Hemicellulases from Penicillium and Talaromyces for lignocellulosic biomass valorization: A review

Distinct metabolites affect the phloem fungal communities in ash trees (Fraxinus spp.) native and nonnative to the highly invasive emerald ash borer (AGRILUS PLANIPENNIS)

Emerald ash borer (EAB, Agrilus planipennis) is an invasive killer of ash trees (Fraxinus spp.) in North America and Europe. Ash species co-evolved with EAB in their native range in Asia are mostly resistant, although the precise mechanism(s) remain unclear. Very little is also known about EAB or ash tree microbiomes. We performed the first joint comparison of phloem mycobiome and metabolites between a native and a nonnative ash species, infested and uninfested with EAB, in conjunction with investigation of larval mycobiome. Phloem mycobiome communities differed between the tree species, but both were unaffected by EAB infestation. Several indicator taxa in the larval gut shared a similarly high relative abundance only with the native host trees. Widely targeted metabolomics revealed 24 distinct metabolites in native trees and 53 metabolites in nonnative trees, respectively, that differed in relative content between infested and uninfested trees only in one species. Interestingly, four metabolites shared a strong relationship with the phloem mycobiomes, majority of which affected only the native trees. Collectively, our results demonstrate a complex interplay between host tree chemistry and mycobiome, and suggest the shared relationships between the mycobiomes of the native host tree and EAB may reflect their shared co-evolution.

Genome Characteristics of the Endophytic Fungus Talaromyces sp. DC2 Isolated from Catharanthus roseus (L.) G. Don

Talaromyces sp. DC2 is an endophytic fungus that was isolated from the stem of Catharanthus roseus (L.) G. Don in Hanoi, Vietnam and is capable of producing vinca alkaloids. This study utilizes the PacBio Sequel technology to completely sequence the whole genome of Talaromyces sp. DC2The genome study revealed that DC2 contains a total of 34.58 Mb spanned by 156 contigs, with a GC content of 46.5%. The identification and prediction of functional protein-coding genes, tRNA, and rRNA were comprehensively predicted and highly annotated using various BLAST databases, including non-redundant (Nr) protein sequence, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Carbohydrate-Active Enzymes (CAZy) databases. The genome of DC2 has a total of 149, 227, 65, 153, 53, and 6 genes responsible for cellulose, hemicellulose, lignin, pectin, chitin, starch, and inulin degradation, respectively. The Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analyses revealed that strain DC2 possesses 20 biosynthetic gene clusters responsible for producing secondary metabolites. The strain DC2 has also been found to harbor the DDC gene encoding aromatic L-amino acid decarboxylase enzyme. Conclusively, this study has provided a comprehensive understanding of the processes involved in secondary metabolites and the ability of the Talaromyces sp. DC2 strain to degrade plant cell walls.

Isolation and Characterization of Xylanase from a Novel Strain, Penicillium menonorum SP10

Xylanase has been applied in various sectors, such as biomass conversion, paper, pulp, textiles, and pharmaceutical industries. This study aimed to isolate and screen potential xylanase-producing fungi from the soil of Suphan Buri Province, Thailand. Fifteen fungi were isolated, and their xylanase activities were tested by the qualitative method. The result showed that isolate SP3, SP10 and SP15 gave high xylanase activity with potency index (PI) of 2.32, 2.01 and 1.82, respectively. These fungi were selected for the xylanase quantitative test, isolate SP10 performed the highest xylanase activity with 0.535 U/mL. Through molecular methods using the β-tubulin gene, isolate SP10 was identified as Penicillium menonorum. The xylanase characteristics from P. menonorum SP10 were determined, including the xylanase isoforms and the optimum pH and temperature. The xylanase isoforms on SDS-PAGE indicated that P. menonorum SP10 produced two xylanases (45 and 54 kDa). Moreover, its xylanase worked optimally at pH 6 and 55 °C while reaching 61% activity at 65 °C. These results proposed P. menonorum SP10 as a good candidate for industrial uses, especially in poultry feed and pulp industries, to improve yield and economic efficiency under slightly acidic and high-temperature conditions.

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

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.

