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Fungal Biodegradation: Strategies, Current Understanding, and Future Prospects: 2nd Edition
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Fungal Biodegradation: Strategies, Current Understanding, and Future Prospects: 2nd Edition

A special issue of Journal of Fungi (ISSN 2309-608X).

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 13786

Special Issue Editors

Dr. Elisabet Aranda

E-Mail Website
Guest Editor
Department of Microbiology, Institute of Water Research, University of Granada, Ramón y Cajal 4, 18071 Granada, Spain
Interests: fungal bioremediation; xenobiotic transformation
Special Issues, Collections and Topics in MDPI journals
Dr. Ramón Alberto Batista-García

E-Mail Website
Guest Editor
Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Ave. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico
Interests: fungal bioremediation; extremophilic fungi; xenobiotic transformation; omics approaches
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The bioremediation of hazardous pollutants has been extensively studied in recent decades, including the potential use of different microorganisms for this purpose. Environmental studies have revealed that fungi are some of the most important players in polluted environments. They can remove a myriad of chemical compounds, including some of the more recalcitrant xenobiotics, such as polycyclic aromatic hydrocarbons (PAHs), dyes, plastics, pharmaceutical active compounds, or heavy metals. Paradoxically, despite their key involvement, fungi are often treated as a black box, and their roles in the transformation of xenobiotics and catabolic pathways remain poorly understood.

We are pleased to invite you to the Special Issue “Fungal Biodegradation: Strategies, Current Understanding, and Future Prospects”. Original research articles, reviews, minireviews, method articles, and short communications are welcome. Research areas may include, but are not limited to: advances in research of fungi with the capability to transform recalcitrant and emerging pollutants; fungal diversity in polluted habitats; fungal ecology and physiology during biotransformation of environmental pollutants; genomics, transcriptomics, proteomics, and metabolomics studies aiming to understand the molecular basis of mycoremediation processes; the potential applicability of fungi to implement bioremediation strategies at different scales; fungal treatment of wastewaters and solid wastes; biotechnological applications focused on biotransformation, removal, and biosorption of pollutants by fungi.

This Special Issue will publish work that contributes to a fuller understanding of the mechanisms of xenobiotic fungal degradation at different levels, from a genetic, transcriptomic, and proteomic point of view. These findings will contribute to the tailoring of bioremediation strategies toward a clean and healthy environment.

Dr. Elisabet Aranda
Dr. Ramón Alberto Batista-García
Guest Editors

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. Journal of Fungi 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 2600 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

  • mycoremediation
  • fungal bioremediation
  • fungi-mediated biotransformation
  • fungi
  • Ascomycota and Basidiomycota
  • xenobiotics and emerging pollutants
  • biotechnological applications
  • omics approaches
 

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Published Papers (5 papers)

