Filamentous Fungi as Excellent Industrial Strains: Development and Applications

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungi in Agriculture and Biotechnology".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 14339

Special Issue Editors


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Guest Editor
Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Paterna, Spain
Interests: fungal biotechnology; fungal synthetic biology; genome editing; fungal biofactories; gene regulation; antifungals; plant biomass conversion; circular economy
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Guest Editor
Food Technology Area, Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, University of Valencia, 46100 Valencia, Spain
Interests: food fermentation; health; nutrition; filamentous fungi; antifungal proteins; mycotoxins; food sustainability
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Filamentous fungi are well known for their ability to produce organic acids, primary and secondary metabolites, enzymes and other proteins with applications in many industrial fields, including food and feed, pulp and paper, detergent, textile, pharmaceutical or biochemical and biofuel industries, among others. Industrial strains are commonly obtained by classical (non-GMO) strategies. However, in the last decades, genetic engineering—including genome editing—has contributed enormously to the development of efficient production strains with several potential applications in industry.

This Special Issue will be dedicated to any type of study (research articles, reviews, brief reports, etc.) that addresses the improvement of filamentous fungi, either through classical or biotechnological techniques, aimed at developing and optimization of filamentous fungal strains for their application at the industrial level. We also welcome papers describing methodologies for the genomic modification of industrially relevant fungal strains.

Dr. Sandra Garrigues
Dr. Mónica Gandía
Guest Editors

Manuscript Submission Information

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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

  • fungal strain improvement
  • classical strain development
  • fungal biotechnology
  • fungal synthetic biology
  • fungal biofactories
  • industrial applications

Related Special Issue

Published Papers (7 papers)

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Research

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14 pages, 2888 KiB  
Article
Effects of Orange Peel Extract on Laccase Activity and Gene Expression in Trametes versicolor
by Simon Vandelook, Berend Bassleer, Elise Elsacker and Eveline Peeters
J. Fungi 2024, 10(6), 370; https://doi.org/10.3390/jof10060370 - 22 May 2024
Viewed by 421
Abstract
The genome of Trametes versicolor encodes multiple laccase isozymes, the expression of which is responsive to various conditions. Here, we set out to investigate the potential of orange peel extract as an inducer of laccase production in this white-rot fungus, in comparison to [...] Read more.
The genome of Trametes versicolor encodes multiple laccase isozymes, the expression of which is responsive to various conditions. Here, we set out to investigate the potential of orange peel extract as an inducer of laccase production in this white-rot fungus, in comparison to the previously identified inducing chemical compound, veratryl alcohol. For four geographically distinct T. versicolor strains, a positive correlation has been observed between their oxidative activity and incubation time in liquid cultures. The addition of 20% orange peel extract or 5 mM veratryl alcohol caused a rapid increase in the oxidative potential of T. versicolor M99 after 24 h, with a more pronounced effect observed for the orange peel extract. To elucidate the underlying molecular mechanisms of the induced laccase activity, a transcriptional gene expression analysis was performed for the seven individual laccase genes in T. versicolor, revealing the upregulation of several laccase genes in response to the addition of each inducer. Notably, the gene encoding TvLac5 demonstrated a substantial upregulation in response to the addition of 20% orange peel extract, likely contributing to the observed increase in its oxidative potential. In conclusion, our results demonstrate that orange peels are a promising agro-industrial side stream for implementation as inducing agents in large-scale laccase production with T. versicolor. Full article
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12 pages, 1465 KiB  
Article
Agrobacterium tumefaciens-Mediated Transformation of the Aquatic Fungus Phialemonium inflatum FBCC-F1546
by Jonghan Yoon, Youngjun Kim, Seoyeon Kim, Haejun Jeong, Jiyoon Park, Min-Hye Jeong, Sangkyu Park, Miju Jo, Sunmin An, Jiwon Park, Seol-Hwa Jang, Jaeduk Goh and Sook-Young Park
J. Fungi 2023, 9(12), 1158; https://doi.org/10.3390/jof9121158 - 1 Dec 2023
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Abstract
Phialemonium inflatum is a useful fungus known for its ability to mineralise lignin during primary metabolism and decompose polycyclic aromatic hydrocarbons (PAHs). However, no functional genetic analysis techniques have been developed yet for this fungus, specifically in terms of transformation. In this study, [...] Read more.
Phialemonium inflatum is a useful fungus known for its ability to mineralise lignin during primary metabolism and decompose polycyclic aromatic hydrocarbons (PAHs). However, no functional genetic analysis techniques have been developed yet for this fungus, specifically in terms of transformation. In this study, we applied an Agrobacterium tumefaciens-mediated transformation (ATMT) system to P. inflatum for a functional gene analysis. We generated 3689 transformants using the binary vector pSK1044, which carried either the hygromycin B phosphotransferase (hph) gene or the enhanced green fluorescent protein (eGFP) gene to label the transformants. A Southern blot analysis showed that the probability of a single copy of T-DNA insertion was approximately 50% when the co-cultivation of fungal spores and Agrobacterium tumefaciens cells was performed at 24–36 h, whereas at 48 h, it was approximately 35.5%. Therefore, when performing gene knockout using the ATMT system, the co-cultivation time was reduced to ≤36 h. The resulting transformants were mitotically stable, and a PCR analysis confirmed the genes’ integration into the transformant genome. Additionally, hph and eGFP gene expressions were confirmed via PCR amplification and fluorescence microscopy. This optimised transformation system will enable functional gene analyses to study genes of interest in P. inflatum. Full article
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13 pages, 1238 KiB  
Article
Interaction between a Martian Regolith Simulant and Fungal Organic Acids in the Biomining Perspective
by Michele Vezzola, Solveig Tosi, Enrico Doria, Mattia Bonazzi, Matteo Alvaro and Alessio Sanfilippo
J. Fungi 2023, 9(10), 976; https://doi.org/10.3390/jof9100976 - 28 Sep 2023
Viewed by 880
Abstract
The aim of this study was to evaluate the potential of Aspergillus tubingensis in extracting metals from rocks simulating Martian regolith through biomining. The results indicated that the fungal strain produced organic acids, particularly oxalic acid, in the first five days, leading to [...] Read more.
The aim of this study was to evaluate the potential of Aspergillus tubingensis in extracting metals from rocks simulating Martian regolith through biomining. The results indicated that the fungal strain produced organic acids, particularly oxalic acid, in the first five days, leading to a rapid reduction in the pH of the culture medium. This acidic medium is ideal for bioleaching, a process that employs acidolysis and complexolysis to extract metals from rocks. Additionally, the strain synthesized siderophores, molecules capable of mobilizing metals from solid matrices, as verified by the blue CAS colorimetric test. The secretion of siderophores in the culture medium proved advantageous for biomining. The siderophores facilitated the leaching of metal ions, such as manganese, from the rock matrix into the acidified water solution. In addition, the susceptibility of the Martian regolith simulant to the biomining process was assessed by determining the particle size distribution, acid composition after treatment, and geochemical composition of the rock. Although the preliminary results demonstrate successful manganese extraction, further research is required to optimize the extraction technique. To conclude, the A. tubingensis strain exhibits promising abilities in extracting metals from rocks through biomining. Its use could prove useful in future in situ mining operations and environmental remediation efforts. Further research is required to optimize the process and evaluate its feasibility on a larger scale. Full article
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15 pages, 3704 KiB  
Article
Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi
by Jiajia Li, Ad Wiebenga, Anna Lipzen, Vivian Ng, Sravanthi Tejomurthula, Yu Zhang, Igor V. Grigoriev, Mao Peng and Ronald P. de Vries
J. Fungi 2023, 9(8), 860; https://doi.org/10.3390/jof9080860 - 18 Aug 2023
Cited by 3 | Viewed by 1883
Abstract
Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as [...] Read more.
Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications. Full article
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Review

