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Biodegradation of Pollutants in the Environment: Omics Approaches 2.0

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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: closed (30 November 2023) | Viewed by 26219

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Dr. Irina Sousa Moreira

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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
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Dear Colleagues,

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

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 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 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 the biodegradation of pollutants, particularly concerning the use of omics tools and understanding molecular mechanisms, are welcome.

Dr. Irina Sousa Moreira
Guest Editor

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Keywords

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

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Biodegradation of Pollutants in the Environment: Omics Approaches in International Journal of Molecular Sciences (8 articles)

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Research

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18 pages, 7404 KiB

Open AccessArticle

Comparative Genomic and Transcriptomic Analysis of Phenol Degradation and Tolerance in Acinetobacter lwoffii through Adaptive Evolution

by Nan Xu, Xiaojing Yang, Qiyuan Yang and Minliang Guo

Int. J. Mol. Sci. 2023, 24(22), 16529; https://doi.org/10.3390/ijms242216529 - 20 Nov 2023

Cited by 3 | Viewed by 1558

Abstract

Microorganism-based methods have been widely applied for the treatment of phenol-polluted environments. The previously isolated Acinetobacter lwoffii NL1 strain could completely degrade 0.5 g/L phenol within 12 h, but not higher concentrations of phenol. In this study, we developed an evolutionary strain NL115, through adaptive laboratory evolution, which possessed improved degradation ability and was able to degrade 1.5 g/L phenol within 12 h. Compared with that of the starting strain NL1, the concentration of degradable phenol by the developed strain increased three-fold; its phenol tolerance was also enhanced. Furthermore, comparative genomics showed that sense mutations mainly occurred in genes encoding alkyl hydroperoxide reductase, phenol hydroxylase, 30S ribosomal protein, and mercury resistance operon. Comparative transcriptomics between A. lwoffii NL115 and NL1 revealed the enrichment of direct degradation, stress resistance, and vital activity processes among the metabolic responses of A. lwoffii adapted to phenol stress. Among these, all the upregulated genes (log₂fold-change > 5) encoded peroxidases. A phenotypic comparison of A. lwoffii NL1 and NL115 found that the adapted strain NL115 exhibited strengthened antioxidant capacity. Furthermore, the increased enzymatic activities of phenol hydroxylase and alkyl hydroperoxide reductase in A. lwoffii NL115 validated their response to phenol. Overall, this study provides insight into the mechanism of efficient phenol degradation through adaptive microbial evolution and can help to drive improvements in phenol bioremediation. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 2.0)

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17 pages, 7206 KiB

Open AccessArticle

Optimizing Eco-Friendly Degradation of Polyvinyl Chloride (PVC) Plastic Using Environmental Strains of Malassezia Species and Aspergillus fumigatus

by Heba A. El-Dash, Nehal E. Yousef, Abeer A. Aboelazm, Zuhier A. Awan, Galal Yahya and Amira M. El-Ganiny

Int. J. Mol. Sci. 2023, 24(20), 15452; https://doi.org/10.3390/ijms242015452 - 22 Oct 2023

Cited by 12 | Viewed by 2460

Abstract

Worldwide, huge amounts of plastics are being introduced into the ecosystem, causing environmental pollution. Generally, plastic biodegradation in the ecosystem takes hundreds of years. Hence, the isolation of plastic-biodegrading microorganisms and finding optimum conditions for their action is crucial. The aim of the current study is to isolate plastic-biodegrading fungi and explore optimum conditions for their action. Soil samples were gathered from landfill sites; 18 isolates were able to grow on SDA. Only 10 isolates were able to the degrade polyvinyl chloride (PVC) polymer. Four isolates displayed promising depolymerase activity. Molecular identification revealed that three isolates belong to genus Aspergillus, and one isolate was Malassezia sp. Three isolates showed superior PVC-biodegrading activity (Aspergillus-2, Aspergillus-3 and Malassezia) using weight reduction analysis and SEM. Two Aspergillus strains and Malassezia showed optimum growth at 40 °C, while the last strain grew better at 30 °C. Two Aspergillus isolates grew better at pH 8–9, and the other two isolates grow better at pH 4. Maximal depolymerase activity was monitored at 50 °C, and at slightly acidic pH in most isolates, FeCl₃ significantly enhanced depolymerase activity in two Aspergillus isolates. In conclusion, the isolated fungi have promising potential to degrade PVC and can contribute to the reduction of environmental pollution in eco-friendly way. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 2.0)

