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New Opportunities in Fungal Biotechnology

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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 (15 August 2022) | Viewed by 29619

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Dr. Dominik Mojzita

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VTT Technical Research Centre of Finland, Industrial biotechnology and food, Espoo, Finland
Interests: synthetic biology; fungal biotechnology; genetic engineering; gene expression; recombinant protein production; novel fungal production hosts

Special Issue Information

Dear Colleagues,

There is a long history of biotechnological use of fungi. Since ancient times, fungi have been used for processing and the production of various foods. More recently, fungi have been employed as important workhorses in industrial biotechnology—ranging from the production of recombinant enzymes to the production of biochemicals and fuels. Fungi are also used as hosts to produce life-saving biopharmaceuticals such as insulin. Interestingly, the spectrum of applications where fungi play an essential role is expanding vigorously. We have witnessed novel applications such as cellular agriculture which involves the production of recombinant animal proteins and other compounds for use in food—aiming at providing more economical and environmentally friendly ways to obtain substitutes for meat and dairy products. Furthermore, there are novel uses of fungi either as production hosts or in material applications such as “fungal leather” where fungal biomass is utilized.

Apart from exciting new scientific findings, the ongoing developments bring along significant investments and business. The field of fungal biotech is “mushrooming” with new ambitious start-up companies, while at the same time, established biotech companies are adapting their operations to the new markets as well. Together with the growing demand, the challenges also grow as the requirements for the yield and quality of the products must match expectations and regulations. It is obvious that new production technologies, including establishing novel hosts and approaches, are needed to fulfill these expectations.

This Special Issue will be dedicated to novel fungal hosts and novel ways how to utilize these hosts for production of various compounds. Emphasis will be given to new techniques for heterologous gene expression, metabolic engineering, strain development, and cultivation methods to broaden the portfolio of the current approaches and to highlight the potential of the fungal kingdom for current and future biotechnology.

Dr. Dominik Mojzita
Guest Editor

Manuscript Submission Information

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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 biotechnology
synthetic biology
yeast
filamentous fungi
production host development
recombinant protein production
bioconversion
heterologous gene expression
metabolic engineering
metabolic modeling
fungal-based materials
bioprocess development

Published Papers (10 papers)

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Research

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18 pages, 3246 KiB

Open AccessArticle

Biotransformation of the Fluoroquinolone, Levofloxacin, by the White-Rot Fungus Coriolopsis gallica

by Amal Ben Ayed, Imen Akrout, Quentin Albert, Stéphane Greff, Charlotte Simmler, Jean Armengaud, Mélodie Kielbasa, Annick Turbé-Doan, Delphine Chaduli, David Navarro, Emmanuel Bertrand, Craig B. Faulds, Mohamed Chamkha, Amina Maalej, Héla Zouari-Mechichi, Giuliano Sciara, Tahar Mechichi and Eric Record

J. Fungi 2022, 8(9), 965; https://doi.org/10.3390/jof8090965 - 15 Sep 2022

Cited by 10 | Viewed by 2508

Abstract

The wastewater from hospitals, pharmaceutical industries and more generally human and animal dejections leads to environmental releases of antibiotics that cause severe problems for all living organisms. The aim of this study was to investigate the capacity of three fungal strains to biotransform the fluoroquinolone levofloxacin. The degradation processes were analyzed in solid and liquid media. Among the three fungal strains tested, Coriolopsis gallica strain CLBE55 (BRFM 3473) showed the highest removal efficiency, with a 15% decrease in antibiogram zone of inhibition for Escherichia coli cultured in solid medium and 25% degradation of the antibiotic in liquid medium based on high-performance liquid chromatography (HPLC). Proteomic analysis suggested that laccases and dye-decolorizing peroxidases such as extracellular enzymes could be involved in levofloxacin degradation, with a putative major role for laccases. Degradation products were proposed based on mass spectrometry analysis, and annotation suggested that the main product of biotransformation of levofloxacin by Coriolopsis gallica is an N-oxidized derivative. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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17 pages, 1593 KiB

