed. In particular, this study addresses the key adaptation mechanisms, whole-cell, enzymatic degradation, and non-enzymatic pathways in aerobic, anaerobic, and combination conditions of extremophiles in dye degradation and decolorization. Furthermore, they have special metabolic pathways and protein frameworks that contribute significantly to the complete mineralization and decolorization of the dye when all functions are turned on. The high potential efficiency of microbial degradation by unculturable and multi-enzyme-producing extremophiles remains a question that needs to be answered in practical research. Full article
(This article belongs to the Special Issue Microbial Biodegradation of Toxic Pollutants)
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