Industrial Use of Cell Wall Degrading Enzymes: The Fine Line Between Production Strategy and Economic Feasibility

Hydrolysis of ionic liquid-treated substrate with an Iocasia fonsfrigidae strain SP3-1 endoglucanase

Recently, we reported the discovery of a novel endoglucanase of the glycoside hydrolase family 12 (GH12), designated IfCelS12A, from the haloalkaliphilic anaerobic bacterium Iocasia fonsfrigidae strain SP3-1, which was isolated from a hypersaline pond in the Samut Sakhon province of Thailand (ca. 2017). IfCelS12A exhibits high substrate specificity on carboxymethyl cellulose and amorphous cellulose but low substrate specificity on b-1,3;1,4-glucan. Unlike some endoglucanases of the GH12 family, IfCelS12A does not exhibit hydrolytic activity on crystalline cellulose (i.e., Avicel™). High-Pressure Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) analyses of products resulting from IfCelS12-mediated hydrolysis indicate mode of action for this enzyme. Notably, IfCelS12A preferentially hydrolyzes cellotetraoses, cellopentaoses, and cellohexaoses with negligible activity on cellobiose or cellotriose. Kinetic analysis with cellopentaose and barely b-D-glucan as cellulosic substrates were conducted. On cellopentaose, IfCelS12A demonstrates a 16-fold increase in activity (KM = 0.27 mM; kcat = 0.36 s-1; kcat/KM = 1.34 mM-1 s-1) compared to the enzymatic hydrolysis of barley b-D-glucan (KM: 0.04 mM, kcat: 0.51 s-1, kcat/KM = 0.08 mM-1 s-1). Moreover, IfCelS12A enzymatic efficacy is stable in hypersaline sodium chlorids (NaCl) solutions (up to 10% NaCl). Specifically, IfCel12A retains notable activity after 24 h at 2M NaCl (10% saline solution). IfCelS12A used as a cocktail component with other cellulolytic enzymes and in conjunction with mobile sequestration platform technology offers additional options for deconstruction of ionic liquid-pretreated cellulosic feedstock. KEY POINTS: • IfCelS12A from an anaerobic alkaliphile Iocasia fronsfrigidae shows salt tolerance • IfCelS12A in cocktails with other enzymes efficiently degrades cellulosic biomass • IfCelS12A used with mobile enzyme sequestration platforms enhances hydrolysis.

Chitinases: expanding the boundaries of knowledge beyond routinized chitin degradation

Chitinases, enzymes that degrade chitin, have long been studied for their role in various biological processes. They play crucial roles in the moulting process of invertebrates, the digestion of chitinous food, and defense against chitin-bearing pathogens. Additionally, chitinases are involved in physiological functions in crustaceans, such as chitinous food digestion, moulting, and stress response. Moreover, chitinases are universally distributed in organisms from viruses to mammals and have diverse functions including tissue degradation and remodeling, nutrition uptake, pathogen invasion, and immune response regulation. The discovery of these diverse functions expands our understanding of the biological significance and potential applications of chitinases. However, recent research has shown that chitinases possess several other functions beyond just chitin degradation. Their potential as biopesticides, therapeutic agents, and tools for bioremediation underscores their significance in addressing global challenges. More importantly, we noted that they may be applied as bioweapons if ethical regulations regarding production, engineering and application are overlooked.

Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments

Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.

Endogenous cell wall degrading enzyme LytD is important for the biocontrol activity of Bacillus subtilis

Autolysins are endogenous cell wall degrading enzymes (CWDEs) in bacteria that remodel the peptidoglycan layer of its own cell wall. In the Bacillus subtilis genome, at least 35 autolysin genes have been identified. However, the study of their roles in bacterial physiology has been hampered by their complexity and functional redundancy. B. subtilis GLB191 is an effective biocontrol strain against grape downy mildew disease, the biocontrol effect of which results from both direct effect against the pathogen and stimulation of the plant defense. In this study, we show that the autolysin N-acetylglucosaminidase LytD, a major autolysin of vegetative growth in B. subtilis, plays an important role in its biocontrol activity against grape downy mildew. Disruption of lytD resulted in reduced suppression of the pathogen Plasmopara viticola and stimulation of the plant defense. LytD is also shown to affect the biofilm formation and colonization of B. subtilis on grape leaves. This is the first report that demonstrates the role of an endogenous CWDE in suppressing plant disease infection of a biological control microorganism. These findings not only expand our knowledge on the biological function of autolysins but also provide a new target to promote the biocontrol activity of B. subtilis.

Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs

BACKGROUND

Sesarmid crabs dominate mangrove habitats as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory are not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove ecosystems. Although endogenous cellulase expressions were reported in crabs, it remains unknown if endogenous enzymes alone can complete the whole lignocellulolytic pathway, or if they also depend on the contribution from the intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach.

RESULTS

Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs with different dietary preferences revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab gut microbiomes have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. Herbivorous and detritivorous crabs showed highly similar CAZyme composition despite dissimilarities in taxonomic profiles observed in both groups, suggesting a stronger selection force on gut microbiota by functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of gut microbiota in supplementing nitrogen that is deficient in plant diet.