Open AccessArticle

Genome-Wide Screening and Stability Verification of the Robust Internal Control Genes for RT-qPCR in Filamentous Fungi

by Yayong Yang, Xinyu Xu, Zhuohan Jing, Jun Ye, Hui Li, Xiaoyu Li, Lei Shi, Mengyu Chen, Tengyun Wang, Baogui Xie and Yongxin Tao

J. Fungi 2022, 8(9), 952; https://doi.org/10.3390/jof8090952 - 10 Sep 2022

Cited by 4 | Viewed by 2017

Abstract

In real-time quantitative PCR (RT-qPCR), internal control genes (ICGs) are crucial for normalization. This study screened 6 novel ICGs: Pre-mRNA-splicing factor cwc15 (Cwf15); ER associated DnaJ chaperone (DnaJ); E3 ubiquitin-protein ligase NEDD4 (HUL4); ATP-binding cassette, subfamily B (MDR/TAP), member 1 (VAMP); Exosome complex exonuclease DIS3/RRP44 (RNB); V-type H⁺-transporting ATPase sub-unit A (V-ATP) from the 22-transcriptome data of 8 filamentous fungi. The six novel ICGs are all involved in the basic biological process of cells and share the different transcription levels from high to low. In order to further verify the stability of ICGs candidates, the six novel ICGs as well as three traditional housekeeping genes: β-actin (ACTB); β-tubulin (β-TUB); glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH) and the previously screened reference genes: SPRY-domain-containing protein (SPRYp); Ras-2 protein (Ras); Vacuolar protein sorting protein 26 (Vps26) were evaluated by geNorm and NormFinder statistical algorithms. RT-qPCR of 12 ICGs were performed at different developmental stages in Flammulina filiformis and under different treatment conditions in Neurospora crassa. The consistent results of the two algorithms suggested that the novel genes, RNB, V-ATP, and VAMP, showed the highest stability in F. filiformis and N. crassa. RNB, V-ATP, and VAMP have high expression stability and universal applicability and therefore have great potential as ICGs for standardized calculation in filamentous fungi. The results also provide a novel guidance for the screening stable reference genes in RT-qPCR and a wide application in gene expression analysis of filamentous fungi. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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20 pages, 3767 KiB

Open AccessArticle

Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides

by Maggie Gortikov, Elizabeta Yakubovich, Zheng Wang, Francesc López-Giráldez, Yujia Tu, Jeffrey P. Townsend and Oded Yarden

J. Fungi 2022, 8(8), 854; https://doi.org/10.3390/jof8080854 - 15 Aug 2022

Cited by 3 | Viewed by 2216

Abstract

The nature of saprophytic and mycoparasitic hyphal growth of Trichoderma spp. has been studied extensively, yet its initiation via conidial germination in this genus is less well understood. Using near-synchronous germinating cultures of Trichoderma asperelloides, we followed the morphological progression from dormant conidia to initial polar growth to germling formation and to evidence for first branching. We found that the stage-specific transcriptional profile of T. asperelloides is one of the most dynamic described to date: transcript abundance of over 5000 genes—comprising approximately half of the annotated genome—was unremittingly reduced in the transition from dormancy to polar growth. Conversely, after the onset of germination, the transcript abundance of approximately a quarter of the genome was unremittingly elevated during the transition from elongation to initial branching. These changes are a testimony to the substantial developmental events that accompany germination. Bayesian network analysis identified several chitinase- and glucanase-encoding genes as active transcriptional hubs during germination. Furthermore, the expression of specific members of the chitin synthase and glucan elongase families was significantly increased during germination in the presence of Rhizoctonia solani—a known host of the mycoparasite—indicating that host recognition can occur during the early stages of mycoparasite development. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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19 pages, 2036 KiB

Open AccessArticle

Increased Attraction and Stability of Beauveria bassiana-Formulated Microgranules for Aedes aegypti Biocontrol

by Norma Zamora-Avilés, Alonso A. Orozco-Flores, Ricardo Gomez-Flores, Maribel Domínguez-Gámez, Mario A. Rodríguez-Pérez and Patricia Tamez-Guerra

