Fungal Enzymes and Yeasts for Conversion of Plant Biomass to Bioenergy and High-Value Products

Advanced Fungal Biotechnologies in Accomplishing Sustainable Development Goals (SDGs): What Do We Know and What Comes Next?

The present era has witnessed an unprecedented scenario with extreme climate changes, depleting natural resources and rising global food demands and its widespread societal impact. From providing bio-based resources to fulfilling socio-economic necessities, tackling environmental challenges, and ecosystem restoration, microbes exist as integral members of the ecosystem and influence human lives. Microbes demonstrate remarkable potential to adapt and thrive in climatic variations and extreme niches and promote environmental sustainability. It is important to mention that advances in fungal biotechnologies have opened new avenues and significantly contributed to improving human lives through addressing socio-economic challenges. Microbe-based sustainable innovations would likely contribute to the United Nations sustainable development goals (SDGs) by providing affordable energy (use of agro-industrial waste by microbial conversions), reducing economic burdens/affordable living conditions (new opportunities by the creation of bio-based industries for a sustainable living), tackling climatic changes (use of sustainable alternative fuels for reducing carbon footprints), conserving marine life (production of microbe-based bioplastics for safer marine life) and poverty reduction (microbial products), among other microbe-mediated approaches. The article highlights the emerging trends and future directions into how fungal biotechnologies can provide feasible and sustainable solutions to achieve SDGs and address global issues.

Apiospora arundinis, a panoply of carbohydrate-active enzymes and secondary metabolites

The Apiospora genus comprises filamentous fungi with promising potential, though its full capabilities remain undiscovered. In this study, we present the first genome assembly of an Apiospora arundinis isolate, demonstrating a highly complete and contiguous assembly estimated to 48.8 Mb, with an N99 of 3.0 Mb. Our analysis predicted a total of 15,725 genes, with functional annotations for 13,619 of them, revealing a fungus capable of producing very high amounts of carbohydrate-active enzymes (CAZymes) and secondary metabolites. Through transcriptomic analysis, we observed differential gene expression in response to varying growth media, with several genes related to carbohydrate metabolism showing significant upregulation when the fungus was cultivated on a hay-based medium. Finally, our metabolomic analysis unveiled a fungus capable of producing a diverse array of metabolites.

Solid-State Fermentation with White Rot Fungi (Pleurotus Species) Improves the Chemical Composition of Highland Barley Straw as a Ruminant Feed and Enhances In Vitro Rumen Digestibility

Lignin degradation is important for enhancing the digestibility and improving the nutritive quality of ruminant feeds. White rot fungi are well known for their bioconversion of lignocellulosic biomass. The objective of this paper was to evaluate whether Lentinus sajor-caju, Pleurotus ostreatus, Phyllotopsis rhodophylla, Pleurotus djamor, Pleurotus eryngii, and Pleurotus citrinopileatus treatments altered the chemical compositions of highland barley straw constituents and enhanced their nutritional value as a ruminant feed. All white rot fungi significantly increased the relative crude protein (CP), ethyl ether extract (EE), starch, soluble protein (SP), and non-protein nitrogen (NPN) contents but decreased the ash, neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and acid detergent insoluble protein (ADFIP) contents. In addition, L. sajor-caju treatment increased (p < 0.001) the levels of PA, PB2, PB3, CA, CB1, CB2, and CNSC, but reduced (p < 0.001) the PC and CC in the solid-state fermentation of highland barley straw. Maximum ligninlysis (50.19%) was optimally produced in the presence of 1.53% glucose and 2.29% urea at 22.72 ℃. The in vitro dry matter digestibility and total volatile fatty acid concentrations of fermented highland barley straw, as well as the fermentability, were optimized and improved with L. sajor-caju, which degraded the lignocellulose and improved the nutritional value of highland barley straw as a ruminant feed.