Expression and Characterization of Two α-l-Arabinofuranosidases from Talaromyces amestolkiae: Role of These Enzymes in Biomass Valorization

α-l-arabinofuranosidases are glycosyl hydrolases that catalyze the break between α-l-arabinofuranosyl substituents or between α-l-arabinofuranosides and xylose from xylan or xylooligosaccharide backbones. While they belong to several glycosyl hydrolase (GH) families, there are only 24 characterized GH62 arabinofuranosidases, making them a small and underrepresented group, with many of their features remaining unknown. Aside from their applications in the food industry, arabinofuranosidases can also aid in the processing of complex lignocellulosic materials, where cellulose, hemicelluloses, and lignin are closely linked. These materials can be fully converted into sugar monomers to produce secondary products like second-generation bioethanol. Alternatively, they can be partially hydrolyzed to release xylooligosaccharides, which have prebiotic properties. While endoxylanases and β-xylosidases are also necessary to fully break down the xylose backbone from xylan, these enzymes are limited when it comes to branched polysaccharides. In this article, two new GH62 α-l-arabinofuranosidases from Talaromyces amestolkiae (named ARA1 and ARA-2) have been heterologously expressed and characterized. ARA-1 is more sensitive to changes in pH and temperature, whereas ARA-2 is a robust enzyme with wide pH and temperature tolerance. Both enzymes preferentially act on arabinoxylan over arabinan, although ARA-1 has twice the catalytic efficiency of ARA-2 on this substrate. The production of xylooligosaccharides from arabinoxylan catalyzed by a T. amestolkiae endoxylanase was significantly increased upon pretreatment of the polysaccharide with ARA-1 or ARA-2, with the highest synergism values reported to date. Finally, both enzymes (ARA-1 or ARA-2 and endoxylanase) were successfully applied to enhance saccharification by combining them with a β-xylosidase already characterized from the same fungus.

Distinct lignocellulolytic enzymes produced by Trichoderma harzianum in response to different pretreated substrates

In order to optimize the composition of enzyme cocktail for improving the hydrolytic efficiency of lignocellulose, different substrates were tested as inducers for producing lignocellulolytic enzymes by Trichoderma harzianum EM0925 in this study. As results, ultrafine grinding or steam explosion pretreated substrates can induce T. harzianum EM0925 to secret holo lignocellulolytic enzymes; acid treated substrate can induce cellobiohydrolase; while alkali or sodium chlorite treated substrates can induce β-xylosidase specifically. Furthermore, the combination of enzyme cocktails with different hydrolysis characteristics can further improve the hydrolysis efficiency, since 100% yields of glucose and xylose were obtained simultaneously from ultrafine grinding treated corn stover at low enzyme dosage (1.2 mg proteins/g substrate). This study for the first time demonstrated an effective solution that specific-pretreated substrates can be used as inducers for specific enzyme production by T. harzianum, which provided new idea and potential strategy for the construction of highly-efficient lignocellulolytic enzyme cocktails.

Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation

The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.

Insights into the capability of the lignocellulolytic enzymes of Penicillium parvum 4-14 to saccharify corn bran after alkaline hydrogen peroxide pretreatment

BACKGROUND

Corn bran is a major agro-industrial byproduct from corn starch processing. It contains abundant arabinoxylan that can be converted into value-added chemicals via biotechnology. Corn bran arabinoxylan (CBAX) is one of the most recalcitrant xylans for enzymatic degradation due to its particular heterogeneous nature. The present study aimed to investigate the capability of the filamentous fungus Penicillium parvum 4-14 to enzymatically saccharify CBAX and reveal the fungal carbohydrate-active enzyme (CAZyme) repertoire by genome sequencing and secretome analysis.

