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Special Issue "Biodegradation of Pollutants in the Environment: Omics Approaches"

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

Deadline for manuscript submissions: 30 April 2022.

Special Issue Editor

Dr. Irina Moreira
E-Mail Website
Guest Editor
CBQF—Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Porto, Portugal
Interests: environmental microbiology; biodegradation; fluoroaromatics; emerging contaminants; metabolic pathways; aerobic granular sludge; bioreactors
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Special Issue Information

Dear Colleagues,

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 pollution sources. In recent decades, omics disciplines, such as genomics, proteomics, metabolomics, metagenomics and transcriptomics, have emerged as scientific tools to understand the mechanisms of biodegradation processes, namely, the elucidation of genes and enzymes involved in the degradation of and tolerance to xenobiotics, the identification of intermediate and final metabolites of degradation pathways, and the identification of key microorganisms from communities involved in the degradation. This knowledge allows one not only to deepen the understanding of the biodegradation processes but also to optimize the efficiency of degradation and the isolation of degrading strains for use in biotechnological applications for bioremediation proposes.

Reviews and original articles focused on biodegradation of pollutants focused on the use of omics tools and understanding molecular mechanisms are welcome. 

Dr. Irina 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 papers will be 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • Pollutants
  • Genomics
  • Proteomics
  • Metabolomics
  • Metagenomics
  • Transcriptomics
  • Degrading microorganisms
  • Metabolic pathway of degradation

Published Papers (3 papers)

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Research

Article
Occurrence of Textile Dyes and Metals in Tunisian Textile Dyeing Effluent: Effects on Oxidative Stress Status and Histological Changes in Balb/c Mice
Int. J. Mol. Sci. 2021, 22(22), 12568; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212568 - 22 Nov 2021
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Abstract
Although it is known that textile wastewater contains highly toxic contaminants whose effects in humans represent public health problems in several countries, studies involving mammal species are scarce. This study was aimed to evaluate the toxicity profile of 90-days oral administration of textile [...] Read more.
Although it is known that textile wastewater contains highly toxic contaminants whose effects in humans represent public health problems in several countries, studies involving mammal species are scarce. This study was aimed to evaluate the toxicity profile of 90-days oral administration of textile dyeing effluent (TDE) on oxidative stress status and histological changes of male mice. The TDE was collected from the textile plant of Monastir, Tunisia and evaluated for the metals, aromatic amines, and textile dyes using analytical approaches. Metal analysis by ICP-MS showed that the tested TDE exhibited very high levels of Cr, As, and Sr, which exceeded the wastewater emission limits prescribed by WHO and Tunisian authority. The screening of TDE through UPLC-MS/MS confirmed the presence of two textile dyes: a triphenylmethane dye (Crystal violet) and a disperse azo dye (Disperse yellow 3). Exposure to TDE significantly altered the malondialdehyde (MDA), Conjugated dienes (CDs), Sulfhydryl proteins (SHP) and catalase levels in the hepatic and renal tissues. Furthermore, histopathology observation showed that hepatocellular and renal lesions were induced by TDE exposure. The present study concluded that TDE may involve induction of oxidative stress which ensues in pathological lesions in several vital organs suggesting its high toxicity. Metals and textile dyes may be associated with the observed toxicological effects of the TDE. These pollutants, which may have seeped into surrounding rivers in Monastir city, can cause severe health malaise in wildlife and humans. Full article
(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches)
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Article
Bisphenol A Removal by the Fungus Myrothecium roridumIM 6482—Analysis of the Cellular and Subcellular Level
Int. J. Mol. Sci. 2021, 22(19), 10676; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910676 - 01 Oct 2021
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Abstract
Bisphenol (BPA) is a key ingredient in the production of epoxy resins and some types of plastics, which can be released into the environment and alter the endocrine systems of wildlife and humans. In this study, the ability of the fungus M. roridum [...] Read more.
Bisphenol (BPA) is a key ingredient in the production of epoxy resins and some types of plastics, which can be released into the environment and alter the endocrine systems of wildlife and humans. In this study, the ability of the fungus M. roridumIM 6482 to BPA elimination was investigated. LC-MS/MS analysis showed almost complete removal of BPA from the growth medium within 72 h of culturing. Products of BPA biotransformation were identified, and their estrogenic activity was found to be lower than that of the parent compound. Extracellular laccase activity was identified as the main mechanism of BPA elimination. It was observed that BPA induced oxidative stress in fungal cells manifested as the enhancement in ROS production, membranes permeability and lipids peroxidation. These oxidative stress markers were reduced after BPA biodegradation (72 h of culturing). Intracellular proteome analyses performed using 2-D electrophoresis and MALDI-TOF/TOF technique allowed identifying 69 proteins in a sample obtained from the BPA containing culture. There were mainly structural and regulator proteins but also oxidoreductive and antioxidative agents, such as superoxide dismutase and catalase. The obtained results broaden the knowledge on BPA elimination by microscopic fungi and may contribute to the development of BPA biodegradation methods. Full article
(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches)
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Article
Adaption and Degradation Strategies of Methylotrophic 1,4-Dioxane Degrading Strain Xanthobacter sp. YN2 Revealed by Transcriptome-Scale Analysis
Int. J. Mol. Sci. 2021, 22(19), 10435; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910435 - 28 Sep 2021
Viewed by 415
Abstract
Biodegradation of 1,4-dioxane (dioxane) contamination has gained much attention for decades. In our previous work, we isolated a highly efficient dioxane degrader, Xanthobacter sp. YN2, but the underlying mechanisms of its extraordinary degradation performance remained unresolved. In this study, we performed a comparative [...] Read more.
Biodegradation of 1,4-dioxane (dioxane) contamination has gained much attention for decades. In our previous work, we isolated a highly efficient dioxane degrader, Xanthobacter sp. YN2, but the underlying mechanisms of its extraordinary degradation performance remained unresolved. In this study, we performed a comparative transcriptome analysis of YN2 grown on dioxane and citrate to elucidate its genetic degradation mechanism and investigated the transcriptomes of different dioxane degradation stages (T0, T24, T48). We also analyzed the transcriptional response of YN2 over time during which the carbon source switched from citrate to dioxane. The results indicate that strain YN2 was a methylotroph, which provides YN2 a major advantage as a pollutant degrader. A large number of genes involved in dioxane metabolism were constitutively expressed prior to dioxane exposure. Multiple genes related to the catabolism of each intermediate were upregulated by treatment in response to dioxane. Glyoxylate metabolism was essential during dioxane degradation by YN2, and the key intermediate glyoxylate was metabolized through three routes: glyoxylate carboligase pathway, malate synthase pathway, and anaplerotic ethylmalonyl–CoA pathway. Genes related to quorum sensing and transporters were significantly upregulated during the early stages of degradation (T0, T24) prior to dioxane depletion, while the expression of genes encoding two-component systems was significantly increased at late degradation stages (T48) when total organic carbon in the culture was exhausted. This study is the first to report the participation of genes encoding glyoxalase, as well as methylotrophic genes xoxF and mox, in dioxane metabolism. The present study reveals multiple genetic and transcriptional strategies used by YN2 to rapidly increase biomass during growth on dioxane, achieve high degradation efficiency and tolerance, and adapt to dioxane exposure quickly, which provides useful information regarding the molecular basis for efficient dioxane biodegradation. Full article
(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches)
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