Transcriptomic insights into the roles of the transcription factors Clr1, Clr2 and Clr4 in lignocellulose degradation of the thermophilic fungal platform Thermothelomyces thermophilus

Introduction: Thermothelomyces thermophilus, formerly known as Myceliophthora thermophila, is used in industry to produce lignocellulolytic enzymes and heterologous proteins. However, the transcriptional network driving the expression of these proteins remains elusive. As a first step to systematically uncover this network, we investigated growth, protein secretion, and transcriptomic fingerprints of strains deficient in the cellulolytic transcriptional regulators Clr1, Clr2, and Clr4, respectively. Methods: The genes encoding Clr1, Clr2, and Clr4 were individually deleted using split marker or the CRISPR/Cas12a technology and the resulting strains as well as the parental strain were cultivated in bioreactors under chemostat conditions using glucose as the carbon source. During steady state conditions, cellulose was added instead of glucose to study the genetic and cellular responses in all four strains to the shift in carbon source availability. Results: Notably, the clr1 and clr2 deletion strains were unable to continue to grow on cellulose, demonstrating a key role of both regulators in cellulose catabolism. Their transcriptomic fingerprints uncovered not only a lack of cellulase gene expression but also reduced expression of genes predicted to encode hemicellulases, pectinases, and esterases. In contrast, the growth of the clr4 deletion strain was very similar compared to the parental strain. However, a much stronger expression of cellulases, hemicellulases, pectinases, and esterases was observed. Discussion: The data gained in this study suggest that both transcriptional regulators Clr1 and Clr2 activate the expression of genes predicted to encode cellulases as well as hemicellulases, pectinases, and esterases. They further suggest that Clr1 controls the basal expression of cellulases and initiates the main lignocellulolytic response to cellulose via induction of clr2 expression. In contrast, Clr4 seems to act as a repressor of the lignocellulolytic response presumably via controlling clr2 expression. Comparative transcriptomics in all four strains revealed potentially new regulators in carbohydrate catabolism and lignocellulolytic enzyme expression that define a candidate gene list for future analyses.

Fungal Ligninolytic Enzymes and Their Application in Biomass Lignin Pretreatment

Lignocellulosic biomass is a significant source of sustainable fuel and high-value chemical production. However, due to the complex cross-linked three-dimensional network structure, lignin is highly rigid to degradation. In natural environments, the degradation is performed by wood-rotting fungi. The process is slow, and thus, the use of lignin degradation by fungi has not been regarded as a feasible technology in the industrial lignocellulose treatment. Fungi produce a wide variety of ligninolytic enzymes that can be directly introduced in industrial processing of lignocellulose. Within this study, screening of ligninolytic enzyme production using decolorization of ABTS and Azure B dyes was performed for 10 fungal strains with potentially high enzyme production abilities. In addition to standard screening methods, media containing lignin and hay biomass as carbon sources were used to determine the change in enzyme production depending on the substrate. All selected fungi demonstrated the ability to adapt to a carbon source limitation; however, four strains indicated the ability to secrete ligninolytic enzymes in all experimental conditions-Irpex lacteus, Pleurotus dryinus, Bjerkandera adusta, and Trametes versicolor-respectively displayed a 100%, 82.7%, 82.7%, and 55% oxidation of ABTS on lignin-containing media and 100%, 87.9%, 78%, and 70% oxidation of ABTS on hay-containing media after 168 h of incubation. As a result, the most potent strains of fungi were selected to produce lignocellulose-degrading enzymes and to demonstrate their potential application in biological lignocellulose pretreatment.

Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line

BACKGROUND

The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study.

RESULTS

Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively.

CONCLUSIONS

This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.