RESULTS

CBAX1 and CBAX2 with different branching degrees, together with corn bran residue (CBR) were generated from corn bran after alkaline hydrogen peroxide (AHP) pretreatment and graded ethanol precipitation. The protein blends E_CBAX1, E_CBAX2, and E_CBR were produced by the fungus grown on CBAX1, CBAX2, or CBR, respectively. Under the optimal conditions, E_CBAX1 released more than 80% xylose and arabinose from CBAX1 and CBAX2. Almost complete saccharification of the arabinoxylans was achieved by combining E_CBAX1 and a commercial enzyme cocktail Cellic®CTec3. Approximately 89% glucose, 64% xylose, and 64% arabinose were liberated from CBR by E_CBR. The combination of E_CBR with Cellic®CTec3 enhanced the saccharification of CBR, with conversion ratios of 97% for glucose, 81% for xylose, and 76% for arabinose. A total of 376 CAZymes including plentiful lignocellulolytic enzymes were predicted in P. parvum based on the fungal genomic sequence (25.8 Mb). Proteomic analysis indicated that the expression of CAZymes in P. parvum varied between CBAX1 and CBR, and the fungus produced complete cellulases, numerous hemicellulases, as well as high levels of glycosidases under the culture conditions.

CONCLUSIONS

This investigation disclosed the CAZyme repertoire of P. parvum at the genomic and proteomic levels, and elaborated on the promising potential of fungal lignocellulolytic enzymes upon saccharification of corn bran biomass after AHP pretreatment.

Botryosphaeriaceae gene machinery: Correlation between diversity and virulence

The Botryosphaeriaceae family comprises numerous fungal pathogens capable of causing economically meaningful diseases in a wide range of crops. Many of its members can live as endophytes and turn into aggressive pathogens following the onset of environmental stress events. Their ability to cause disease may rely on the production of a broad set of effectors, such as cell wall-degrading enzymes, secondary metabolites, and peptidases. Here, we conducted comparative analyses of 41 genomes representing six Botryosphaeriaceae genera to provide insights into the genetic features linked to pathogenicity and virulence. We show that these Botryosphaeriaceae genomes possess a large diversity of carbohydrate-active enzymes (CAZymes; 128 families) and peptidases (45 families). Botryosphaeria, Neofusicoccum, and Lasiodiplodia presented the highest number of genes encoding CAZymes involved in the degradation of the plant cell wall components. The genus Botryosphaeria also exhibited the highest abundance of secreted CAZymes and peptidases. Generally, the secondary metabolites gene cluster profile was consistent in the Botryosphaeriaceae family, except for Diplodia and Neoscytalidium. At the strain level, Neofusicoccum parvum NpBt67 stood out among all the Botryosphaeriaceae genomes, presenting a higher number of secretome constituents. In contrast, the Diplodia strains showed the lowest richness of the pathogenicity- and virulence-related genes, which may correlate with their low virulence reported in previous studies. Overall, these results contribute to a better understanding of the mechanisms underlying pathogenicity and virulence in remarkable Botryosphaeriaceae species. Our results also support that Botryosphaeriaceae species could be used as an interesting biotechnological tool for lignocellulose fractionation and bioeconomy.

A novel fusion transcription factor drives high cellulase and xylanase production on glucose in Trichoderma reesei

To reduce the high cost of (hemi)cellulase production in lignocellulose biorefining, it is important to develop strategies to enhance enzyme productivity from economic and also readily manipulatable carbon sources. In this study, an artificial transcription factor XT was designed by fusing the DNA binding domain of Xyr1 to the transactivation domain of Tmac1. When overexpressed in Trichoderma reesei QM9414 Δxyr1, the XT recombinant strain (OEXT) greatly improved (hemi)cellulase production on repressing glucose compared with QM9414 on Avicel with 1.7- and 8.2-fold increases in pNPCase and xylanase activity, respectively. Both activities were even higher (0.9- and 33.8-fold higher, respectively) than the recombinant strain similarly overexpressing Xyr1. The dramatically enhanced xylanase activities in OEXT resulted from the elevated expression of various hemicellulases in the secretome. Moreover, the enzyme cocktail from OEXT improved the saccharification efficiency toward corn stover by 60% compared with enzymes from QM9414 with equal volume loading.

Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization

Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.