CONCLUSIONS

Endosymbiotic microbes play an important role in lignocellulose degradation in most crab species. Their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity in digesting mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in the crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrates.

Exploring the partial degradation of polysaccharides: Structure, mechanism, bioactivities, and perspectives

Polysaccharides are promising biomolecules with lowtoxicity and diverse bioactivities in food processing and clinical drug development. However, an essential prerequisite for their applications is the fine structure characterization. Due to the complexity of polysaccharide structure, partial degradation is a powerful tool for fine structure analysis, which can effectively provide valid information on the structure of backbone and branching glycosidic fragments of complex polysaccharides. This review aims to conclude current methods of partial degradation employed for polysaccharide structural characterization, discuss the molecular mechanisms, and describe the molecular structure and solution properties of degraded polysaccharides. In addition, the effects of polysaccharide degradation on the conformational relationships between the molecular structure and bioactivities, such as antioxidant, antitumor, and immunomodulatory activities, are also discussed. Finally, we summarize the prospects and current challenges for the partial degradation of polysaccharides. This review will be of great value for the scientific elucidation of polysaccharide fine structures and potential applications.

Development of sustainable downstream processing for nutritional oil production

Nutritional oils (mainly omega-3 fatty acids) are receiving increased attention as critical supplementary compounds for the improvement and maintenance of human health and wellbeing. However, the predominant sources of these oils have historically shown numerous limitations relating to desirability and sustainability; hence the crucial focus is now on developing smarter, greener, and more environmentally favourable alternatives. This study was undertaken to consider and assess the numerous prevailing and emerging techniques implicated across the stages of fatty acid downstream processing. A structured and critical comparison of the major classes of disruption methodology (physical, chemical, thermal, and biological) is presented, with discussion and consideration of the viability of new extraction techniques. Owing to a greater desire for sustainable industrial practices, and a desperate need to make nutritional oils more available; great emphasis has been placed on the discovery and adoption of highly sought-after 'green' alternatives, which demonstrate improved efficiency and reduced toxicity compared to conventional practices. Based on these findings, this review also advocates new forays into application of novel nanomaterials in fatty acid separation to improve the sustainability of nutritional oil downstream processing. In summary, this review provides a detailed overview of the current and developing landscape of nutritional oil; and concludes that adoption and refinement of these sustainable alternatives could promptly allow for development of a more complete 'green' process for nutritional oil extraction; allowing us to better meet worldwide needs without costing the environment.

Biotechnological development of Trichoderma-based formulations for biological control

Trichoderma spp. are a genus of well-known fungi that promote healthy growth and modulate different functions in plants, as well as protect against various plant pathogens. The application of Trichoderma and its propagules as a biological control method can therefore help to reduce the use of chemical pesticides and fertilizers in agriculture. This review critically discusses and analyzes groundbreaking innovations over the past few decades of biotechnological approaches to prepare active formulations containing Trichoderma. The use of various carrier substances is covered, emphasizing their effects on enhancing the shelf life, viability, and efficacy of the final product formulation. Furthermore, the use of processing techniques such as freeze drying, fluidized bed drying, and spray drying are highlighted, enabling the development of stable, light-weight formulations. Finally, promising microencapsulation techniques for maximizing the performance of Trichoderma spp. during application processes are discussed, leading to the next-generation of multi-functional biological control formulations. KEY POINTS: • The development of carrier substances to encapsulate Trichoderma propagules is highlighted. • Advances in biotechnological processes to prepare Trichoderma-containing formulations are critically discussed. • Current challenges and future outlook of Trichoderma-based formulations in the context of biological control are presented.

A pectin-based photoactivated bactericide nanosystem for achieving an improved utilization rate, photostability and targeted delivery of hematoporphyrin

Photoactivated pesticides have many advantages, such as high activity, low toxicity, and no drug resistance. However, poor photostability and a low utilization rate limit their practical application. Herein, the photosensitizer hematoporphyrin (HP) was used as a photoactivated pesticide, covalently linked with pectin (PEC) via ester bonds, to prepare an amphiphilic polymer pro-bactericide, and subsequently self-assembled in aqueous solutions to obtain an esterase-triggered nanobactericide delivery system. The fluorescence quenching effect due to the aggregation of HP in nanoparticles (NPs) enabled the inhibition of photodegradation of HP in this system. Esterase stimulation could trigger HP release and increase its photodynamic activity. Antibacterial assays have shown that the NPs had potent antibacterial capacity, almost completely inactivating bacteria after 60 min of exposure to light. The NPs had good adherence to the leaves. Safety assessment indicated that the NPs have no obvious toxic effects on plants. Antibacterial studies on plants have shown that the NPs have excellent antibacterial effects on infected plants. These results provide a new strategy for obtaining a photoactivated bactericide nanosystem with a high utilization rate and good photostability and targeting ability.