J. Fungi 2022, 8(8), 828; https://doi.org/10.3390/jof8080828 - 08 Aug 2022

Cited by 1 | Viewed by 1733

Abstract

Aedes aegypti (Linn.) incidence has increased in recent years, causing human viral diseases such as dengue, which are often fatal. Beauveria bassiana (Bals., Vuillemin) efficacy for Ae. aegypti biological control has been evidenced but it relies on host susceptibility and strain virulence. We hypothesized that B. bassiana conidia microgranular formulations (MGF) with the additives acetone, lactic acid, and sugar increase Ae. aegypti adult exposure, thus improving their biocontrol effectiveness. Beauveria bassiana strain four (BBPTG4) conidia stability was assessed after 0 d, 5 d, and 30 d storage at 25 °C ± 2 °C with additives or in MGF after 91 d of storage at 25 °C ± 2 °C or 4 °C ± 1 °C, whereas mortality was evaluated after adult exposure to MGF + conidia, using home-made traps. Additives did not show toxicity to conidia. In addition, we observed that sugar in MGF increased Ae. aegypti adults’ attraction and their viability resulted in a 3-fold reduction after 5 d and 1- to 4-fold decrease after 30 d of storage, and formulations were less attractive (p < 0.05). Conidia stability was higher on MGF regardless of the storage temperature, losing up to 2.5-fold viability after 91 d. In conclusion, BBPTG4 infected and killed Ae. aegypti, whereas MGF attracting adults resulted in 42.2% mortality, increasing fungus auto dissemination potential among infected surviving adults. It is necessary to further evaluate MGF against Ae. aegypti in the field. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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25 pages, 34466 KiB

Open AccessArticle

RNA-Seq Provides Insights into the Mechanisms Underlying Ilyonectria robusta Responding to Secondary Metabolites of Bacillus methylotrophicus NJ13

by Xiang Li, Mengtao Li, Xiangkai Liu, Yilin Jiang, Dongfang Zhao, Jie Gao, Zhenhui Wang, Yun Jiang and Changqing Chen

J. Fungi 2022, 8(8), 779; https://doi.org/10.3390/jof8080779 - 26 Jul 2022

Cited by 2 | Viewed by 1701

Abstract

(1) Background: Ilyonectria robusta can cause ginseng to suffer from rusty root rot. Secondary metabolites (SMs) produced by Bacillus methylotrophicus NJ13 can inhibit the mycelial growth of I. robusta. However, the molecular mechanism of the inhibition and response remains unclear. (2) Methods: Through an in vitro trial, the effect of B. methylotrophicus NJ13’s SMs on the hyphae and conidia of I. robusta was determined. The change in the physiological function of I. robusta was evaluated in response to NJ13’s SMs by measuring the electrical conductivity, malondialdehyde (MDA) content, and glucose content. The molecular interaction mechanism of I. robusta’s response to NJ13’s SMs was analyzed by using transcriptome sequencing. (3) Results: NJ13’s SMs exhibited antifungal activity against I. robusta: namely, the hyphae swelled and branched abnormally, and their inclusions leaked out due to changes in the cell membrane permeability and the peroxidation level; the EC₅₀ value was 1.21% (v/v). In transcripts at 4 dpi and 7 dpi, the number of differentially expressed genes (DEGs) (|log₂(fold change)| > 1, p adj ≤ 0.05) was 1960 and 354, respectively. NJ13’s SMs affected the glucose metabolism pathway, and the sugar-transporter-related genes were downregulated, which are utilized by I. robusta for energy production. The cell wall structure of I. robusta was disrupted, and chitin-synthase-related genes were downregulated. (4) Conclusions: A new dataset of functional responses of the ginseng pathogenic fungus I. robusta was obtained. The results will benefit the development of targeted biological fungicides for I. robusta and the study of the molecular mechanisms of interaction between biocontrol bacteria and phytopathogenic fungi. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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12 pages, 3926 KiB

Open AccessArticle

Thermo-Mechanical and Fungi Treatment as an Alternative Lignin Degradation Method for Bambusa oldhamii and Guadua angustifolia Fibers

by Luis Garzón, Jorge I. Fajardo, Román Rodriguez-Maecker, Ernesto Delgado Fernández and Darío Cruz