Metagenomic analysis reveals the microbial degradation mechanism during kitchen waste biodrying

Biodrying is a treatment to remove moisture using bio-heat generated during organic degradation. Organic matter degradation and microbial metabolism were studied during the whole kitchen waste biodrying, using metagenomic analysis. After the 25-day biodrying process, carbohydrate, protein and lipid contents decreased by 83.7%, 27.8% and 79.3%, respectively, and their degradation efficiencies increased after the thermophilic phase. Lipase activity exceeded 10 mmol d^-1 g^-1 throughout biodrying. Cellulase and lipase activities recovered by 2.21% and 5.77%, respectively, after the thermophilic phase, while the protease activity had a maximum increment of 347%. Metabolic analysis revealed that carbohydrate, amino acid and lipid metabolism was possibly inhibited by the high temperature, but the relative abundances of related predicted functions recovered by more than 0.9%, 7% and 11%, respectively, by the end of biodrying. Protein function prediction suggests that β-oxidation, fatty acid biosynthesis, and the degradation of cellulose and chitin were possibly enhanced during the thermophilic phase. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that leucine, isoleucine and lysine could ultimately degraded to acetyl-CoA. Weissella, Aeribacillus and Bacillus were the genera with the most enriched functional genes during the whole biodrying process. These findings help elucidate the microbial degradation processes during biodrying, which provides further scientific support for improving the application of biodrying products.

Production of cellulosic ethanol and value-added products from corn fiber

Corn fiber, a by-product from the corn processing industry, mainly composed of residual starch, cellulose, and hemicelluloses, is a promising raw material for producing cellulosic ethanol and value-added products due to its abundant reserves and low costs of collection and transportation. Now, several technologies for the production of cellulosic ethanol from corn fiber have been reported, such as the D3MAX process, Cellerate™ process, etc., and part of the technologies have also been used in industrial production in the United States. The ethanol yields range from 64 to 91% of the theoretical maximum, depending on different production processes. Because of the multicomponent of corn fiber and the complex structures highly substituted by a variety of side chains in hemicelluloses of corn fiber, however, there are many challenges in cellulosic ethanol production from corn fiber, such as the low conversion of hemicelluloses to fermentable sugars in enzymatic hydrolysis, high production of inhibitors during pretreatment, etc. Some technologies, including an effective pretreatment process for minimizing inhibitors production and maximizing fermentable sugars recovery, production of enzyme preparations with suitable protein compositions, and the engineering of microorganisms capable of fermenting hexose and pentose in hydrolysates and inhibitors tolerance, etc., need to be further developed. The process integration of cellulosic ethanol and value-added products also needs to be developed to improve the economic benefits of the whole process. This review summarizes the status and progresses of cellulosic ethanol production and potential value-added products from corn fiber and presents some challenges in this field at present.

Molecular advances in microbial α-galactosidases: challenges and prospects

α-Galactosidase (α-D-galactosidase galactohydrolase; EC 3.2.1.22), is an industrially important enzyme that hydrolyzes the galactose residues in galactooligosaccharides and polysaccharides. The industrial production of α-galactosidase is currently insufficient owing to the high production cost, low production efficiency and low enzyme activity. Recent years have witnessed an increase in the worldwide research on molecular techniques to improve the production efficiency of microbial α-galactosidases. Cloning and overexpression of the gene sequences coding for α-galactosidases can not only increase the enzyme yield but can confer industrially beneficial characteristics to the enzyme protein. This review focuses on the molecular advances in the overexpression of α-galactosidases in bacterial and yeast/fungal expression systems. Recombinant α-galactosidases have improved biochemical and hydrolytic properties compared to their native counterparts. Metabolic engineering of microorganisms to produce high yields of α-galactosidase can also assist in the production of value-added products. Developing new variants of α-galactosidases through directed evolution can yield enzymes with increased catalytic activity and altered regioselectivity. The bottlenecks in the recombinant production of α-galactosidases are also discussed. The knowledge about the hurdles in the overexpression of recombinant proteins illuminates the emerging possibilities of developing a successful microbial cell factory and widens the opportunities for the production of industrially beneficial α-galactosidases.

Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms

Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms.