Carbohydrate-active enzymes in animal feed

Considering an ever-growing global population, which hit 8 billion people in the fall of 2022, it is essential to find solutions to avoid the competition between human food and animal feed for croplands. Agricultural co-products have become important components of the circular economy with their use in animal feed. Their implementation was made possible by the addition of exogenous enzymes in the diet, especially carbohydrate-active enzymes (CAZymes). In this review, we describe the diversity and versatility of microbial CAZymes targeting non-starch polysaccharides to improve the nutritional potential of diets containing cereals and protein meals. We focused our attention on cellulases, hemicellulases, pectinases which were often found to be crucial in vivo. We also highlight the performance and health benefits brought by the exogenous addition of enzymatic cocktails containing CAZymes in the diets of monogastric animals. Taking the example of the well-studied commercial cocktail Rovabio™, we discuss the evolution, constraints and future challenges faced by feed enzymes suppliers. We hope that this review will promote the use and development of enzyme solutions for industries to sustainably feed humans in the future.

Stoichiometric balance ratio of cellobiose and gentiobiose induces cellulase production in Talaromyces cellulolyticus

BACKGROUND

The exact mechanism by which fungal strains sense insoluble cellulose is unknown, but research points to the importance of transglycosylation products generated by fungi during cellulose breakdown. Here, we used multi-omics approach to identify the transglycosylation metabolites and determine their function in cellulase induction in a model strain, Talaromyces cellulolyticus MTCC25456.

RESULTS

Talaromyces sp. is a novel hypercellulolytic fungal strain. Based on genome scrutiny and biochemical analysis, we predicted the presence of cellulases on the surface of its spores. We performed metabolome analysis to show that these membrane-bound cellulases act on polysaccharides to form a mixture of disaccharides and their transglycosylated derivatives. Inevitably, a high correlation existed between metabolite data and the KEGG enrichment analysis of differentially expressed genes in the carbohydrate metabolic pathway. Analysis of the contribution of the transglycosylation product mixtures to cellulase induction revealed a 57% increase in total cellulase. Further research into the metabolites, using in vitro induction tests and response surface methodology, revealed that Talaromyces sp. produces cell wall-breaking enzymes in response to cellobiose and gentiobiose as a stimulant. Precisely, a 2.5:1 stoichiometric ratio of cellobiose to gentiobiose led to a 2.4-fold increase in cellulase synthesis. The application of the optimized inducers in cre knockout strain significantly increased the enzyme output.

CONCLUSION

This is the first study on the objective evaluation and enhancement of cellulase production using optimized inducers. Inducer identification and genetic engineering boosted the cellulase production in the cellulolytic fungus Talaromyces sp.

Radical cation scavenging activity of berberine bridge enzyme-like oligosaccharide oxidases acting on short cell wall fragments

Oligogalacturonide-oxidases (OGOXs) and cellodextrin-oxidase (CELLOX) are plant berberine bridge enzyme-like oligosaccharide-oxidases (OSOXs) that oxidize, respectively, oligogalacturonides (OGs) and cellodextrins (CDs), thereby inactivating their elicitor nature and concomitantly releasing H₂O₂. Little is known about the physiological role of OSOX activity. By using an ABTS^·+-reduction assay, we identified a novel reaction mechanism through which the activity of OSOXs on cell wall oligosaccharides scavenged the radical cation ABTS^·+ with an efficiency dependent on the type and length of the oxidized oligosaccharide. In contrast to the oxidation of longer oligomers such as OGs (degree of polymerization from 10 to 15), the activity of OSOXs on short galacturonan- and cellulose-oligomers (degree of polymerization ≤ 4) successfully counteracted the radical cation-generating activity of a fungal laccase, suggesting that OSOXs can generate radical cation scavenging activity in the apoplast with a power proportional to the extent of degradation of the plant cell wall, with possible implications for redox homeostasis and defense against oxidative stress.

Cellobiose elicits immunity in lettuce conferring resistance to Botrytis cinerea

Cellobiose is the primary product of cellulose hydrolysis and is expected to function as a type of pathogen/damage-associated molecular pattern in evoking plant innate immunity. In this study, cellobiose was demonstrated to be a positive regulator in the immune response of lettuce, but halted autoimmunity when lettuce was exposed to concentrations of cellobiose >60 mg l-1. When lettuce plants were infected by Botrytis cinerea, cellobiose endowed plants with enhanced pre-invasion resistance by activating high β-1,3-glucanase and antioxidative enzyme activities at the initial stage of pathogen infection. Cellobiose-activated core regulatory factors such as EDS1, PTI6, and WRKY70, as well as salicylic acid signaling, played an indispensable role in modulating plant growth-defense trade-offs. Transcriptomics data further suggested that the cellobiose-activated plant-pathogen pathways are involved in microbe/pathogen-associated molecular pattern-triggered immune responses. Genes encoding receptor-like kinases, transcription factors, and redox homeostasis, phytohormone signal transduction, and pathogenesis-related proteins were also up- or down-regulated by cellobiose. Taken together, the findings of this study demonstrated that cellobiose serves as an elicitor to directly activate disease-resistance-related cellular functions. In addition, multiple genes have been identified as potential modulators of the cellobiose-induced immune response, which could aid understanding of underlying molecular events.

Managing the Transition to Widespread Metagenomic Monitoring: Policy Considerations for Future Biosurveillance

The technological possibilities and future public health importance of metagenomic sequencing have received extensive attention, but there has been little discussion about the policy and regulatory issues that need to be addressed if metagenomic sequencing is adopted as a key technology for biosurveillance. In this article, we introduce metagenomic monitoring as a possible path to eventually replacing current infectious disease monitoring models. Many key enablers are technological, whereas others are not. We therefore highlight key policy challenges and implementation questions that need to be addressed for "widespread metagenomic monitoring" to be possible. Policymakers must address pitfalls like fragmentation of the technological base, private capture of benefits, privacy concerns, the usefulness of the system during nonpandemic times, and how the future systems will enable better response. If these challenges are addressed, the technological and public health promise of metagenomic sequencing can be realized.