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25 pages, 8997 KiB

Open AccessArticle

Bacteria, Fungi, and Enzymes in Soil Treated with Sulcotrione and Terbuthylazine

by Małgorzata Baćmaga, Jadwiga Wyszkowska, Agata Borowik and Jan Kucharski

Int. J. Mol. Sci. 2023, 24(19), 14469; https://doi.org/10.3390/ijms241914469 - 23 Sep 2023

Cited by 3 | Viewed by 1438

Abstract

Soil’s biological equilibrium, disturbed by the uncontrolled penetration of pesticides, can be restored by the activity of native microorganisms, which show abilities in neutralizing these xenobiotics. Therefore, this research is necessary in the search for new microorganisms used in the process of the bioremediation of contaminated soils. The aim of this study was to evaluate the effects of the herbicides, Sulcogan 300 SC, Tezosar 500 SC, and Sulcotrek 500 SC, applied to soil at the manufacturers’ recommended dosage as well as 10-fold higher, on the abundance of microorganisms, the diversity and structure of bacterial and fungal communities, the activity of soil enzymes, and the growth and development of Zea mays L. It was found that herbicides in contaminating amounts stimulated the proliferation of organotrophic bacteria and inhibited the growth of fungi. Organotrophic bacteria and actinobacteria were represented by K-strategies and fungi by r-strategies. Bacteria belonging to the phylum, Actinobacteriota, represented by the genus, Cellulosimicrobium, were most abundant in the soil, while among the fungi, it was the phylum, Ascomycota, represented by the genus, Humicola and Chaetomium. The herbicides decreased urease activity while increasing arylsulfatase and acid phosphatase activity. They had a positive effect on the growth and development of Zea mays L., as evidenced by an increase in the values of the plant tolerance index (TI) and the maize leaf greenness index (SPAD). The results indicate that soil microorganisms and enzymes are suitable indicators reflecting the quality of herbicide-treated soil. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 2.0)

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15 pages, 3040 KiB

Open AccessArticle

Evaluation of the Different Nutritional and Environmental Parameters on Microbial Pyrene Degradation by Mangrove Culturable Bacteria

by Manzoor Ahmad, Juan Ling, Jianping Yin, Luxiang Chen, Qingsong Yang, Weiguo Zhou, Yuhang Zhang, Xiaofang Huang, Imran Khan and Junde Dong

Int. J. Mol. Sci. 2023, 24(9), 8282; https://doi.org/10.3390/ijms24098282 - 5 May 2023

Cited by 6 | Viewed by 2076

Abstract

Mangrove ecosystems play curial roles in providing many ecological services and alleviating global climate change. However, they are in decline globally, mainly threatened by human activities and global warming, and organic pollutants, especially PAHs, are among the crucial reasons. Microbial remediation is a cost-effective and environmentally friendly way of alleviating PAH contamination. Therefore, understanding the effects of environmental and nutritional parameters on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) is significant for the bioremediation of PAH contamination. In the present study, five bacterial strains, designated as Bp1 (Genus Rhodococcus), Sp8 (Genus Nitratireductor), Sp13 (Genus Marinobacter), Sp23 (Genus Pseudonocardia), and Sp24 (Genus Mycolicibacterium), have been isolated from mangrove sediment and their ring hydroxylating dioxygenase (RHD) genes have been successfully amplified. Afterward, their degradation abilities were comprehensively evaluated under normal cultural (monoculture and co-culture) and different nutritional (tryptone, yeast extract, peptone, glucose, sucrose, and NPK fertilizer) and environmental (cetyl trimethyl ammonium bromide (CTAB), sodium dodecyl sulfate (SDS)) parameters, as well with different co-contaminants (phenanthrene and naphthalene) and heavy metals (Cd²⁺, Cu²⁺, Fe³⁺, Ni²⁺, Mg²⁺, Mn²⁺, and Co²⁺). The results showed that strain Sp24 had the highest pyrene degradation rate (85%) in the monoculture experiment after being cultured for 15 days. Adding nitrogen- and carbon-rich sources, including tryptone, peptone, and yeast extract, generally endorsed pyrene degradation. In contrast, the effects of carbon sources (glucose and sucrose) on pyrene degradation were distinct for different bacterial strains. Furthermore, the addition of NPK fertilizer, SDS, Tween-80, phenanthrene, and naphthalene enhanced the bacterial abilities of pyrene removal significantly (p < 0.05). Heavy metals significantly reduced all bacterial isolates’ degradation potentials (p < 0.05). The bacterial consortia containing high bio-surfactant-producing strains showed substantially higher pyrene degradation. Moreover, the consortia of three and five bacterial strains showed more degradation efficiency than those of two bacterial strains. These results provide helpful microbial resources for mangrove ecological remediation and insight into optimized culture strategies for the microbial degradation of PAHs. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 2.0)

