International Journal of Molecular Sciences

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2 pages, 184 KiB

Open AccessEditorial

Biodegradation of Pollutants in the Environment: Omics Approaches

by Irina S. Moreira

Int. J. Mol. Sci. 2023, 24(10), 8815; https://doi.org/10.3390/ijms24108815 - 16 May 2023

Viewed by 803

Abstract

This special edition intends to highlight how omics approaches have been used in biodegradation studies to understand the mechanisms involved and improve biodegradation processes [...] Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches)

Research

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16 pages, 4243 KiB

Open AccessArticle

Biodegradation and Metabolic Pathway of 17β-Estradiol by Rhodococcus sp. ED55

by Irina S. Moreira, Sapia Murgolo, Giuseppe Mascolo and Paula M. L. Castro

Int. J. Mol. Sci. 2022, 23(11), 6181; https://doi.org/10.3390/ijms23116181 - 31 May 2022

Cited by 5 | Viewed by 1454

Abstract

Endocrine disrupting compounds (EDCs) in the environment are considered a motif of concern, due to the widespread occurrence and potential adverse ecological and human health effects. The natural estrogen, 17β-estradiol (E2), is frequently detected in receiving water bodies after not being efficiently removed [...] Read more.

Endocrine disrupting compounds (EDCs) in the environment are considered a motif of concern, due to the widespread occurrence and potential adverse ecological and human health effects. The natural estrogen, 17β-estradiol (E2), is frequently detected in receiving water bodies after not being efficiently removed in conventional wastewater treatment plants (WWTPs), promoting a negative impact for both the aquatic ecosystem and human health. In this study, the biodegradation of E2 by Rhodococcus sp. ED55, a bacterial strain isolated from sediments of a discharge point of WWTP in Coloane, Macau, was investigated. Rhodococcus sp. ED55 was able to completely degrade 5 mg/L of E2 in 4 h in a synthetic medium. A similar degradation pattern was observed when the bacterial strain was used in wastewater collected from a WWTP, where a significant improvement in the degradation of the compound occurred. The detection and identification of 17 metabolites was achieved by means of UPLC/ESI/HRMS, which proposed a degradation pathway of E2. The acute test with luminescent marine bacterium Aliivibrio fischeri revealed the elimination of the toxicity of the treated effluent and the standardized yeast estrogenic (S-YES) assay with the recombinant strain of Saccharomyces cerevisiae revealed a decrease in the estrogenic activity of wastewater samples after biodegradation. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches)

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26 pages, 21503 KiB

Open AccessArticle

Effect of Separate and Combined Toxicity of Bisphenol A and Zinc on the Soil Microbiome

by Magdalena Zaborowska, Jadwiga Wyszkowska, Agata Borowik and Jan Kucharski

Int. J. Mol. Sci. 2022, 23(11), 5937; https://doi.org/10.3390/ijms23115937 - 25 May 2022

Cited by 12 | Viewed by 1949

Abstract

The research objective was established by taking into account common sources of soil contamination with bisphenol A (B) and zinc (Zn²⁺), as well as the scarcity of data on the effect of metabolic pathways involved in the degradation of organic compounds [...] Read more.

The research objective was established by taking into account common sources of soil contamination with bisphenol A (B) and zinc (Zn²⁺), as well as the scarcity of data on the effect of metabolic pathways involved in the degradation of organic compounds on the complexation of zinc in soil. Therefore, the aim of this study was to determine the spectrum of soil homeostasis disorders arising under the pressure of both the separate and combined toxicity of bisphenol A and Zn²⁺. With a broad pool of indicators, such as indices of the effect of xenobiotics (IF_X), humic acid (IF_H), plants (IF_P), colony development (CD), ecophysiological diversity (EP), the Shannon–Weaver and the Simpson indices, as well as the index of soil biological fertility (BA₂₁), the extent of disturbances was verified on the basis of enzymatic activity, microbiological activity, and structural diversity of the soil microbiome. A holistic character of the study was achieved, having determined the indicators of tolerance (IT) of Sorghum Moench (S) and Panicum virgatum (P), the ratio of the mass of their aerial parts to roots (PR), and the SPAD leaf greenness index. Bisphenol A not only failed to perform a complexing role towards Zn²⁺, but in combination with this heavy metal, had a particularly negative effect on the soil microbiome and enzymatic activity. The NGS analysis distinguished certain unique genera of bacteria in all objects, representing the phyla Actinobacteriota and Proteobacteria, as well as fungi classified as members of the phyla Ascomycota and Basidiomycota. Sorghum Moench (S) proved to be more sensitive to the xenobiotics than Panicum virgatum (P). Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches)