Potential Fungi Isolated From Anti-biodegradable Chinese Medicine Residue to Degrade Lignocellulose

Traditional Chinese medicine is one of the ancient medicines which is popular in Asian countries, among which the residue produced by the use of anti-biodegradables is endless, and causes significant adverse impacts on the environment. However, the high acidity of anti-biodegradable residues and some special biological activities make it difficult for microorganisms to survive, resulting in a very low degradation rate of lignocellulose in naturally stacked residues, which directly impedes the degradation of residues. We aimed to identify the fungal strains that efficiently biodegrade anti-biodegradable residue and see the possibility to improve the biodegradation of it and other agricultural wastes by co-cultivating these fungi. We isolated 302 fungal strains from anti-biodegradable residue to test hydrolysis ability. Finally, we found Coniochaeta sp., Fomitopsis sp., Nemania sp., Talaromyces sp., Phaeophlebiopsis sp. which inhabit the anti-biodegradable residues are capable of producing higher concentrations of extracellular enzymes. Synergistic fungal combinations (viz., Fomitopsis sp. + Phaeophlebiopsis sp.; Talaromyces sp. + Coniochaeta sp. + Fomitopsis sp.; Talaromyces sp. + Fomitopsis sp. + Piloderma sp. and Talaromyces sp. + Nemania sp. + Piloderma sp.) have better overall degradation effect on lignocellulose. Therefore, these fungi and their combinations have strong potential to be further developed for bioremediation and biological enzyme industrial production.

Fungal Proteases as Emerging Biocatalysts to Meet the Current Challenges and Recent Developments in Biomedical Therapies: An Updated Review

With the increasing world population, demand for industrialization has also increased to fulfill humans' living standards. Fungi are considered a source of essential constituents to produce the biocatalytic enzymes, including amylases, proteases, lipases, and cellulases that contain broad-spectrum industrial and emerging applications. The present review discussed the origin, nature, mechanism of action, emerging aspects of genetic engineering for designing novel proteases, genome editing of fungal strains through CRISPR technology, present challenges and future recommendations of fungal proteases. The emerging evidence revealed that fungal proteases show a protective role to many environmental exposures and discovered that an imbalance of protease inhibitors and proteases in the epithelial barriers leads to the protection of chronic eosinophilic airway inflammation. Moreover, mitoproteases recently were found to execute intense proteolytic processes that are crucial for mitochondrial integrity and homeostasis function, including mitochondrial biogenesis, protein synthesis, and apoptosis. The emerging evidence revealed that CRISPR/Cas9 technology had been successfully developed in various filamentous fungi and higher fungi for editing of specific genes. In addition to medical importance, fungal proteases are extensively used in different industries such as foods to prepare butter, fruits, juices, and cheese, and to increase their shelf life. It is concluded that hydrolysis of proteins in industries is one of the most significant applications of fungal enzymes that led to massive usage of proteomics.

Developing a Sustainable and Circular Bio-Based Economy in EU: By Partnering Across Sectors, Upscaling and Using New Knowledge Faster, and For the Benefit of Climate, Environment & Biodiversity, and People & Business

This paper gives an overview of development of the EU-bioeconomy, 2014–2020. The Vision of the new Circular Bio-based Economy, CBE is presented: Unlocking the full potential of all types of sustainably sourced biomass, crop residues, industrial side-streams, and wastes by transforming it into value-added products. The resulting product portfolio consists of a wide spectrum of value-added products, addressing societal and consumer needs. Food and feed, bio-based chemicals, materials, health-promoting products; and bio-based fuels. The pillars of CBE are described, including biotechnology, microbial production, enzyme technology, green chemistry, integrated physical/chemical processing, policies, conducive framework conditions and public private partnerships. Drivers of CBE are analyzed: Biomass supply, biorefineries, value chain clusters, rural development, farmers, foresters and mariners; urgent need for climate change mitigation and adaptation, and stopping biodiversity loss. Improved framework conditions can be drivers but also obstacles if not updated to the era of circularity. Key figures, across the entire BBI-JU project portfolio (2014–2020) are provided, including expansion into biomass feedstocks, terrestrial and aquatic, and an impressive broadening of bio-based product portfolio, including higher-value, health-promoting products for man, animal, plants and soil. Parallel to this, diversification of industrial segments and types of funding instruments developed, reflecting industrial needs and academic research involvement. Impact assessment is highlighted. A number of specific recommendations are given; e.g., including international win/win CBE-collaborations, as e.g., expanding African EU collaboration into CBE. In contrast to fossil resources biological resources are found worldwide. In its outset, circular bio-based economy, can be implemented all over, in a just manner, not the least stimulating rural development.