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17 pages, 1532 KiB

Open AccessArticle

Biodegradation and Metabolic Pathway of the Neonicotinoid Insecticide Thiamethoxam by Labrys portucalensis F11

by Oumeima Boufercha, Ana R. Monforte, Allaoueddine Boudemagh, António C. Ferreira, Paula M. L. Castro and Irina S. Moreira

Int. J. Mol. Sci. 2022, 23(22), 14326; https://doi.org/10.3390/ijms232214326 - 18 Nov 2022

Cited by 3 | Viewed by 2221

Abstract

Thiamethoxam (TMX) is an effective neonicotinoid insecticide. However, its widespread use is detrimental to non-targeted organisms and water systems. This study investigates the biodegradation of this insecticide by Labrys portucalensis F11. After 30 days of incubation in mineral salt medium, L. portucalensis F11 was able to remove 41%, 35% and 100% of a supplied amount of TMX (10.8 mg L⁻¹) provided as the sole carbon and nitrogen source, the sole carbon and sulfur source and as the sole carbon source, respectively. Periodic feeding with sodium acetate as the supplementary carbon source resulted in faster degradation of TMX (10.8 mg L⁻¹); more than 90% was removed in 3 days. The detection and identification of biodegradation intermediates was performed by UPLC-QTOF/MS/MS. The chemical structure of 12 metabolites is proposed. Nitro reduction, oxadiazine ring cleavage and dechlorination are the main degradation pathways proposed. After biodegradation, toxicity was removed as indicated using Aliivibrio fischeri and by assessing the synthesis of an inducible β-galactosidase by an E. coli mutant (Toxi-Chromo test). L. portucalensis F11 was able to degrade TMX under different conditions and could be effective in bioremediation strategies. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 2.0)

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12 pages, 1102 KiB

Open AccessArticle

PUF-Immobilized Bjerkandera adusta DSM 3375 as a Tool for Bioremediation of Creosote Oil Contaminated Soil

by Katarzyna Struszczyk-Świta, Piotr Drożdżyński, Karolina Murawska and Olga Marchut-Mikołajczyk

Int. J. Mol. Sci. 2022, 23(20), 12441; https://doi.org/10.3390/ijms232012441 - 18 Oct 2022

Cited by 2 | Viewed by 2104

Abstract

Creosote oil, a byproduct of coal distillation, is primarily composed of aromatic compounds that are difficult to degrade, such as polycyclic aromatic hydrocarbons, phenolic compounds, and N-, S-, and O-heterocyclic compounds. Despite its toxicity and carcinogenicity, it is still often used to impregnate wood, which has a particularly negative impact on the condition of the soil in plants that impregnate wooden materials. Therefore, a rapid, effective, and eco-friendly technique for eliminating the creosote in this soil must be developed. The research focused on obtaining a preparation of Bjerkandera adusta DSM 3375 mycelium immobilized in polyurethane foam (PUF). It contained mold cells in the amount of 1.10 ± 0.09 g (DW)/g of the carrier. The obtained enzyme preparation was used in the bioremediation of soil contaminated with creosote (2% w/w). The results showed that applying the PUF-immobilized mycelium of B. adusta DSM 3375 over 5, 10, and 15 weeks of bioremediation, respectively, removed 19, 30, and 35% of creosote from the soil. After 15 weeks, a 73, 79, and 72% level of degradation of fluoranthene, pyrene, and fluorene, respectively, had occurred. The immobilized cells have the potential for large-scale study, since they can degrade creosote oil in soil. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 2.0)