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16 pages, 3087 KiB  
Review
Aspergillus oryzae as a Cell Factory: Research and Applications in Industrial Production
by Zeao Sun, Yijian Wu, Shihua Long, Sai Feng, Xiao Jia, Yan Hu, Maomao Ma, Jingxin Liu and Bin Zeng
J. Fungi 2024, 10(4), 248; https://doi.org/10.3390/jof10040248 - 26 Mar 2024
Viewed by 1390
Abstract
Aspergillus oryzae, a biosafe strain widely utilized in bioproduction and fermentation technology, exhibits a robust hydrolytic enzyme secretion system. Therefore, it is frequently employed as a cell factory for industrial enzyme production. Moreover, A. oryzae has the ability to synthesize various secondary [...] Read more.
Aspergillus oryzae, a biosafe strain widely utilized in bioproduction and fermentation technology, exhibits a robust hydrolytic enzyme secretion system. Therefore, it is frequently employed as a cell factory for industrial enzyme production. Moreover, A. oryzae has the ability to synthesize various secondary metabolites, such as kojic acid and L-malic acid. Nevertheless, the complex secretion system and protein expression regulation mechanism of A. oryzae pose challenges for expressing numerous heterologous products. By leveraging synthetic biology and novel genetic engineering techniques, A. oryzae has emerged as an ideal candidate for constructing cell factories. In this review, we provide an overview of the latest advancements in the application of A. oryzae-based cell factories in industrial production. These studies suggest that metabolic engineering and optimization of protein expression regulation are key elements in realizing the widespread industrial application of A. oryzae cell factories. It is anticipated that this review will pave the way for more effective approaches and research avenues in the future implementation of A. oryzae cell factories in industrial production. Full article
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16 pages, 1578 KiB  
Review
Synthetic Biology Tools for Engineering Aspergillus oryzae
by Hui Yang, Chaonan Song, Chengwei Liu and Pengchao Wang
J. Fungi 2024, 10(1), 34; https://doi.org/10.3390/jof10010034 - 3 Jan 2024
Viewed by 1960
Abstract
For more than a thousand years, Aspergillus oryzae has been used in traditional culinary industries, including for food fermentation, brewing, and flavoring. In recent years, A. oryzae has been extensively used in deciphering the pathways of natural product synthesis and value-added compound bioproduction. [...] Read more.
For more than a thousand years, Aspergillus oryzae has been used in traditional culinary industries, including for food fermentation, brewing, and flavoring. In recent years, A. oryzae has been extensively used in deciphering the pathways of natural product synthesis and value-added compound bioproduction. Moreover, it is increasingly being used in modern biotechnology industries, such as for the production of enzymes and recombinant proteins. The investigation of A. oryzae has been significantly accelerated through the successive application of a diverse array of synthetic biology techniques and methodologies. In this review, the advancements in biological tools for the synthesis of A. oryzae, including DNA assembly technologies, gene expression regulatory elements, and genome editing systems, are discussed. Additionally, the challenges associated with the heterologous expression of A. oryzae are addressed. Full article
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33 pages, 873 KiB  
Review
Strategies for the Development of Industrial Fungal Producing Strains
by Sonia Salazar-Cerezo, Ronald P. de Vries and Sandra Garrigues
J. Fungi 2023, 9(8), 834; https://doi.org/10.3390/jof9080834 - 8 Aug 2023
Cited by 7 | Viewed by 5834
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by [...] Read more.
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed. Full article
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