Evaluation of the chemical constituents and potential biological activities of Cunninghamella blakesleeana

The aim of this work is to evaluate the chemical constituents and potential biological activists of Cunninghamella blakesleeana. Three fatty acids were isolated using column chromatography and identified as palmitic acid (F1), oleic acid (F2) and stearic acid (F3) in addition to other two steroidal compounds; α-amyrin (A4), and β-sitosterol (A5). Using GC, ten fatty acids were detected the major fatty acid obtained was stearic acid (74.61%) while palmitic acid was the second high percentage (10.35%), and the least percentage obtained was arachidic acid (0.07%). C. blakesleeana extract showed in-vitro antimicrobial activities against some microorganisms. The highest activity of C. blakesleeana total extract was reported against Staphylococcus aureus (18.3 ± 0.03 mm.) followed by Streptococcus pyogenes (15.3 ± 0.05), while the lowest were for both Candida albicans & Pseudomonas aeruginosa (6.7 ± 0.06 and 5.9.0 ± 0.9 mm. respectively). The three isolated compounds (F1-3) showed activities against Staphylococcus aureus, Penicillium expansum, and Salmonella typhimurium only. The highest activity was aganist Staphylococcus aureus (13.0 ± 0.1 mm.). The highest effect was obtained by compound F3 (stearic acid) (15.0 ± 0.5 mm.), and compound F1 (oleic acid) (13.0 ± 0.1 mm.) and F2 (palmitic acid) 11.0 ± 0.3 mm. The total ethanol extract of the investigated fungus was safe up to 5000 mg kg⁻¹ and did not produce any significant change in liver and kidney functions after oral administration (400 mg kg⁻¹) for 14 consecutive days. The results reported the isolation of some fungal new driving compounds which has been not isolated before from Cunninghamella species in addition to their correlated new biological activities.

Growing a circular economy with fungal biotechnology: a white paper

Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture and beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions. Fungal biotechnology has, thus, the potential to make a significant contribution to climate change mitigation and meeting the United Nation’s sustainable development goals through the rational improvement of new and established fungal cell factories. The White Paper presented here is the result of the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019. This paper highlights discussions on current opportunities and research challenges in fungal biotechnology and aims to inform scientists, educators, the general public, industrial stakeholders and policymakers about the current fungal biotech revolution.

A comparative study of the enzymatic hydrolysis of batch organosolv-pretreated birch and spruce biomass

A shift towards a sustainable and green society is vital to reduce the negative effects of climate change associated with increased CO₂ emissions. Lignocellulosic biomass is both renewable and abundant, but is recalcitrant to deconstruction. Among the methods of pretreatment available, organosolv (OS) delignifies cellulose efficiently, significantly improving its digestibility by enzymes. We have assessed the hydrolysability of the cellulose-rich solid fractions from OS-pretreated spruce and birch at 2% w/v loading (dry matter). Almost complete saccharification of birch was possible with 80 mg enzyme preparation/g_solids (12 FPU/g_solids), while the saccharification yield for spruce was only 70%, even when applying 60 FPU/g_solids. As the cellulose content is enriched by OS, the yield of glucose was higher than in their steam-exploded counterparts. The hydrolysate was a transparent liquid due to the absence of phenolics and was also free from inhibitors. OS pretreatment holds potential for use in a large-scale, closed-loop biorefinery producing fuels from the cellulose fraction and platform chemicals from the hemicellulose and lignin fractions respectively.