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Biodegradation of Pollutants in the Environment: Omics Approaches 3.0
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Biodegradation of Pollutants in the Environment: Omics Approaches 3.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Toxicology".

Deadline for manuscript submissions: 20 June 2025 | Viewed by 2844

Special Issue Editor

Dr. Irina Sousa Moreira

E-Mail Website
Guest Editor
CBQF—Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, 4169-005 Porto, Portugal
Interests: environmental microbiology; biodegradation; fluoroaromatics; emerging contaminants; metabolic pathways; aerobic granular sludge; bioreactors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of the 2021 Special Issue “Biodegradation of Pollutants in the Environment: Omics Approaches” and the 2023 Special Issue “Biodegradation of Pollutants in the Environment: Omics Approaches 2.0”.

Biodegradation by microorganisms is considered a cost-effective and environmentally friendly process for the removal of contaminants from natural ecosystems, as well as for preventing their release from sources of pollution. In recent decades, omics disciplines, such as genomics, proteomics, metabolomics, metagenomics and transcriptomics, have emerged as scientific tools for understanding the mechanisms of biodegradation processes, namely, the elucidation of genes and enzymes involved in the degradation of and tolerance to xenobiotics, the identification of the intermediate and final metabolites of degradation pathways and the identification of key microorganisms from the communities involved in the degradation. This knowledge allows not only the deepening of the understanding of biodegradation processes but also the optimization of the efficiency of degradation and the isolation of degrading strains for use in biotechnological applications for bioremediation proposes.

Reviews and original articles focused on the biodegradation of pollutants, particularly concerning the use of omics tools and the examination of molecular mechanisms, are welcome.

Dr. Irina Sousa Moreira
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.

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Keywords

  • biodegradation
  • pollutants
  • genomics
  • proteomics
  • metabolomics
  • metagenomics
  • transcriptomics
  • degrading microorganisms
  • metabolic pathway of degradation

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Published Papers (3 papers)

