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Microorganisms
Special Issues
Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants
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Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants

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

Deadline for manuscript submissions: closed (31 May 2024) | Viewed by 7415

Special Issue Editor

Dr. Anna Muratova

E-Mail Website
Guest Editor
Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), Saratov 410049, Russia
Interests: bacterial degradation of PAHs and oil hydrocarbons; biodegradation enzymes; bioremediation; plant-microbe interactions; plant-microbial metabolisms of organic pollutants; phytoremediation

Special Issue Information

Dear Colleagues,

The development of modern technologies leads to the continued saturation of the environment with various organic and inorganic compounds, the diversity and quantity of which are constantly increasing. The large-scale and long-term use of naturally, synthetically, and unintentionally produced organic compounds turns them into hazardous pollutants, with different resistances to biotic and abiotic decomposition in the environment. For example, despite their natural origin, large volumes of oil production, transportation, and processing all over the world have made petroleum hydrocarbons one of the largest and most dangerous pollutants. The widespread use of synthetic pesticides, pharmaceuticals, and plastics also increases the water and land areas contaminated with them. Phenols, polycyclic aromatic hydrocarbons (PAHs), and heterocyclic compounds such as phenol, pyridine, p-nitrophenol, trichloroethylene, and dimethyl phthalate (DMP) are a major environmental problem around the world. In addition, the scale of environmental pollution is increasing with a new generation of persistent organic pollutants, including polybrominated diphenyl ethers (PBDE), polychlorinated naphthalenes (PCNs), and perfluorochemicals (PFCs). The persistence of such compounds, classified as persistent organic pollutants (POPs), in the environment represents a long-term danger to human and wildlife health. The biological decomposition of hazardous organic pollutants caused by living organisms is the only way to counteract their accumulation in nature. The purposeful use of flexible metabolic processes of microorganisms makes it possible to ensure the complete and cost-effective removal of pollutants from the environment.

This Special Issue of Microorganisms welcomes original research and review articles that present the latest advances in the microbial degradation of hazardous organic contaminants. The topics that fit the scope of the Special Issue are as follows:

- Taxonomic diversity of microorganisms degrading hazardous organic contaminants.

- Degradation pathways (including enzymes and metabolites) of hazardous organic contaminants.

- Influence of biotic (interactions of microorganisms with plants, fungi, and among themselves) and abiotic (environmental conditions and the presence of various additives) factors on the degradation of hazardous organic contaminants.

- Selection and study of microorganisms degrading new synthetic compounds.

- Genomics as a way for improving biodegradation of hazardous organic contaminants.

- Use of metagenomics, metatranscriptomics, metabolomics, and metaproteomics to predict the catabolic potential of microorganisms in a polluted environment.

Papers on other relevant topics are also welcome.

Dr. Anna Muratova
Guest Editor

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
  • persistent organic pollutants
  • microbial enzymes for biodegradation
  • metabolic pathways of pollutants
  • pollutant catabolism genes

Published Papers (6 papers)