QM/MM investigation of the catalytic mechanism of processive endoglucanase Cel9G from Clostridium cellulovorans

Carbohydrate degradation catalyzed by glucoside hydrolases (GHs) is a major mechanism in biomass conversion. GH family 9 endoglucanase (Cel9G) from Clostridium cellulovorans, a typical multimodular enzyme, contains a catalytic domain closely linked to a family 3c carbohydrate-binding module (CBM3c). Unlike the conventional behavior proposed for other carbohydrate-binding modules, CBM3c has a direct impact on catalytic activity. In this work, extensive molecular dynamics (MD) simulations were employed to clarify the functional role of CBM3c. Furthermore, the detailed catalytic mechanism of Cel9G was investigated at the atomistic level using the combined quantum mechanical and molecular mechanical (QM/MM) method. Based on these simulations, owing to the rigidity of the peptide linker, CBM3c may affect the enzymatic activity via direct interactions with alpha helix 4 of GH9, especially with the K123 and H125 residues. In addition, using cellohexaose as a substrate, the QM/MM MD simulations confirmed that this enzyme can cleave the β-1,4-glycosidic linkage via an inverting mechanism. An oxocarbenium ion-like transition state was located with a barrier height of 19.6 kcal mol^-1. Furthermore, the G(-1) pyranose unit preferentially adopted a distorted ¹S₅/⁴H₅ conformer in the enzyme-substrate complex. For the cleavage of the glycosidic bond, we were able to identify a plausible route (¹S₅/⁴H₅ → [⁴H₅/⁴E]^# → ⁴C₁) from the reactant to the product at the G(-1) site.

Lessons from Biomass Valorization for Improving Plastic-Recycling Enzymes

Synthetic polymers such as plastics exhibit numerous advantageous properties that have made them essential components of our daily lives, with plastic production doubling every 15 years. The relatively low cost of petroleum-based polymers encourages their single use and overconsumption. Synthetic plastics are recalcitrant to biodegradation, and mismanagement of plastic waste leads to their accumulation in the ecosystem, resulting in a disastrous environmental footprint. Enzymes capable of depolymerizing plastics have been reported recently that may provide a starting point for eco-friendly plastic recycling routes. However, some questions remain about the mechanisms by which enzymes can digest insoluble solid substrates. We review the characterization and engineering of plastic-eating enzymes and provide some comparisons with the field of lignocellulosic biomass valorization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Fungal Cell Factories for Efficient and Sustainable Production of Proteins and Peptides

Filamentous fungi are a large and diverse taxonomically group of microorganisms found in all habitats worldwide. They grow as a network of cells called hyphae. Since filamentous fungi live in very diverse habitats, they produce different enzymes to degrade material for their living, for example hydrolytic enzymes to degrade various kinds of biomasses. Moreover, they produce defense proteins (antimicrobial peptides) and proteins for attaching surfaces (hydrophobins). Many of them are easy to cultivate in different known setups (submerged fermentation and solid-state fermentation) and their secretion of proteins and enzymes are often much larger than what is seen from yeast and bacteria. Therefore, filamentous fungi are in many industries the preferred production hosts of different proteins and enzymes. Edible fungi have traditionally been used as food, such as mushrooms or in fermented foods. New trends are to use edible fungi to produce myco-protein enriched foods. This review gives an overview of the different kinds of proteins, enzymes, and peptides produced by the most well-known fungi used as cell factories for different purposes and applications. Moreover, we describe some of the challenges that are important to consider when filamentous fungi are optimized as efficient cell factories.

Effects of Microbial Inoculation with Different Indigenous Bacillus Species on Physicochemical Characteristics and Bacterial Succession during Short-Term Composting

Bacillus accelerates lignocellulose degradation, promotes the stabilization and resource utilization of compost by secreting enzymes, and plays an important role in compost formation and quality control. This study evaluated enzyme activity, lignocellulosic degradation, and bacterial succession in composting inoculated with different microbial Bacillus agents. They were identified as B. licheniformis, B. subtilis, B. thermoamylovorans, B. thermoruber, and B. hisashii. Four treatments were established, including a CK (uninoculated microorganisms), A (B. licheniformis, B. subtilis, B. thermoamylovorans,and B. hisashii), B (B. subtilis, B. thermoamylovorans, B. thermoruber, and B. hisashii), and C (B. subtilis, B. thermoamylovorans, and B. hisashii), and the composting lasted 7–14 days. Lignin and cellulose degradation rates in B during composting were 17.1% and 36.7% at the cooling stage, respectively. Redundancy analysis showed that degradation of lignocellulose in the thermophilic stage was mainly related to the secretion of lignocellulose-degrading enzymes after microbial inoculation. 16S rRNA sequencing revealed that Bacillus (20.3%) and Thermobifida (20.2%) were the dominant genera. Inoculation with a combination including B. thermoruber was a feasible way to increase lignocellulose degradation and promote maturity in sewage sludge composting.