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20 pages, 5263 KiB  
Article
Comparative Genomics, Transcriptome, and Prokaryotic Expression Analysis of alkB1_1 in Acinetobacter vivianii KJ-1: Revealing the Mechanism of Petroleum Hydrocarbon Degradation
by Qiannan Cui, Yali Zhang, Jie Wang, Jianing Wang, Qingqing Zhao, Fanyong Song, Leilei Wang, Wen Zhang and Yujie Huang
Int. J. Mol. Sci. 2025, 26(9), 4083; https://doi.org/10.3390/ijms26094083 - 25 Apr 2025
Viewed by 146
Abstract
The present study aimed to comprehensively dissect the petroleum hydrocarbon degradation mechanism of Acinetobacter vivianii KJ-1. The isolated and identified strain was able to proliferate using diesel as the sole carbonaceous substrate. Via comparative genomics, an in-depth analysis was performed to elucidate the [...] Read more.
The present study aimed to comprehensively dissect the petroleum hydrocarbon degradation mechanism of Acinetobacter vivianii KJ-1. The isolated and identified strain was able to proliferate using diesel as the sole carbonaceous substrate. Via comparative genomics, an in-depth analysis was performed to elucidate the genome similarities and disparities between this strain and related strains, thereby uncovering a core genome as well as genes with uncharacterized functions. Transcriptome analysis, carried out under different substrate conditions (C16, diesel, sodium acetate) manifested distinct gene expression modalities. A multitude of genes associated with alkane metabolism were differentially expressed, among which alkB1_1 and alkB1_2 was conspicuously upregulated. Prokaryotic expression of alkB1_1 was implemented, and the enzyme activity of the recombinant protein peaked at a pH level of approximately 7.0 and within a temperature range of 30 to 40 °C. The recombinant strain was shown to possess the ability to degrade n-hexadecane. Collectively, this research not only augments the understanding of the degradation mechanism of A. vivianii KJ-1 but also provides a fundamental basis for developing bioremediation strategies targeting petroleum hydrocarbon-contaminated environments. Full article
(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 3.0)
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15 pages, 4167 KiB  
Article
Proteome Changes Induced by Iprodione Exposure in the Pesticide-Tolerant Pseudomonas sp. C9 Strain Isolated from a Biopurification System
by Pamela Donoso-Piñol, Gabriela Briceño, Joseph A. M. Evaristo, Fábio C. S. Nogueira, Heidi Schalchli and María Cristina Diez
Int. J. Mol. Sci. 2024, 25(19), 10471; https://doi.org/10.3390/ijms251910471 - 28 Sep 2024
Viewed by 891
Abstract
Iprodione is a pesticide that belongs to the dicarboximide fungicide family. This pesticide was designed to combat various agronomical pests; however, its use has been restricted due to its environmental toxicity and risks to human health. In this study, we explored the proteomic [...] Read more.
Iprodione is a pesticide that belongs to the dicarboximide fungicide family. This pesticide was designed to combat various agronomical pests; however, its use has been restricted due to its environmental toxicity and risks to human health. In this study, we explored the proteomic changes in the Pseudomonas sp. C9 strain when exposed to iprodione, to gain insights into the affected metabolic pathways and enzymes involved in iprodione tolerance and biodegradation processes. As a result, we identified 1472 differentially expressed proteins in response to iprodione exposure, with 978 proteins showing significant variations. We observed that the C9 strain upregulated the expression of efflux pumps, enhancing its tolerance to iprodione and other harmful compounds. Peptidoglycan-binding proteins LysM, glutamine amidotransferase, and protein Ddl were similarly upregulated, indicating their potential role in altering and preserving bacterial cell wall structure, thereby enhancing tolerance. We also observed the presence of hydrolases and amidohydrolases, essential enzymes for iprodione biodegradation. Furthermore, the exclusive identification of ABC transporters and multidrug efflux complexes among proteins present only during iprodione exposure suggests potential counteraction against the inhibitory effects of iprodione on downregulated proteins. These findings provide new insights into iprodione tolerance and biodegradation by the Pseudomonas sp. C9 strain. Full article
(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 3.0)
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16 pages, 2784 KiB  
Article
Biodegradation of Photocatalytic Degradation Products of Sulfonamides: Kinetics and Identification of Intermediates
by Daria Madej-Knysak, Ewa Adamek and Wojciech Baran
Int. J. Mol. Sci. 2024, 25(12), 6688; https://doi.org/10.3390/ijms25126688 - 18 Jun 2024
Viewed by 1098
Abstract
Sulfonamides can be effectively removed from wastewater through a photocatalytic process. However, the mineralization achieved by this method is a long-term and expensive process. The effect of shortening the photocatalytic process is the partial degradation and formation of intermediates. The purpose of this [...] Read more.
Sulfonamides can be effectively removed from wastewater through a photocatalytic process. However, the mineralization achieved by this method is a long-term and expensive process. The effect of shortening the photocatalytic process is the partial degradation and formation of intermediates. The purpose of this study was to evaluate the sensitivity and transformation of photocatalytic reaction intermediates in aerobic biological processes. Sulfadiazine and sulfamethoxazole solutions were used in the study, which were irradiated in the presence of a TiO2-P25 catalyst. The resulting solutions were then aerated after the addition of river water or activated sludge suspension from a commercial wastewater treatment plant. The reaction kinetics were determined and fifteen products of photocatalytic degradation of sulfonamides were identified. Most of these products were further transformed in the presence of activated sludge suspension or in water taken from the river. They may have been decomposed into other organic and inorganic compounds. The formation of biologically inactive acyl derivatives was observed in the biological process. However, compounds that are more toxic to aquatic organisms than the initial drugs can also be formed. After 28 days, the sulfamethoxazole concentration in the presence of activated sludge was reduced by 66 ± 7%. Sulfadiazine was practically non-biodegradable under the conditions used. The presented results confirm the advisability of using photocatalysis as a process preceding biodegradation. Full article
(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 3.0)
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