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Research

23 pages, 4610 KiB  
Article
Phenanthrene-Degrading and Nickel-Resistant Neorhizobium Strain Isolated from Hydrocarbon-Contaminated Rhizosphere of Medicago sativa L.
by Sergey Golubev, Margarita Rasterkovskaya, Irina Sungurtseva, Andrey Burov and Anna Muratova
Microorganisms 2024, 12(8), 1586; https://doi.org/10.3390/microorganisms12081586 - 4 Aug 2024
Viewed by 253
Abstract
Pollutant degradation and heavy-metal resistance may be important features of the rhizobia, making them promising agents for environment cleanup biotechnology. The degradation of phenanthrene, a three-ring polycyclic aromatic hydrocarbon (PAH), by the rhizobial strain Rsf11 isolated from the oil-polluted rhizosphere of alfalfa and [...] Read more.
Pollutant degradation and heavy-metal resistance may be important features of the rhizobia, making them promising agents for environment cleanup biotechnology. The degradation of phenanthrene, a three-ring polycyclic aromatic hydrocarbon (PAH), by the rhizobial strain Rsf11 isolated from the oil-polluted rhizosphere of alfalfa and the influence of nickel ions on this process were studied. On the basis of whole-genome and polyphasic taxonomy, the bacterium Rsf11 represent a novel species of the genus Neorhizobium, so the name Neorhizobium phenanthreniclasticum sp. nov. was proposed. Analysis of phenanthrene degradation by the Rsf1 strain revealed 1-hydroxy-2-naphthoic acid as the key intermediate and the activity of two enzymes apparently involved in PAH degradation. It was also shown that the nickel resistance of Rsf11 was connected with the extracellular adsorption of metal by EPS. The joint presence of phenanthrene and nickel in the medium reduced the degradation of PAH by the microorganism, apparently due to the inhibition of microbial growth but not due to the inhibition of the activity of the PAH degradation enzymes. Genes potentially involved in PAH catabolism and nickel resistance were discovered in the microorganism studied. N. phenanthreniclasticum strain Rsf11 can be considered as a promising candidate for use in the bioremediation of mixed PAH–heavy-metal contamination. Full article
(This article belongs to the Special Issue Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants)
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15 pages, 6224 KiB  
Article
Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile
by Akzhigit Mashzhan, Aida Kistaubayeva, Rubén Javier-López, Akerke Bissenbay and Nils-Kåre Birkeland
Microorganisms 2024, 12(7), 1277; https://doi.org/10.3390/microorganisms12071277 - 23 Jun 2024
Viewed by 660
Abstract
Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov. strain KAk was isolated from a geothermal hot spring located in Kazakhstan. Growth occurred at temperatures ranging from 50 to 80 °C, with approximately 70 °C as optimum. It also thrived in pH conditions ranging from 4.0 [...] Read more.
Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov. strain KAk was isolated from a geothermal hot spring located in Kazakhstan. Growth occurred at temperatures ranging from 50 to 80 °C, with approximately 70 °C as optimum. It also thrived in pH conditions ranging from 4.0 to 9.0, with the best growth occurring at 6.8. Under optimal conditions in a glucose-containing medium, the cells were predominantly observed singly, in pairs, or less frequently in chains, and did not form endospores. However, under conditions involving growth with merino wool or feathers, or under suboptimal conditions, the cells of strain KAk exhibited a notably elongated and thinner morphology, with lengths ranging from 5 to 8 µm, and spores were observed. The KAk strain exhibited efficient degradation of feather keratin and merino wool at temperatures ranging from 65 to 70 °C. Analysis of the 16S rRNA gene sequence placed KAk within the genus Caldanaerobacter, family Thermoanaerobacteraceae, with the highest similarity to C. subterraneus subsp. tengcongensis MB4T (98.84% sequence identity). Furthermore, our analysis of the draft genome sequence indicated a genome size of 2.4 Mbp, accompanied by a G+C value of 37.6 mol%. This study elucidated the physiological and genomic characteristics of strain KAk, highlighting its keratinolytic capabilities and distinctiveness compared to other members of the genus Caldanaerobacter. Full article
(This article belongs to the Special Issue Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants)
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18 pages, 6226 KiB  
Article
Genomic Insights into the Microbial Agent Streptomyces albidoflavus MGMM6 for Various Biotechnology Applications
by Roderic Gilles Claret Diabankana, Mikhail Frolov, Saparmyradov Keremli, Shamil Zavdatovich Validov and Daniel Mawuena Afordoanyi
Microorganisms 2023, 11(12), 2872; https://doi.org/10.3390/microorganisms11122872 - 27 Nov 2023
Cited by 1 | Viewed by 1400
Abstract
Microbial biotechnology plays a crucial role in improving industrial processes, particularly in the production of compounds with diverse applications. In this study, we used bioinformatic approaches to analyze the genomic architecture of Streptomyces albidoflavus MGMM6 and identify genes involved in various metabolic pathways [...] Read more.
Microbial biotechnology plays a crucial role in improving industrial processes, particularly in the production of compounds with diverse applications. In this study, we used bioinformatic approaches to analyze the genomic architecture of Streptomyces albidoflavus MGMM6 and identify genes involved in various metabolic pathways that have significant biotechnological potential. Genome mining revealed that MGMM6 consists of a linear chromosome of 6,932,303 bp, with a high G+C content of 73.5%, lacking any plasmid contigs. Among the annotated genes, several are predicted to encode enzymes such as dye peroxidase, aromatic ring-opening dioxygenase, multicopper oxidase, cytochrome P450 monooxygenase, and aromatic ring hydroxylating dioxygenases which are responsible for the biodegradation of numerous endogenous and xenobiotic pollutants. In addition, we identified genes associated with heavy metal resistance, such as arsenic, cadmium, mercury, chromium, tellurium, antimony, and bismuth, suggesting the potential of MGMM6 for environmental remediation purposes. The analysis of secondary metabolites revealed the presence of multiple biosynthesis gene clusters responsible for producing compounds with potent antimicrobial and metal-chelating activities. Furthermore, laboratory tests conducted under controlled conditions demonstrated the effectiveness of MGMM6 in inhibiting phytopathogenic microbes, decolorizing and degrading aromatic triphenylmethane dyes, particularly Blue Brilliant G250, from wastewater by up to 98 ± 0.15%. Overall, the results of our study highlight the promising biotechnological potential of S. albidoflavus MGMM6. Full article