A Fungal Versatile GH10 Endoxylanase and Its Glycosynthase Variant: Synthesis of Xylooligosaccharides and Glycosides of Bioactive Phenolic Compounds

The study of endoxylanases as catalysts to valorize hemicellulosic residues and to obtain glycosides with improved properties is a topic of great industrial interest. In this work, a GH10 β-1,4-endoxylanase (XynSOS), from the ascomycetous fungus Talaromyces amestolkiae, has been heterologously produced in Pichia pastoris, purified, and characterized. rXynSOS is a highly glycosylated monomeric enzyme of 53 kDa that contains a functional CBM1 domain and shows its optimal activity on azurine cross-linked (AZCL)-beechwood xylan at 70 °C and pH 5. Substrate specificity and kinetic studies confirmed its versatility and high affinity for beechwood xylan and wheat arabinoxylan. Moreover, rXynSOS was capable of transglycosylating phenolic compounds, although with low efficiencies. For expanding its synthetic capacity, a glycosynthase variant of rXynSOS was developed by directed mutagenesis, replacing its nucleophile catalytic residue E236 by a glycine (rXynSOS-E236G). This novel glycosynthase was able to synthesize β-1,4-xylooligosaccharides (XOS) of different lengths (four, six, eight, and ten xylose units), which are known to be emerging prebiotics. rXynSOS-E236G was also much more active than the native enzyme in the glycosylation of a broad range of phenolic compounds with antioxidant properties. The interesting capabilities of rXynSOS and its glycosynthase variant make them promising tools for biotechnological applications.

Microbial α-galactosidases: Efficient biocatalysts for bioprocess technology

Galactomannans, abundantly present in plant biomass, can be used as renewable fermentation feedstock for biorefineries working for the production of bioethanol and other value-added products. The complete and efficient bioconversion of biomass to fermentable sugars for the generation of biofuels and other value-added products require the concerted action of accessory enzymes like α-galactosidases, which can work in cohesion with other carbohydrases in an enzyme cocktail. In the paper industry, α-galactosidases enhance the bleaching effect of endo-β-1,4-mannanases on softwood kraft pulp. Microbial α-galactosidases also find applications in the treatment of legume foods, recovery of sucrose from sugar beet syrup, improving the rheological properties of galactomannans, and synthesis of α-galactooligosaccharides to be used as functional food ingredients. Owing to their industrial applications, there is a surge in the research focused on α-galactosidases. The current review illustrates the diverse industrial applications of microbial α-galactosidases and their challenges and prospects.

The enzyme interactome concept in filamentous fungi linked to biomass valorization

Biomass represents an abundant and inexpensive source of sugars and aromatic compounds that can be used as raw materials for conversion into value-added bioproducts. Filamentous fungi are sources of plant cell wall degrading enzymes in nature. Understanding the interactions between enzymes is crucial for optimizing biomass degradation processes. Herein, the concept of the interactome is presented as a holistic approach that depicts the interactions among enzymes, substrates, metabolites, and inhibitors. The interactome encompasses several stages of biomass degradation, starting with the sensing of the substrate and the subsequent synthesis of hydrolytic and oxidative enzymes (fungus-substrate interaction). Enzyme-enzyme interactions are exemplified in the complex processes of lignocellulosic biomass degradation. The enzyme-substrate-metabolite-inhibitor interaction also provides a better understanding of biomass conversion, allowing bioproduct production from recalcitrant agro-industrial residues, thus bringing greater value to residual biomass. Finally, technological applications are presented for optimizing the interactome at various levels.