Characterization of two 1,3-β-glucan-modifying enzymes from Penicillium sumatraense reveals new insights into 1,3-β-glucan metabolism of fungal saprotrophs

BACKGROUND

1,3-β-glucan is a polysaccharide widely distributed in the cell wall of several phylogenetically distant organisms, such as bacteria, fungi, plants and microalgae. The presence of highly active 1,3-β-glucanases in fungi evokes the biological question on how these organisms can efficiently metabolize exogenous sources of 1,3-β-glucan without incurring in autolysis.

RESULTS

To elucidate the molecular mechanisms at the basis of 1,3-β-glucan metabolism in fungal saprotrophs, the putative exo-1,3-β-glucanase G9376 and a truncated form of the putative glucan endo-1,3-β-glucosidase (ΔG7048) from Penicillium sumatraense AQ67100 were heterologously expressed in Pichia pastoris and characterized both in terms of activity and structure. G9376 efficiently converted laminarin and 1,3-β-glucan oligomers into glucose by acting as an exo-glycosidase, whereas G7048 displayed a 1,3-β-transglucanase/branching activity toward 1,3-β-glucan oligomers with a degree of polymerization higher than 5, making these oligomers more recalcitrant to the hydrolysis acted by exo-1,3-β-glucanase G9376. The X-ray crystallographic structure of the catalytic domain of G7048, solved at 1.9 Å of resolution, consists of a (β/α)₈ TIM-barrel fold characteristic of all the GH17 family members. The catalytic site is in a V-shaped cleft containing the two conserved catalytic glutamic residues. Molecular features compatible with the activity of G7048 as 1,3-β-transglucanase are discussed.

CONCLUSIONS

The antagonizing activity between ΔG7048 and G9376 indicates how opportunistic fungi belonging to Penicillium genus can feed on substrates similar for composition and structure to their own cell wall without incurring in a self-deleterious autohydrolysis.

Xylanase Inhibitors: Defense Players in Plant Immunity with Implications in Agro-Industrial Processing

Xylanase inhibitors (XIs) are plant cell wall proteins largely distributed in monocots that inhibit the hemicellulose degrading activity of microbial xylanases. XIs have been classified into three classes with different structures and inhibition specificities, namely Triticum aestivum xylanase inhibitors (TAXI), xylanase inhibitor proteins (XIP), and thaumatin-like xylanase inhibitors (TLXI). Their involvement in plant defense has been established by several reports. Additionally, these inhibitors have considerable economic relevance because they interfere with the activity of xylanases applied in several agro-industrial processes. Previous reviews highlighted the structural and biochemical properties of XIs and hypothesized their role in plant defense. Here, we aimed to update the information on the genomic organization of XI encoding genes, the inhibition properties of XIs against microbial xylanases, and the structural properties of xylanase-XI interaction. We also deepened the knowledge of XI regulation mechanisms in planta and their involvement in plant defense. Finally, we reported the recently studied strategies to reduce the negative impact of XIs in agro-industrial processes and mentioned their allergenicity potential.

Plant Extraction in Water: Towards Highly Efficient Industrial Applications

Since the beginning of this century, the world has experienced a growing need for enabling techniques and more environmentally friendly protocols that can facilitate more rational industrial production. Scientists are faced with the major challenges of global warming and safeguarding water and food quality. Organic solvents are still widely used and seem to be hard to replace, despite their enormous environmental and toxicological impact. The development of water-based strategies for the extraction of primary and secondary metabolites from plants on a laboratory scale is well documented, with several intensified processes being able to maximize the extraction power of water. Technologies, such as ultrasound, hydrodynamic cavitation, microwaves and pressurized reactors that achieve subcritical water conditions can dramatically increase extraction rates and yields. In addition, significant synergistic effects have been observed when using combined techniques. Due to the limited penetration depth of microwaves and ultrasonic waves, scaling up entails changes to reactor design. Nevertheless, the rich academic literature from laboratory-scale investigations may contribute to the engineering work involved in maximizing mass/energy transfer. In this article, we provide an overview of current and innovative techniques for solid-liquid extraction in water for industrial applications, where continuous and semi-continuous processes can meet the high demands for productivity, profitability and quality.