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22 pages, 2494 KiB

Open AccessArticle

Microbial Consortia and Mixed Plastic Waste: Pangenomic Analysis Reveals Potential for Degradation of Multiple Plastic Types via Previously Identified PET Degrading Bacteria

by Sabrina Edwards, Rosa León-Zayas, Riyaz Ditter, Helen Laster, Grace Sheehan, Oliver Anderson, Toby Beattie and Jay L. Mellies

Int. J. Mol. Sci. 2022, 23(10), 5612; https://doi.org/10.3390/ijms23105612 - 17 May 2022

Cited by 20 | Viewed by 7247

Abstract

The global utilization of single-use, non-biodegradable plastics, such as bottles made of polyethylene terephthalate (PET), has contributed to catastrophic levels of plastic pollution. Fortunately, microbial communities are adapting to assimilate plastic waste. Previously, our work showed a full consortium of five bacteria capable [...] Read more.

The global utilization of single-use, non-biodegradable plastics, such as bottles made of polyethylene terephthalate (PET), has contributed to catastrophic levels of plastic pollution. Fortunately, microbial communities are adapting to assimilate plastic waste. Previously, our work showed a full consortium of five bacteria capable of synergistically degrading PET. Using omics approaches, we identified the key genes implicated in PET degradation within the consortium’s pangenome and transcriptome. This analysis led to the discovery of a novel PETase, EstB, which has been observed to hydrolyze the oligomer BHET and the polymer PET. Besides the genes implicated in PET degradation, many other biodegradation genes were discovered. Over 200 plastic and plasticizer degradation-related genes were discovered through the Plastic Microbial Biodegradation Database (PMBD). Diverse carbon source utilization was observed by a microbial community-based assay, which, paired with an abundant number of plastic- and plasticizer-degrading enzymes, indicates a promising possibility for mixed plastic degradation. Using RNAseq differential analysis, several genes were predicted to be involved in PET degradation, including aldehyde dehydrogenases and several classes of hydrolases. Active transcription of PET monomer metabolism was also observed, including the generation of polyhydroxyalkanoate (PHA)/polyhydroxybutyrate (PHB) biopolymers. These results present an exciting opportunity for the bio-recycling of mixed plastic waste with upcycling potential. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches)

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15 pages, 1203 KiB

Open AccessArticle

Occurrence of Textile Dyes and Metals in Tunisian Textile Dyeing Effluent: Effects on Oxidative Stress Status and Histological Changes in Balb/c Mice

by Nosra Methneni, Khawla Ezdini, Nouha Ben Abdeljelil, Joris Van Loco, Kathy Van den Houwe, Riheb Jabeur, Ons Fekih Sallem, Ahlem Jaziri, Mercedes Fernandez-Serrano, Nezar H. Khdary and Hedi Ben Mansour

Int. J. Mol. Sci. 2021, 22(22), 12568; https://doi.org/10.3390/ijms222212568 - 22 Nov 2021

Cited by 7 | Viewed by 2190

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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16 pages, 4235 KiB

Open AccessArticle

Bisphenol A Removal by the Fungus Myrothecium roridumIM 6482—Analysis of the Cellular and Subcellular Level

by Anna Jasińska, Adrian Soboń, Sylwia Różalska and Paulina Średnicka

Int. J. Mol. Sci. 2021, 22(19), 10676; https://doi.org/10.3390/ijms221910676 - 1 Oct 2021

Cited by 8 | Viewed by 1801

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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17 pages, 2678 KiB

Open AccessArticle

Adaption and Degradation Strategies of Methylotrophic 1,4-Dioxane Degrading Strain Xanthobacter sp. YN2 Revealed by Transcriptome-Scale Analysis

by Yingning Wang, Fang Ma, Jixian Yang, Haijuan Guo, Delin Su and Lan Yu

Int. J. Mol. Sci. 2021, 22(19), 10435; https://doi.org/10.3390/ijms221910435 - 28 Sep 2021

Cited by 4 | Viewed by 1839

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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Review

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22 pages, 1484 KiB

Open AccessReview

Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review

by Siti Suhailah Sharuddin, Norhayati Ramli, Mohd Zulkhairi Mohd Yusoff, Nor Azlan Nor Muhammad, Li Sim Ho and Toshinari Maeda

Int. J. Mol. Sci. 2022, 23(7), 3737; https://doi.org/10.3390/ijms23073737 - 29 Mar 2022

Cited by 11 | Viewed by 3097

Abstract

While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a [...] Read more.

While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches)

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