Lignocellulose biomass bioconversion during composting: Mechanism of action of lignocellulase, pretreatment methods and future perspectives

Composting is a biodegradation and transformation process that converts lignocellulosic biomass into value-added products, such as humic substances (HSs). However, the recalcitrant nature of lignocellulose hinders the utilization of cellulose and hemicellulose, decreasing the bioconversion efficiency of lignocellulose. Pretreatment is an essential step to disrupt the structure of lignocellulosic biomass. Many pretreatment methods for composting may cause microbial inactivation and death. Thus, the pretreatment methods suitable for composting can promote the degradation and transformation of lignocellulosic biomass. Therefore, this review summarizes the pretreatment methods suitable for composting. Microbial consortium pretreatment, Fenton pretreatment and surfactant-assisted pretreatment for composting may improve the bioconversion process. Microbial consortium pretreatment is a cost-effective pretreatment method to enhance HSs yields during composting. On the other hand, the efficiency of enzyme production during composting is very important for the degradation of lignocellulose, whose action mechanism is unknown. Therefore, this review describes the mechanism of action of lignocellulase, the predominant microbes producing lignocellulase and their related genes. Finally, optimizing pretreatment conditions and increasing enzymatic hydrolysis to improve the quality of composts by controlling suitable microenvironmental factors and core target microbial activities as a research focus in the bioconversion of lignocellulose during composting in the future.

Lytic Polysaccharide Monooxygenase from Talaromyces amestolkiae with an Enigmatic Linker-like Region: The Role of This Enzyme on Cellulose Saccharification

The first lytic polysaccharide monooxygenase (LPMO) detected in the genome of the widespread ascomycete Talaromyces amestolkiae (TamAA9A) has been successfully expressed in Pichia pastoris and characterized. Molecular modeling of TamAA9A showed a structure similar to those from other AA9 LPMOs. Although fungal LPMOs belonging to the genera Penicillium or Talaromyces have not been analyzed in terms of regioselectivity, phylogenetic analyses suggested C1/C4 oxidation which was confirmed by HPAEC. To ascertain the function of a C-terminal linker-like region present in the wild-type sequence of the LPMO, two variants of the wild-type enzyme, one without this sequence and one with an additional C-terminal carbohydrate binding domain (CBM), were designed. The three enzymes (native, without linker and chimeric variant with a CBM) were purified in two chromatographic steps and were thermostable and active in the presence of H2O2. The transition midpoint temperature of the wild-type LPMO (Tm = 67.7 °C) and its variant with only the catalytic domain (Tm = 67.6 °C) showed the highest thermostability, whereas the presence of a CBM reduced it (Tm = 57.8 °C) and indicates an adverse effect on the enzyme structure. Besides, the potential of the different T. amestolkiae LPMO variants for their application in the saccharification of cellulosic and lignocellulosic materials was corroborated.

Effects of different fermentation assisted enzyme treatments on the composition, microstructure and physicochemical properties of wheat straw used as a substitute for peat in nursery substrates

To solve the central problems caused by traditional composting treatments, such as long-time consumption and poor regulation effects, this study used three fermentation methods and four enzymes to develop rapid and directional regulation methods to convert wheat straw into a suitable substrate. The results showed that the mixed anaerobic method led to better pH (4.39-5.75) and EC values (1.27-1.89 mS/cm) in the straw substrates, while the aerobic method retained more nutrients and increased lignin and cellulose contents by 5.07-8.04% and 1.52-3.32%. The cellulase mixed with hemicellulase or laccase treatments all increased the crystallinity by 0.45-7.23%. The TG/DTG results showed that all treatments decreased the initial straw glass transition temperature, particularly when using the mixed anaerobic method, with decreases of 10.63-25.48 °C. Overall, mixed anaerobic fermentation and multiple enzymes, including cellulase, have been suggested as alternative biological modification methods for straw substrates.