An Insight into Microbial Inoculants for Bioconversion of Waste Biomass into Sustainable "Bio-Organic" Fertilizers: A Bibliometric Analysis and Systematic Literature Review

The plant-microbe holobiont has garnered considerable attention in recent years, highlighting its importance as an ecological unit. Similarly, manipulation of the microbial entities involved in the rhizospheric microbiome for sustainable agriculture has also been in the limelight, generating several commercial bioformulations to enhance crop yield and pest resistance. These bioformulations were termed biofertilizers, with the consistent existence and evolution of different types. However, an emerging area of interest has recently focused on the application of these microorganisms for waste valorization and the production of "bio-organic" fertilizers as a result. In this study, we performed a bibliometric analysis and systematic review of the literature retrieved from Scopus and Web of Science to determine the type of microbial inoculants used for the bioconversion of waste into "bio-organic" fertilizers. The Bacillus, Acidothiobacillus species, cyanobacterial biomass species, Aspergillus sp. and Trichoderma sp. were identified to be consistently used for the recovery of nutrients and bioconversion of wastes used for the promotion of plant growth. Cyanobacterial strains were used predominantly for wastewater treatment, while Bacillus, Acidothiobacillus, and Aspergillus were used on a wide variety of wastes such as sawdust, agricultural waste, poultry bone meal, crustacean shell waste, food waste, and wastewater treatment plant (WWTP) sewage sludge ash. Several bioconversion strategies were observed such as submerged fermentation, solid-state fermentation, aerobic composting, granulation with microbiological activation, and biodegradation. Diverse groups of microorganisms (bacteria and fungi) with different enzymatic functionalities such as chitinolysis, lignocellulolytic, and proteolysis, in addition to their plant growth promoting properties being explored as a consortium for application as an inoculum waste bioconversion to fertilizers. Combining the efficiency of such functional and compatible microbial species for efficient bioconversion as well as higher plant growth and crop yield is an enticing opportunity for "bio-organic" fertilizer research.

Stimulating fungal cell wall integrity by exogenous β-glucanase to improve the production of fungal natural products

The low production of natural products (NPs) is still the critical restrictive factor in exploiting their potential large-scale applications and a barrier to isolating and identifying other meaningful products. Given that the stimulation of cell wall integrity (CWI) has become a novel strategy to modulate the production of microbial natural products, herein, exogenous β-glucanase treatment was developed as an external cell wall β-glucan stress to stimulate the fungal CWI, and then to improve the production of fungal NPs. It was found that the production of fungal NPs cercosporin and sophorolipids, biosynthesized by Cercospora sp. and Starmerella bombicola, respectively, was significantly improved by the treatment of β-glucanase under a controllable dose. Moreover, it demonstrated that β-glucanase had an ability to stimulate fungal CWI through slight fungal superficial damage, thus facilitating the secretion of NPs. We expected that this easy-operating method to stimulate fungal CWI could be feasible to improve more fungal NPs production. KEY POINTS: • Exogenous β-glucanase stimulated the fungal cell wall integrity • Changing fungal cell walls modulated natural product production • β-glucanase with potential universal effects on more fungal natural products.

Interplay between the microalgae Micrasterias radians and its symbiont Dyadobacter sp. HH091

Based on previous research, related to detailed insight into mutualistic collaboration of microalga and its microbiome, we established an artificial plant-bacteria system of the microalga Micrasterias radians MZCH 672 and the bacterial isolate Dyadobacter sp. HH091. The bacteria, affiliated with the phylum Bacteroidota, strongly stimulated growth of the microalga when it was added to axenic algal cultures. For further advances, we studied the isolate HH091 and its interaction with the microalga M. radians using transcriptome and extensive genome analyses. The genome of HH091 contains predicted polysaccharide utilizing gene clusters co-working with the type IX secretion system (T9SS) and conceivably involved in the algae-bacteria liaison. Here, we focus on characterizing the mechanism of T9SS, implementing the attachment and invasion of microalga by Dyadobacter sp. HH091. Omics analysis exposed T9SS genes: gldK, gldL, gldM, gldN, sprA, sprE, sprF, sprT, porU and porV. Besides, gld genes not considered as the T9SS components but required for gliding motility and protein secretion (gldA, gldB, gldD, gldF, gldG, gldH, gldI, gldJ), were also identified at this analysis. A first model of T9SS apparatus of Dyadobacter was proposed in a course of this research. Using the combination of fluorescence labeling of Dyadobacter sp. HH091, we examined the bacterial colonisation and penetration into the cell wall of the algal host M. radians MZCH 672.

Berberine Bridge Enzyme-like Oligosaccharide Oxidases Act as Enzymatic Transducers Between Microbial Glycoside Hydrolases and Plant Peroxidases

Oligogalacturonide (OG)-oxidase 1 (OGOX1) and cellodextrin (CD)-oxidase (CELLOX) are plant berberine bridge enzyme-like oligosaccharide oxidases that oxidize OGs and CDs, cell-wall fragments with the nature of damage-associated molecular patterns. The oxidation of OGs and CDs attenuates their elicitor activity and concomitantly releases H₂O₂. By using a multiple enzyme-based assay, we demonstrate that the H₂O₂ generated downstream of the combined action between a fungal polygalacturonase and OGOX1 or an endoglucanase and CELLOX can be directed by plant peroxidases (PODs) either towards a reaction possibly involved in plant defense, such as the oxidation of monolignol or a reaction possibly involved in a developmental event, such as the oxidation of auxin (indole-3-acetic acid), pointing to OGOX1 and CELLOX as enzymatic transducers between microbial glycoside hydrolases and plant PODs. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Fusarium graminearum as a producer of xylanases with low cellulases when grown on wheat bran

•

Endophytic fungi of cacao had important xylanase activity when grown on wheat bran.

•

F. graminearum strain Ec220 produced xylanases with low cellulolytic activity.

•

Xylanase production was optimized using response surface methodology.