J. Fungi 2022, 8(4), 399; https://doi.org/10.3390/jof8040399 - 14 Apr 2022

Cited by 2 | Viewed by 1845

Abstract

Different strategies have been used to degrade the molecular structure of lignins in natural fibers. Both chemical and biological processes can obtain different types of lignins for industrial use. In this study, a variation of the spectral intensity of the thermo-mechanical and fungi-modified Bambusa oldhamii (giant bamboo) and Guadua angustifolia Kunt fibers were examined via Fouriertransform infrared spectroscopy. The giant bamboo and Guadua angustifolia Kunt specimens were modified using a non-chemical alternative steam pressure method for degrading lignins, followed by mechanical sieving to obtain fibers of different lengths. The obtained fibers were treated with the Fusarium incarnatum-equiseti MF18MH45591 strain in a 21 d degradation process. The samples were subjected to Fouriertransform infrared spectroscopy before and after the strain treatment. The intensity variation was found to be in the spectral range of 1200 cm⁻¹ to 1800 cm⁻¹, in which lignin components are commonly found in most plant species. A multivariate analysis of the principal components of the treated and untreated control samples confirmed the changes in the spectral region of interest, which were associated with the thermo-mechanical and fungal treatment. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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12 pages, 1629 KiB

Open AccessArticle

Fungal Fermented Palm Kernel Expeller as Feed for Black Soldier Fly Larvae in Producing Protein and Biodiesel

by Chin Seng Liew, Chung Yiin Wong, Eman A. Abdelfattah, Ratchaprapa Raksasat, Hemamalini Rawindran, Jun Wei Lim, Worapon Kiatkittipong, Kunlanan Kiatkittipong, Mardawani Mohamad, Peter Nai Yuh Yek, Herma Dina Setiabudi, Chin Kui Cheng and Su Shiung Lam

J. Fungi 2022, 8(4), 332; https://doi.org/10.3390/jof8040332 - 23 Mar 2022

Cited by 13 | Viewed by 3643

Abstract

Being the second-largest country in the production of palm oil, Malaysia has a massive amount of palm kernel expeller (PKE) leftover. For that purpose, black soldier fly larvae (BSFL) are thus employed in this study to valorize the PKE waste. More specifically, this work elucidated the effects of the pre-fermentation of PKE via different amounts of Rhizopus oligosporus to enhance PKE palatability for the feeding of BSFL. The results showed that fermentation successfully enriched the raw PKE and thus contributed to the better growth of BSFL. BSFL grew to be 34% heavier at the optimum inoculum volume of 0.5 mL/10 g dry weight of PKE as compared to the control. Meanwhile, excessive fungal inoculum induced competition between BSFL and R. oligosporus, resulting in a reduction in BSFL weight. Under optimum feeding conditions, BSFL also registered the highest lipid yield (24.7%) and protein yield (44.5%). The biodiesel derived from BSFL lipid had also shown good compliance with the European biodiesel standard EN 14214. The high saturated fatty acid methyl esters (FAMEs) content (C12:0, C14:0, C16:0) in derived biodiesel made it highly oxidatively stable. Lastly, the superior degradation rate of PKE executed by BSFL further underpinned the sustainable conversion process in attaining valuable larval bioproducts. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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Review

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19 pages, 1270 KiB

Open AccessReview

Nature’s Most Fruitful Threesome: The Relationship between Yeasts, Insects, and Angiosperms

by Eduardo D. Fenner, Thamarys Scapini, Mariana da Costa Diniz, Anderson Giehl, Helen Treichel, Sergio Álvarez-Pérez and Sérgio L. Alves, Jr.