(This article belongs to the Special Issue Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants)
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18 pages, 3554 KiB  
Article
Genome Analysis and Physiology of Pseudomonas sp. Strain OVF7 Degrading Naphthalene and n-Dodecane
by Anastasia A. Ivanova, Olesya I. Sazonova, Anton N. Zvonarev, Yanina A. Delegan, Rostislav A. Streletskii, Lidia A. Shishkina, Alexander G. Bogun and Anna A. Vetrova
Microorganisms 2023, 11(8), 2058; https://doi.org/10.3390/microorganisms11082058 - 10 Aug 2023
Cited by 2 | Viewed by 1440
Abstract
The complete genome of the naphthalene- and n-alkane-degrading strain Pseudomonas sp. strain OVF7 was collected and analyzed. Clusters of genes encoding enzymes for the degradation of naphthalene and n-alkanes are localized on the chromosome. Based on the Average Nucleotide Identity and [...] Read more.
The complete genome of the naphthalene- and n-alkane-degrading strain Pseudomonas sp. strain OVF7 was collected and analyzed. Clusters of genes encoding enzymes for the degradation of naphthalene and n-alkanes are localized on the chromosome. Based on the Average Nucleotide Identity and digital DNA–DNA Hybridization compared with type strains of the group of fluorescent pseudomonads, the bacterium studied probably belongs to a new species. Using light, fluorescent, and scanning electron microscopy, the ability of the studied bacterium to form biofilms of different architectures when cultured in liquid mineral medium with different carbon sources, including naphthalene and n-dodecane, was demonstrated. When grown on a mixture of naphthalene and n-dodecane, the strain first consumed naphthalene and then n-dodecane. Cultivation of the strain on n-dodecane was characterized by a long adaptation phase, in contrast to cultivation on naphthalene and a mixture of naphthalene and n-dodecane. Full article
(This article belongs to the Special Issue Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants)
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16 pages, 3513 KiB  
Article
Isolation and Genomic Analysis of 3-Chlorobenzoate-Degrading Bacteria from Soil
by Ifat Ara, Ryota Moriuchi, Hideo Dohra, Kazuhide Kimbara, Naoto Ogawa and Masaki Shintani
Microorganisms 2023, 11(7), 1684; https://doi.org/10.3390/microorganisms11071684 - 28 Jun 2023
Cited by 1 | Viewed by 1421
Abstract
The compound 3-chlorobenzoate (3-CBA) is a hazardous industrial waste product that can harm human health and the environment. This study investigates the physiological and genetic potential for 3-chlorobenzoate (3-CBA) degradation. Six 3-CBA Gram-negative degraders with different degradation properties belonging to the genera Caballeronia [...] Read more.
The compound 3-chlorobenzoate (3-CBA) is a hazardous industrial waste product that can harm human health and the environment. This study investigates the physiological and genetic potential for 3-chlorobenzoate (3-CBA) degradation. Six 3-CBA Gram-negative degraders with different degradation properties belonging to the genera Caballeronia, Paraburkholderia and Cupriavidus were isolated from the soil. The representative strains Caballeronia 19CS4-2 and Paraburkholderia 19CS9-1 showed higher maximum specific growth rates (µmax, h−1) than Cupriavidus 19C6 and degraded 5 mM 3-CBA within 20–28 h. Two degradation products, chloro-cis,cis-muconate and maleylacetate, were detected in all isolates using high-performance liquid chromatography and mass spectrometry. Genomic analyses revealed the presence of cbe and tfd gene clusters in strains 19CS4-2 and 19CS9-1, indicating that they probably metabolized the 3-CBA via the chlorocatechol ortho-cleavage pathway. Strain 19C6 possessed cbe genes, but not tfd genes, suggesting it might have a different chlorocatechol degradation pathway. Putative genes for the metabolism of 3-hydroxybenzoate via gentisate were found only in 19C6, which utilized the compound as a sole carbon source. 19C6 exhibited distinct characteristics from strains 19CS4-2 and 19CS9-1. The results confirm that bacteria can degrade 3-CBA and improve our understanding of how they contribute to environmental 3-CBA biodegradation. Full article
(This article belongs to the Special Issue Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants)
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12 pages, 3207 KiB  
Article
Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91
by Wei Xiang, Shan Hong, Yanfen Xue and Yanhe Ma
Microorganisms 2023, 11(6), 1537; https://doi.org/10.3390/microorganisms11061537 - 9 Jun 2023
Cited by 1 | Viewed by 1549
Abstract
Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate [...] Read more.
Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate the functional role of alkB1 and alkB2 genes in the n-alkane degradation of strain CH91. RT-qPCR analyses revealed that the two genes were induced by n-alkanes ranging from C16 to C36 and the expression of the alkB2 gene was up-regulated much higher than that of alkB1. The knockout of the alkB1 or alkB2 gene in strain CH91 resulted in the obvious reduction of growth and degradation rates on C16-C36 n-alkanes and the alkB2 knockout mutant exhibited lower growth and degradation rate than the alkB1 knockout mutant. When gene alkB1 or alkB2 was heterologously expressed in Pseudomonas fluorescens KOB2Δ1, the two genes could restore its alkane degradation activity. These results demonstrated that both alkB1 and alkB2 genes were responsible for C16-C36 n-alkanes’ degradation of strain CH91, and alkB2 plays a more important role than alkB1. The functional characteristics of the two alkB genes in the degradation of a broad range of n-alkanes make them potential gene candidates for engineering the bacteria used for bioremediation of petroleum hydrocarbon contaminations. Full article
(This article belongs to the Special Issue Latest Advances in the Microbial Degradation of Hazardous Organic Contaminants)
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