•

Proteomic analysis revealed similarities with previously reported xylanases.

The xylanolytic potential of endophytic fungi isolated from leaves of Theobroma cacao was explored for the first time. Four fungal strains showed significant amounts of xylanase activity and low cellulase levels when grown on wheat bran as the sole carbon source. Strain Ec220 of Fusarium graminearum had the highest xylanase production (1.79 U/ml), whereas its cellulase activity was minimal (0.24 U/ml). Optimal conditions for xylanase production were: 154 h of incubation time, pH 5.79 and 29.8 °C. Furthermore, two protein spots detected by two-dimensional gel electrophoresis showed molecular weights (26.05 and 27.70 kDa) and isoelectric points (6.18 and 9.20) corresponding to previously reported F. graminearum xylanases, Xyl A and Xyl B, respectively. Therefore, endophytic fungi of T. cacao can be an important source of xylanolytic activities when cultured on wheat bran, and xylanases with low cellulases found in strain Ec220 require further characterization as they show promise for possible industrial applications.

Deciphering the role of Trichoderma sp. bioactives in combating the wilt causing cell wall degrading enzyme polygalacturonase produced by Fusarium oxysporum: An in-silico approach

The cell wall degrading enzymes polygalacturonase (PG) secreted by Fusarium oxysporum f. sp. radicis-lycopersici (FOL) is testified to trigger Fusarium crown and root rot disease in tomato crops; instigated due to the degradation of the pectin. Trichoderma sp. is documented as a potential biocontrol agent playing a pivotal role in plant health and disease management. An in-silico approach employing homology modelling, molecular docking, molecular dynamics (MD) simulation and MMPBSA was employed to assess the prospective role of bioactives produced by Trichoderma sp. in combating the PG2 enzyme. The studies revealed that amongst the wide range of bioactives screened, Trichodermamide B produced by T. harzianum and Viridin, Virone, and Trichosetin produced by T. virens emerged as the potential inhibitors of the PG2. Docking results revealed that the complexes possessed most stable energy for Trichodermamide B (-8.1 kcal/mol) followed by Viridin (-7.7 kcal/mol), Virone (-7.1 kcal/mol), and Trichosetin (-7 kcal/mol), respectively. Interaction studies of FOL with T. virens and T. harzianum reported an inhibition of 83.33% and 75.87%, respectively. The structural rigidity and stability of the docked complex was confirmed through MD simulations evaluated across multiple descriptors from the simulation trajectories. Further, MMPBSA analysis validated the results that binding of the enzyme to the screened ligands was spontaneous. The study unravels new insights on the versatile potential of Trichoderma sp. Bioactives as a prospective agent for the inhibition of cell-wall degrading enzymes secreted by phytopathogens. The proposed study can be implemented for design of bioformulations that serve the role of biopesticide, promising a sustainable alternate to chemical-based products.

The Role of Serendipita indica (Piriformospora indica) in Improving Plant Resistance to Drought and Salinity Stresses

Simple Summary

Environmental stresses are one of the biggest threats to modern agriculture, and climate change has heightened the risks of these stresses in different parts of the world. Among all the environmental stresses, salinity and drought are a severe threat to arid and semi-arid regions of the world, and for a long time, scientists have been searching for ways to reduce the risk of these stresses. In recent decades, solutions have been developed to reduce the risk of environmental stress on plants by identifying beneficial soil microorganisms. This study was conducted to identify morphophysiological and molecular changes of plants in coexistence with Serendipita indica and their impact on drought and salinity stress reduction. The study also has investigated the stressors’ impact on plants and the plants’ mechanisms to cope with them; Furthermore, sharing results with researchers provides a clear path for future research.

Abstract

Plant stress is one of the biggest threats to crops, causing irreparable damage to farmers’ incomes; Therefore, finding suitable, affordable, and practical solutions will help the agricultural economy and prevent the loss of millions of tons of agricultural products. Scientists have taken significant steps toward improving farm productivity in the last few decades by discovering how beneficial soil microorganisms enhance plant resistance to environmental stresses. Among these microorganisms is Serendipita indica, which the benefits of coexisting this fungus with plant roots have been extensively explored in recent years. By investigating fungus specification and its effects on plants’ morphological, physiological, and molecular traits, the present study seeks to understand how Serendipita indica affects plant resistance to salinity and drought conditions. Furthermore, this study attempts to identify the unknown mechanisms of action of the coexistence of Serendipita indica with plants in the face of stress using information from previous studies. Thus, it provides a way for future research to assess the impact of this fungus on tackling environmental stresses and enhancing agricultural productivity.

Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola

Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA-DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.

Lytic polysaccharide monooxygenases as powerful tools in enzymatically assisted preparation of nano-scaled cellulose from lignocellulose: A review

Nanocellulose, either in the form of fibers or crystals, constitutes a renewable, biobased, biocompatible material with advantageous mechanical properties that can be isolated from lignocellulosic biomass. Enzyme-assisted isolation of nanocellulose is an attractive, environmentally friendly approach that leads to products of higher quality compared to their chemically prepared counterparts. Lytic polysaccharide monooxygenases (LPMOs) are enzymes that oxidatively cleave the β-1,4-glycosidic bond of polysaccharides upon activation of O₂ or H₂O₂ and presence of an electron donor. Their use for treatment of cellulose fibers towards the preparation of nano-scaled cellulose is related to the ability of LPMOs to create nicking points on the fiber surface, thus facilitating fiber disruption and separation. The aim of this review is to describe the mode of action of LPMOs on cellulose fibers towards the isolation of nanostructures, thus highlighting their great potential for the production of nanocellulose as a novel value added product from lignocellulose.