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26 pages, 8550 KiB

Open AccessArticle

Bacillus subtilis: As an Efficient Bacterial Strain for the Reclamation of Water Loaded with Textile Azo Dye, Orange II

by Muhammad Ikram, Mohammad Naeem, Muhammad Zahoor, Marlia Mohd Hanafiah, Adeleke Abdulrahman Oyekanmi, Noor Ul Islam, Midrar Ullah, Mater H. Mahnashi, Amer Al Ali, Naif A. Jalal, Farkad Bantun, Aiman M. Momenah and Abdul Sadiq

Int. J. Mol. Sci. 2022, 23(18), 10637; https://doi.org/10.3390/ijms231810637 - 13 Sep 2022

Cited by 39 | Viewed by 3757

Abstract

The azo dye orange II is used extensively in the textile sector for coloring fabrics. High concentrations of it are released into aqueous environments through textile effluents. Therefore, its removal from textile wastewater and effluents is necessary. Herein, initially, we tested 11 bacterial strains for their capabilities in the degradation of orange II dye. It was revealed in the preliminary data that B. subtilis can more potently degrade the selected dye, which was thus used in the subsequent experiments. To achieve maximum decolorization, the experimental conditions were optimized whereby maximum degradation was achieved at: a 25 ppm dye concentration, pH 7, a temperature of 35 °C, a 1000 mg/L concentration of glucose, a 1000 mg/L urea concentration, a 666.66 mg/L NaCl concentration, an incubation period of 3 days, and with hydroquinone as a redox mediator at a concentration of 66.66 mg/L. The effects of the interaction of the operational factors were further confirmed using response surface methodology, which revealed that at optimum conditions of pH 6.45, a dye concentration of 17.07 mg/L, and an incubation time of 9.96 h at 45.38 °C, the maximum degradation of orange II can be obtained at a desirability coefficient of 1, estimated using the central composite design (CCD). To understand the underlying principles of degradation of the metabolites in the aliquot mixture at the optimized condition, the study steps were extracted and analyzed using GC-MS(Gas Chromatography Mass Spectrometry), FTIR(Fourier Transform Infrared Spectroscopy), ¹H and carbon 13 NMR(Nuclear Magnetic Resonance Spectroscopy). The GC-MS pattern revealed that the original dye was degraded into o-xylene and naphthalene. Naphthalene was even obtained in a pure state through silica gel column isolation and confirmed using ¹H and ¹³C NMR spectroscopic analysis. Phytotoxicity tests on Vigna radiata were also conducted and the results confirmed that the dye metabolites were less toxic than the parent dye. These results emphasize that B. subtilis should be used as a potential strain for the bioremediation of textile effluents containing orange II and other toxic azo dyes. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 2.0)

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Review

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25 pages, 2208 KiB

Open AccessReview

Biodegradation of Typical Plastics: From Microbial Diversity to Metabolic Mechanisms

by Shiwei Lv, Yufei Li, Sufang Zhao and Zongze Shao

Int. J. Mol. Sci. 2024, 25(1), 593; https://doi.org/10.3390/ijms25010593 - 2 Jan 2024

Cited by 24 | Viewed by 9419

Abstract

Plastic production has increased dramatically, leading to accumulated plastic waste in the ocean. Marine plastics can be broken down into microplastics (<5 mm) by sunlight, machinery, and pressure. The accumulation of microplastics in organisms and the release of plastic additives can adversely affect the health of marine organisms. Biodegradation is one way to address plastic pollution in an environmentally friendly manner. Marine microorganisms can be more adapted to fluctuating environmental conditions such as salinity, temperature, pH, and pressure compared with terrestrial microorganisms, providing new opportunities to address plastic pollution. Pseudomonadota (Proteobacteria), Bacteroidota (Bacteroidetes), Bacillota (Firmicutes), and Cyanobacteria were frequently found on plastic biofilms and may degrade plastics. Currently, diverse plastic-degrading bacteria are being isolated from marine environments such as offshore and deep oceanic waters, especially Pseudomonas spp. Bacillus spp. Alcanivoras spp. and Actinomycetes. Some marine fungi and algae have also been revealed as plastic degraders. In this review, we focused on the advances in plastic biodegradation by marine microorganisms and their enzymes (esterase, cutinase, laccase, etc.) involved in the process of biodegradation of polyethylene terephthalate (PET), polystyrene (PS), polyethylene (PE), polyvinyl chloride (PVC), and polypropylene (PP) and highlighted the need to study plastic biodegradation in the deep sea. Full article

(This article belongs to the Special Issue Biodegradation of Pollutants in the Environment: Omics Approaches 2.0)

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