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Research

15 pages, 2432 KiB  
Article
Characterization of Culturable Mycobiome of Newly Excavated Ancient Wooden Vessels from the Archeological Site of Viminacium, Serbia
by Ivana Djokić, Aleksandar Knežević, Željko Savković, Milica Ljaljević Grbić, Ivica Dimkić, Danka Bukvički, Dragana Gavrilović and Nikola Unković
J. Fungi 2024, 10(5), 343; https://doi.org/10.3390/jof10050343 - 9 May 2024
Viewed by 1291
Abstract
Two ancient wooden vessels, specifically a monoxyle (1st century BCE to 1st century CE) and shipwreck (15th to 17th century CE), were excavated in a well-preserved state east of the confluence of the old Mlava and the Danube rivers (Serbia). The vessels were [...] Read more.
Two ancient wooden vessels, specifically a monoxyle (1st century BCE to 1st century CE) and shipwreck (15th to 17th century CE), were excavated in a well-preserved state east of the confluence of the old Mlava and the Danube rivers (Serbia). The vessels were found in the ground that used to be river sediment and were temporarily stored within the semi-underground exhibition space of Mammoth Park. As part of the pre-conservation investigations, the primary aim of the research presented was to characterize the culturable mycobiomes of two excavated wooden artifacts so that appropriate conservation procedures for alleviating post-excavation fungal infestation could be formulated. Utilizing culture-based methods, a total of 32 fungi from 15 genera were identified, mainly Ascomycota and to a lesser extent Mucoromycota sensu stricto. Soft-rot Ascomycota of genus Penicillium, followed by Aspergillus and Cephalotrichum species, were the most diverse of the isolated fungi. Out of a total of 38 isolates, screened on 7 biodegradation plate assays, 32 (84.21%) demonstrated at least one degradative property. Penicillium solitum had the highest deterioration potential, with a positive reaction in 5 separate plate assays. The obtained results further broaden the limited knowledge on the peculiarities of post-excavation soft-rot decay of archaeological wood and indicate the biochemical mechanisms at the root of post-excavation fungal deterioration. Full article
(This article belongs to the Special Issue Fungal Biodegradation: Strategies, Current Understanding, and Future Prospects: 2nd Edition)
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14 pages, 552 KiB  
Article
Secretome Analysis of Thermothelomyces thermophilus LMBC 162 Cultivated with Tamarindus indica Seeds Reveals CAZymes for Degradation of Lignocellulosic Biomass
by Alex Graça Contato, Tiago Cabral Borelli, Marcos Silveira Buckeridge, Janet Rogers, Steven Hartson, Rolf Alexander Prade and Maria de Lourdes Teixeira de Moraes Polizeli
J. Fungi 2024, 10(2), 121; https://doi.org/10.3390/jof10020121 - 1 Feb 2024
Cited by 2 | Viewed by 1694
Abstract
The analysis of the secretome allows us to identify the proteins, especially carbohydrate-active enzymes (CAZymes), secreted by different microorganisms cultivated under different conditions. The CAZymes are divided into five classes containing different protein families. Thermothelomyces thermophilus is a thermophilic ascomycete, a source of [...] Read more.
The analysis of the secretome allows us to identify the proteins, especially carbohydrate-active enzymes (CAZymes), secreted by different microorganisms cultivated under different conditions. The CAZymes are divided into five classes containing different protein families. Thermothelomyces thermophilus is a thermophilic ascomycete, a source of many glycoside hydrolases and oxidative enzymes that aid in the breakdown of lignocellulosic materials. The secretome analysis of T. thermophilus LMBC 162 cultivated with submerged fermentation using tamarind seeds as a carbon source revealed 79 proteins distributed between the five diverse classes of CAZymes: 5.55% auxiliary activity (AAs); 2.58% carbohydrate esterases (CEs); 20.58% polysaccharide lyases (PLs); and 71.29% glycoside hydrolases (GHs). In the identified GH families, 54.97% are cellulolytic, 16.27% are hemicellulolytic, and 0.05 are classified as other. Furthermore, 48.74% of CAZymes have carbohydrate-binding modules (CBMs). Observing the relative abundance, it is possible to state that only thirteen proteins comprise 92.19% of the identified proteins secreted and are probably the main proteins responsible for the efficient degradation of the bulk of the biomass: cellulose, hemicellulose, and pectin. Full article
(This article belongs to the Special Issue Fungal Biodegradation: Strategies, Current Understanding, and Future Prospects: 2nd Edition)
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21 pages, 5016 KiB  
Article
Decolorization of Textile Azo Dye via Solid-State Fermented Wheat Bran by Lasiodiplodia sp. YZH1
by Ali Borham, Mohammad K. Okla, Mohamed A. El-Tayeb, Ahmed Gharib, Hanan Hafiz, Lei Liu, Chen Zhao, Ruqing Xie, Nannan He, Siwen Zhang, Juanjuan Wang and Xiaoqing Qian
J. Fungi 2023, 9(11), 1069; https://doi.org/10.3390/jof9111069 - 1 Nov 2023
Cited by 2 | Viewed by 2181
Abstract
Textile dyes are one of the major water pollutants released into water in various ways, posing serious hazards for both aquatic organisms and human beings. Bioremediation is a significantly promising technique for dye decolorization. In the present study, the fungal strain Lasiodiplodia sp. [...] Read more.