The effect of enzymatic pretreatment of chickpea on functional properties and antioxidant activity of alkaline protein isolate

Functional properties and antioxidant activity of protein isolates extracted by alkali from chickpea seed after treatment with cellulase and xylanase cocktail and individual arabinofuranosidase were evaluated. Both enzymatic treatments improved recovery of protein by more than 30%, moreover, arabinofuranosidase enabled higher extraction efficiency - above 93%. Protein extracted after treatment with enzyme cocktail showed improved solubility and oil holding capacity by 14% and 80%, respectively, while water holding capacity was increased by 130% after both applied enzymatic pretreatments. The action of enzyme cocktail was more beneficial for improving emulsifying activity and stability of alkaline isolate by 22% and 31%, respectively. Whipping properties of alkaline protein isolate were significantly improved when both enzymatic pretreatments were applied with foam stability increased by 150%. Protein from extractions with arabinofuranosidase and enzyme cocktail expressed enhanced antioxidant activity by 70% and 110%, respectively. Analysis of protein pattern and structural characteristics indicated differences between investigated isolates.

A novel Penicillium sumatraense isolate reveals an arsenal of degrading enzymes exploitable in algal bio-refinery processes

BACKGROUND

Microalgae are coming to the spotlight due to their potential applications in a wide number of fields ranging from the biofuel to the pharmaceutical sector. However, several factors such as low productivity, expensive harvesting procedures and difficult metabolite extractability limit their full utilization at industrial scale. Similarly to the successful employment of enzymatic arsenals from lignocellulolytic fungi to convert lignocellulose into fermentable sugars for bioethanol production, specific algalytic formulations could be used to improve the extractability of lipids from microalgae to produce biodiesel. Currently, the research areas related to algivorous organisms, algal saprophytes and the enzymes responsible for the hydrolysis of algal cell wall are still little explored.

RESULTS

Here, an algal trap method for capturing actively growing microorganisms was successfully used to isolate a filamentous fungus, that was identified by whole-genome sequencing, assembly and annotation as a novel Penicillium sumatraense isolate. The fungus, classified as P. sumatraense AQ67100, was able to assimilate heat-killed Chlorella vulgaris cells by an enzymatic arsenal composed of proteases such as dipeptidyl- and amino-peptidases, β-1,3-glucanases and glycosidases including α- and β-glucosidases, β-glucuronidase, α-mannosidases and β-galactosidases. The treatment of C. vulgaris with the filtrate from P. sumatraense AQ67100 increased the release of chlorophylls and lipids from the algal cells by 42.6 and 48.9%, respectively.

CONCLUSIONS

The improved lipid extractability from C. vulgaris biomass treated with the fungal filtrate highlighted the potential of algal saprophytes in the bioprocessing of microalgae, posing the basis for the sustainable transformation of algal metabolites into biofuel-related compounds.

Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose

The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.

Biochemical and Biotechnological Studies on Xylanase and β‐xylosidase Enzymes Produced by Trichoderma viride Under Solid State Fermentation

The current study concerns with enhancement of xylanase and β-xylosidase activities from lignocellulosic materials by soil derived fungi Trichoderma viride under solid state fermentation (SSF). Xylanase and β-xylosidase activities were found to affected by variety of factors. In this study, some agricultural wastes were selected and used as sources for carbon. Sugar beet pulp (SBP) was at the forefront of these types. Also, various sources for nitrogen were selected to determine the best one. Yeast extract was the best organic source. Maximum xylanase activity took place by using inoculum size 1.8 × 105 spores / ml at 30°C when the pH was 5.5 for eight days of incubation with the addition of 0.1 % of Tween 40. Moreover, spores of Trichoderma viride were irradiated with gamma–rays. The maximum activity was observed upon using 0.7 kilo-gray (kGy). Furthermore, mixed cultures of Trichoderma viride and Penicillium janthenellum (wt / wt) were enhanced xylanase degrading capability. From another standpoint, ammonium sulphate and gel filtration chromatography were the best methods for xylanase purification. Characterizations of the purified enzyme were also selected and studied. It was found that, β-xylosidase enzyme exhibited its maximum activity and stability when the pH was 6 at 40°C by the addition of CaCl2 metal ion. On the other hand, total protein contents and volatile constituents of Trichoderma viride and Penicillium janthenellum were separated and investigated using high performance liquid chromatography (HPLC) and gas chromatography/mass spectrometry (GC/MS) techniques. It was found that, total protein contents for Trichoderma viride and Penicillium janthenellum were represented by fifteen and sixteen amino acids respectively. Also,29 compounds of the total volatile compounds for both Trichoderma viride and Penicillium janthenellum were identified. On the practical and applied field, crude enzyme was a good analyzer for agricultural residues as well showed antifungal and antibacterial effects.