Comparative Analysis of Herbaceous and Woody Cell Wall Digestibility by Pathogenic Fungi

Fungal pathogens have evolved combinations of plant cell-wall-degrading enzymes (PCWDEs) to deconstruct host plant cell walls (PCWs). An understanding of this process is hoped to create a basis for improving plant biomass conversion efficiency into sustainable biofuels and bioproducts. Here, an approach integrating enzyme activity assay, biomass pretreatment, field emission scanning electron microscopy (FESEM), and genomic analysis of PCWDEs were applied to examine digestibility or degradability of selected woody and herbaceous biomass by pathogenic fungi. Preferred hydrolysis of apple tree branch, rapeseed straw, or wheat straw were observed by the apple-tree-specific pathogen Valsa mali, the rapeseed pathogen Sclerotinia sclerotiorum, and the wheat pathogen Rhizoctonia cerealis, respectively. Delignification by peracetic acid (PAA) pretreatment increased PCW digestibility, and the increase was generally more profound with non-host than host PCW substrates. Hemicellulase pretreatment slightly reduced or had no effect on hemicellulose content in the PCW substrates tested; however, the pretreatment significantly changed hydrolytic preferences of the selected pathogens, indicating a role of hemicellulose branching in PCW digestibility. Cellulose organization appears to also impact digestibility of host PCWs, as reflected by differences in cellulose microfibril organization in woody and herbaceous PCWs and variation in cellulose-binding domain organization in cellulases of pathogenic fungi, which is known to influence enzyme access to cellulose. Taken together, this study highlighted the importance of chemical structure of both hemicelluloses and cellulose in host PCW digestibility by fungal pathogens.

Fungal glycosyl hydrolases for sustainable plant biomass valorization: Talaromyces amestolkiae as a model fungus

As the main decomposers and recyclers in nature, fungi secrete complex mixtures of extracellular enzymes for degradation of plant biomass, which is essential for mobilization of the organic carbon fixed by the photosynthesis in vegetal cells. Biotechnology can emulate the closed natural biological cycles, using lignocellulosic biomass as a renewable resource and lignocellulolytic fungal enzymes as catalysts to sustainably produce consumer goods. Cellulose and hemicellulose are the major polysaccharides on Earth, and the main enzymes involved in their hydrolytic depolymerization are cellulases (endoglucanases, cellobiohydrolases, and β-glucosidases) and hemicellulases (mainly endoxylanases and β-xylosidases). This work will focus on the enzymes secreted by the filamentous ascomycete Talaromyces amestolkiae and on some of their biotechnological applications. Their excellent hydrolytic activity was demonstrated by the partial degradation of xylans to prebiotic oligosaccharides by the endoxylanase XynN, or by the saccharification of lignocellulosic wastes to monosaccharides (fermentable to ethanol) either by the whole secretomes or by isolated enzymes used as supplements of commercial cocktails. However, apart from their expected hydrolytic activity, some of the β-glycosidases produced by this strain catalyze the transfer of a sugar molecule to specific aglycons by transglycosylation. As the synthesis of customized glycoconjugates is a major goal for biocatalysis, mutant variants of the β-xyloxidase BxTW1 and the ß-glucosidases BGL-1 and BGL-2 were obtained by directed mutagenesis, substantially improving the regioselective production yields of bioactive glycosides since they showed reduced or null hydrolytic activity.

Current understanding of the inhibition factors and their mechanism of action for the lignocellulosic biomass hydrolysis

Biorefining of lignocellulosic biomass is a relatively new concept but it has strong potential to develop and partially replace the fossil derived fuels and myriad of value products to subsequently reduce the greenhouse gas emissions. However, the energy and cost intensive process of releasing the entrapped fermentable sugars is a major challenge for its commercialization. Various factors playing a detrimental role during enzymatic hydrolysis of biomass are inherent recalcitrance of lignocellulosic biomass, expensive enzymes, sub-optimal enzyme composition, lack of synergistic activity and enzyme inhibition caused by various inhibitors. The current study investigated the mechanism of enzyme inhibition during lignocellulosic biomass saccharification especially at high solid loadings. These inhibition factors are categorized into physio-chemical factors, water-soluble and -insoluble enzyme inhibitors, oligomers and enzyme-lignin binding. Furthermore, different approaches are proposed to alleviate the challenges and improve the enzymatic hydrolysis efficiency such as supplementation with surfactants, synergistic catalytic/non-catalytic proteins, and bioprocess modifications.