J. Fungi 2022, 8(10), 984; https://doi.org/10.3390/jof8100984 - 20 Sep 2022

Cited by 8 | Viewed by 3200

Abstract

The importance of insects for angiosperm pollination is widely recognized. In fact, approximately 90% of all plant species benefit from animal-mediated pollination. However, only recently, a third part player in this story has been properly acknowledged. Microorganisms inhabiting floral nectar, among which yeasts have a prominent role, can ferment glucose, fructose, sucrose, and/or other carbon sources in this habitat. As a result of their metabolism, nectar yeasts produce diverse volatile organic compounds (VOCs) and other valuable metabolites. Notably, some VOCs of yeast origin can influence insects’ foraging behavior, e.g., by attracting them to flowers (although repelling effects have also been reported). Moreover, when insects feed on nectar, they also ingest yeast cells, which provide them with nutrients and protect them from pathogenic microorganisms. In return, insects serve yeasts as transportation and a safer habitat during winter when floral nectar is absent. From the plant’s point of view, the result is flowers being pollinated. From humanity’s perspective, this ecological relationship may also be highly profitable. Therefore, prospecting nectar-inhabiting yeasts for VOC production is of major biotechnological interest. Substances such as acetaldehyde, ethyl acetate, ethyl butyrate, and isobutanol have been reported in yeast volatomes, and they account for a global market of approximately USD 15 billion. In this scenario, the present review addresses the ecological, environmental, and biotechnological outlooks of this three-party mutualism, aiming to encourage researchers worldwide to dig into this field. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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28 pages, 2305 KiB

Open AccessReview

Amazing Fungi for Eco-Friendly Composite Materials: A Comprehensive Review

by Worawoot Aiduang, Athip Chanthaluck, Jaturong Kumla, Kritsana Jatuwong, Sirasit Srinuanpan, Tanut Waroonkun, Rawiwan Oranratmanee, Saisamorn Lumyong and Nakarin Suwannarach

J. Fungi 2022, 8(8), 842; https://doi.org/10.3390/jof8080842 - 11 Aug 2022

Cited by 23 | Viewed by 6704

Abstract

The continually expanding use of plastic throughout our world, along with the considerable increase in agricultural productivity, has resulted in a worrying increase in global waste and related environmental problems. The reuse and replacement of plastic with biomaterials, as well as the recycling of agricultural waste, are key components of a strategy to reduce plastic waste. Agricultural waste is characterized as lignocellulosic materials that mainly consist of cellulose, hemicellulose, and lignin. Saprobe fungi are able to convert agricultural waste into nutrients for their own growth and to facilitate the creation of mycelium-based composites (MBC) through bio-fabrication processes. Remarkably, different fungal species, substrates, and pressing and drying methods have resulted in varying chemical, mechanical, physical, and biological properties of the resulting composites that ultimately vary the functional aspects of the finished MBC. Over the last two decades, several innovative designs have produced a variety of MBC that can be applied across a range of industrial uses including in packaging and in the manufacturing of household items, furniture, and building materials that can replace foams, plastics, and wood products. Materials developed from MBC can be considered highly functional materials that offer renewable and biodegradable benefits as promising alternatives. Therefore, a better understanding of the beneficial properties of MBC is crucial for their potential applications in a variety of fields. Here, we have conducted a brief review of the current findings of relevant studies through an overview of recently published literature on MBC production and the physical, mechanical, chemical, and biological properties of these composites for use in innovative architecture, construction, and product designs. The advantages and disadvantages of various applications of mycelium-based materials (MBM) in various fields have been summarized. Finally, patent trends involving the use of MBM as a new and sustainable biomaterial have also been reviewed. The resulting knowledge can be used by researchers to develop and apply MBC in the form of eco-friendly materials in the future. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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12 pages, 875 KiB

Open AccessReview

Recent Advances in Directed Yeast Genome Evolution

by Zhen Yao, Qinhong Wang and Zongjie Dai

J. Fungi 2022, 8(6), 635; https://doi.org/10.3390/jof8060635 - 15 Jun 2022

Cited by 6 | Viewed by 2464

Abstract

Saccharomyces cerevisiae, as a Generally Recognized as Safe (GRAS) fungus, has become one of the most widely used chassis cells for industrial applications and basic research. However, owing to its complex genetic background and intertwined metabolic networks, there are still many obstacles that need to be overcome in order to improve desired traits and to successfully link genotypes to phenotypes. In this context, genome editing and evolutionary technology have rapidly progressed over the last few decades to facilitate the rapid generation of tailor-made properties as well as for the precise determination of relevant gene targets that regulate physiological functions, including stress resistance, metabolic-pathway optimization and organismal adaptation. Directed genome evolution has emerged as a versatile tool to enable researchers to access desired traits and to study increasingly complicated phenomena. Here, the development of directed genome evolutions in S. cerevisiae is reviewed, with a focus on different techniques driving evolutionary engineering. Full article

(This article belongs to the Special Issue New Opportunities in Fungal Biotechnology)

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