Production of Bulk Chemicals with Biocatalysis: Drivers and Challenges Reflected in Recent Industrial Granted Patents (2015-2020)

The application of biocatalysis and White Biotechnology tools in chemical areas concerning the production of bulk compounds and other related low-added value products (with high volumes) has been gaining importance in recent years. The expected drivers of biocatalysis for these sectors are energy savings, regioselectivity (leading to cleaner products), the possibility of using thermolabile substrates, as well as the generation of less by-products and manageable wastes. This paper explores some recent industrial granted patents related to biocatalysis and bulk chemicals. Several patents have been identified in fields such as biodiesel and esterification reactions, and sugar or furan chemistry. Overall, innovative strategies involve the identification of novel enzymes, the set-up of improved immobilization methods, as well as novel reactor designs that can offer improved performances and economics. The reported examples indicate that biocatalysis can certainly offer opportunities for these areas as well, far from the typical pharmaceutical and fine chemical applications often reported in the literature.

A microalgal-based preparation with synergistic cellulolytic and detoxifying action towards chemical-treated lignocellulose

High-temperature bioconversion of lignocellulose into fermentable sugars has drawn attention for efficient production of renewable chemicals and biofuels, because competing microbial activities are inhibited at elevated temperatures and thermostable cell wall degrading enzymes are superior to mesophilic enzymes. Here, we report on the development of a platform to produce four different thermostable cell wall degrading enzymes in the chloroplast of Chlamydomonas reinhardtii. The enzyme blend was composed of the cellobiohydrolase CBM3GH5 from C. saccharolyticus, the β-glucosidase celB from P. furiosus, the endoglucanase B and the endoxylanase XynA from T. neapolitana. In addition, transplastomic microalgae were engineered for the expression of phosphite dehydrogenase D from Pseudomonas stutzeri, allowing for growth in non-axenic media by selective phosphite nutrition. The cellulolytic blend composed of the glycoside hydrolase (GH) domain GH12/GH5/GH1 allowed the conversion of alkaline-treated lignocellulose into glucose with efficiencies ranging from 14% to 17% upon 48h of reaction and an enzyme loading of 0.05% (w/w). Hydrolysates from treated cellulosic materials with extracts of transgenic microalgae boosted both the biogas production by methanogenic bacteria and the mixotrophic growth of the oleaginous microalga Chlorella vulgaris. Notably, microalgal treatment suppressed the detrimental effect of inhibitory by-products released from the alkaline treatment of biomass, thus allowing for efficient assimilation of lignocellulose-derived sugars by C. vulgaris under mixotrophic growth.

Expression of a Hyperthermophilic Cellobiohydrolase in Transgenic Nicotiana tabacum by Protein Storage Vacuole Targeting

Plant expression of microbial Cell Wall Degrading Enzymes (CWDEs) is a valuable strategy to produce industrial enzymes at affordable cost. Unfortunately, the constitutive expression of CWDEs may affect plant fitness to variable extents, including developmental alterations, sterility and even lethality. In order to explore novel strategies for expressing CWDEs in crops, the cellobiohydrolase CBM3GH5, from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus, was constitutively expressed in N. tabacum by targeting the enzyme both to the apoplast and to the protein storage vacuole. The apoplast targeting failed to isolate plants expressing the recombinant enzyme despite a large number of transformants being screened. On the opposite side, the targeting of the cellobiohydrolase to the protein storage vacuole led to several transgenic lines expressing CBM3GH5, with an enzyme yield of up to 0.08 mg g DW-1 (1.67 Units g DW-1) in the mature leaf tissue. The analysis of CBM3GH5 activity revealed that the enzyme accumulated in different plant organs in a developmental-dependent manner, with the highest abundance in mature leaves and roots, followed by seeds, stems and leaf ribs. Notably, both leaves and stems from transgenic plants were characterized by an improved temperature-dependent saccharification profile.

Dampening the DAMPs: How Plants Maintain the Homeostasis of Cell Wall Molecular Patterns and Avoid Hyper-Immunity

Several oligosaccharide fragments derived from plant cell walls activate plant immunity and behave as typical damage-associated molecular patterns (DAMPs). Some of them also behave as negative regulators of growth and development, and due to their antithetic effect on immunity and growth, their concentrations, activity, time of formation, and localization is critical for the so-called "growth-defense trade-off." Moreover, like in animals, over accumulation of DAMPs in plants provokes deleterious physiological effects and may cause hyper-immunity if the cellular mechanisms controlling their homeostasis fail. Recently, a mechanism has been discovered that controls the activity of two well-known plant DAMPs, oligogalacturonides (OGs), released upon hydrolysis of homogalacturonan (HG), and cellodextrins (CDs), products of cellulose breakdown. The potential homeostatic mechanism involves specific oxidases belonging to the family of berberine bridge enzyme-like (BBE-like) proteins. Oxidation of OGs and CDs not only inactivates their DAMP activity, but also makes them a significantly less desirable food source for microbial pathogens. The evidence that oxidation and inactivation of OGs and CDs may be a general strategy of plants for controlling the homeostasis of DAMPs is discussed. The possibility exists of discovering additional oxidative and/or inactivating enzymes targeting other DAMP molecules both in the plant and in animal kingdoms.