Textile dyes are one of the major water pollutants released into water in various ways, posing serious hazards for both aquatic organisms and human beings. Bioremediation is a significantly promising technique for dye decolorization. In the present study, the fungal strain Lasiodiplodia sp. was isolated from the fruiting bodies of Schizophyllum for the first time. The isolated fungal strain was examined for laccase enzyme production under solid-state fermentation conditions with wheat bran (WB) using ABTS and 2,6-Dimethoxyphenol (DMP) as substrates, then the fermented wheat bran (FWB) was evaluated as a biosorbent for Congo red dye adsorption from aqueous solutions in comparison with unfermented wheat bran. A Box–Behnken design was used to optimize the dye removal by FWB and to analyze the interaction effects between three factors: fermentation duration, pH, and dye concentration. Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM) were applied to study the changes in the physical and chemical characteristics of wheat bran before and after fermentation. An additional experiment was conducted to investigate the ability of the Lasiodiplodia sp. YZH1 to remove Congo red in the dye-containing liquid culture. The results showed that laccase was produced throughout the cultivation, reaching peak activities of ∼6.2 and 22.3 U/mL for ABTS and DMP, respectively, on the fourth day of cultivation. FWB removed 89.8% of the dye (100 mg L−1) from the aqueous solution after 12 h of contact, whereas WB removed only 77.5%. Based on the Box–Behnken design results, FWB achieved 93.08% dye removal percentage under the conditions of 6 days of fermentation, pH 8.5, and 150 mg L−1 of the dye concentration after 24 h. The fungal strain removed 95.3% of 150 mg L−1 of the dye concentration after 8 days of inoculation in the dye-containing liquid culture. These findings indicate that this strain is a worthy candidate for dye removal from environmental effluents. Full article
(This article belongs to the Special Issue Fungal Biodegradation: Strategies, Current Understanding, and Future Prospects: 2nd Edition)
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18 pages, 5273 KiB  
Article
Biodegradation of Low Density Polyethylene by the Fungus Cladosporium sp. Recovered from a Landfill Site
by Zhu Gong, Long Jin, Xingye Yu, Baoteng Wang, Shuang Hu, Honghua Ruan, Yun-Ju Sung, Hyung-Gwan Lee and Fengjie Jin
J. Fungi 2023, 9(6), 605; https://doi.org/10.3390/jof9060605 - 24 May 2023
Cited by 15 | Viewed by 5525
Abstract
Low density polyethylene (LDPE) has been widely used commercially for decades; however, as a non-degradable material, its continuous accumulation has contributed to serious environmental issues. A fungal strain, Cladosporium sp. CPEF-6 exhibiting a significant growth advantage on MSM-LDPE (minimal salt medium), was isolated [...] Read more.
Low density polyethylene (LDPE) has been widely used commercially for decades; however, as a non-degradable material, its continuous accumulation has contributed to serious environmental issues. A fungal strain, Cladosporium sp. CPEF-6 exhibiting a significant growth advantage on MSM-LDPE (minimal salt medium), was isolated and selected for biodegradation analysis. LDPE biodegradation was analyzed by weight loss percent, change in pH during fungal growth, environmental scanning electron microscopy (ESEM), and Fourier transformed infrared spectroscopy (FTIR). Inoculation with the strain Cladosporium sp. CPEF-6 resulted in a 0.30 ± 0.06% decrease in the weight of untreated LDPE (U-LDPE). After heat treatment (T-LDPE), the weight loss of LDPE increased significantly and reached 0.43 ± 0.01% after 30 days of culture. The pH of the medium was measured during LDPE degradation to assess the environmental changes caused by enzymes and organic acids secreted by the fungus. The fungal degradation of LDPE sheets was characterized by ESEM analysis of topographical alterations, such as cracks, pits, voids, and roughness. FTIR analysis of U-LDPE and T-LDPE revealed the appearance of novel functional groups associated with hydrocarbon biodegradation as well as changes in the polymer carbon chain, confirming the depolymerization of LDPE. This is the first report demonstrating the capacity of Cladosporium sp. to degrade LDPE, with the expectation that this finding can be used to ameliorate the negative impact of plastics on the environment. Full article
(This article belongs to the Special Issue Fungal Biodegradation: Strategies, Current Understanding, and Future Prospects: 2nd Edition)
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20 pages, 3976 KiB  
Article
Transcriptomic Analysis of Acetaminophen Biodegradation by Penicillium chrysogenum var. halophenolicum and Insights into Energy and Stress Response Pathways
by Francisco J. Enguita, Sofia Pereira and Ana Lúcia Leitão
J. Fungi 2023, 9(4), 408; https://doi.org/10.3390/jof9040408 - 27 Mar 2023
Cited by 6 | Viewed by 2269
Abstract
(1) Background: Acetaminophen (APAP), an active component of many analgesic and antipyretic drugs, is one of the most concerning trace contaminants in the environment and is considered as an emergent pollutant of marine and aquatic ecosystems. Despite its biodegradability, APAP has become a [...] Read more.
(1) Background: Acetaminophen (APAP), an active component of many analgesic and antipyretic drugs, is one of the most concerning trace contaminants in the environment and is considered as an emergent pollutant of marine and aquatic ecosystems. Despite its biodegradability, APAP has become a recalcitrant compound due to the growth of the global population, the ease of availability, and the inefficient wastewater treatment applied. (2) Methods: In this study, we used a transcriptomic approach to obtain functional and metabolic insights about the metabolization of APAP by a phenol-degrading fungal strain, Penicillium chrysogenum var. halophenolicum. (3) Results: We determined that the transcriptomic profile exhibited by the fungal strain during APAP degradation was very dynamic, being characterized by an abundance of dysregulated transcripts which were proportional to the drug metabolization. Using a systems biology approach, we also inferred the protein functional interaction networks that could be related to APAP degradation. We proposed the involvement of intracellular and extracellular enzymes, such as amidases, cytochrome P450, laccases, and extradiol-dioxygenases, among others. (4) Conclusions: Our data suggested that the fungus could metabolize APAP via a complex metabolic pathway, generating nontoxic metabolites, which demonstrated its potential in the bioremediation of this drug. Full article
(This article belongs to the Special Issue Fungal Biodegradation: Strategies, Current Understanding, and Future Prospects: 2nd Edition)
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