Fungal lignocellulolytic enzymes and lignocellulose: A critical review on their contribution to multiproduct biorefinery and global biofuel research

Date nawah powder as a promising waste for β-mannanase production from a new isolate Aspergillus niger MSSFW, statistically improving production and enzymatic characterization

β-Mannanase producing fungus was isolated from coffee powder waste and identified as Aspergillus niger MSSFW (Gen Bank accession number OR668928). Dates nawah powder as industrial and agricultural waste was the most inducer of β-mannanase production. The Plackett-Burman and Central Composite designs were used to improve β-mannanase titer. Optimization studies enhanced the enzyme yield with approximate 13.50-times. β-Mannanase was purified by Sephadex G-150 gel filtration column and the molecular weight was estimated to be 60 kDa by SDS-PAGE. Crude and purified β-mannanase displayed maximum activity at temperature 60 °C and 50 °C, respectively. Crude β-mannanase showed an activation energy value 2.35-times higher than the purified enzyme. Activation energy for thermal denaturation of the purified β-mannanase was 1.08-times higher than that of the crude enzyme. Purified β-mannanase exhibited higher deactivation rate constant (Kd) and lower half-life (t0.5) and decimal reduction time (D-value) compared with the crude enzyme. Thermodynamic parameters of enthalpy, entropy, and free energy values for crude and purified β-mannanase were calculated. Substrate kinetic parameters suggested that the purified β-mannanase had a strong affinity toward locust bean gum by showing 3.44-times lower Km and 1.99-times higher Vmax compared to the crude enzyme.

Enzymatic hydrolysis of waste streams originating from wastewater treatment plants

BACKGROUND

Achieving climate neutrality is a goal that calls for action in all sectors. The requirements for improving waste management and reducing carbon emissions from the energy sector present an opportunity for wastewater treatment plants (WWTPs) to introduce sustainable waste treatment practices. A common biotechnological approach for waste valorization is the production of sugars from lignocellulosic waste biomass via biological hydrolysis. WWTPs produce waste streams such as sewage sludge and screenings which have not yet been fully explored as feedstocks for sugar production yet are promising because of their carbohydrate content and the lack of lignin structures. This study aims to explore the enzymatic hydrolysis of various waste streams originating from WWTPs by using a laboratory-made and a commercial cellulolytic enzyme cocktail for the production of sugars. Additionally, the impact of lipid and protein recovery from sewage sludge prior to the hydrolysis was assessed.

RESULTS

Treatment with a laboratory-made enzyme cocktail produced by Irpex lacteus (IL) produced 31.2 mg sugar per g dry wastewater screenings. A commercial enzyme formulation released 101 mg sugar per g dry screenings, corresponding to 90% degree of saccharification. There was an increase in sugar levels for all sewage substrates during the hydrolysis with IL enzyme. Lipid and protein recovery from primary and secondary sludge prior to the hydrolysis with IL enzyme was not advantageous in terms of sugar production.

CONCLUSIONS

The laboratory-made fungal IL enzyme showed its versatility and possible application beyond the typical lignocellulosic biomass. Wastewater screenings are well suited for valorization through sugar production by enzymatic hydrolysis. Saccharification of screenings represents a viable strategy to divert this waste stream from landfill and achieve the waste treatment and renewable energy targets set by the European Union. The investigation of lipid and protein recovery from sewage sludge showed the challenges of integrating resource recovery and saccharification processes.

Transcriptome-wide analysis of a superior xylan degrading isolate Penicillium oxalicum 5-18 revealed active lignocellulosic degrading genes

Lignocellulose biomass raw materials have a high value in energy conversion. Recently, there has been growing interest in using microorganisms to secret a series of enzymes for converting low-cost biomass into high-value products such as biofuels. We previously isolated a strain of Penicillium oxalicun 5-18 with promising lignocellulose-degrading capability. However, the mechanisms of lignocellulosic degradation of this fungus on various substrates are still unclear. In this study, we performed transcriptome-wide profiling and comparative analysis of strain 5-18 cultivated in liquid media with glucose (Glu), xylan (Xyl) or wheat bran (WB) as sole carbon source. In comparison to Glu culture, the number of differentially expressed genes (DEGs) induced by WB and Xyl was 4134 and 1484, respectively, with 1176 and 868 genes upregulated. Identified DEGs were enriched in many of the same pathways in both comparison groups (WB vs. Glu and Xly vs. Glu). Specially, 118 and 82 CAZyme coding genes were highly upregulated in WB and Xyl cultures, respectively. Some specific pathways including (Hemi)cellulose metabolic processes were enriched in both comparison groups. The high upregulation of these genes also confirmed the ability of strain 5-18 to degrade lignocellulose. Co-expression and co-upregulated of genes encoding CE and AA CAZy families, as well as other (hemi)cellulase revealed a complex degradation strategy in this strain. Our findings provide new insights into critical genes, key pathways and enzyme arsenal involved in the biomass degradation of P. oxalicum 5-18.

Advances in Applications of Polysaccharides and Polysaccharide-Based Materials

Polysaccharides, complex carbohydrates composed of long chains of residues of sugar molecules, have garnered significant attention in recent years due to their diverse applications across various industries [...].

Caatinga, Amazon and Atlantic Forest as natural sources for microbial lignocellulolytic enzymes

Brazilian biomes are important sources for environmental microorganisms, including efficient metabolic machineries, like actinomycetes. These bacteria are known for their abilities to produce many bioactive compounds, including enzymes with multiple industrial applications. The present work aimed to evaluate lignocellulolytic abilities of actinomycetes isolated from soil and rhizosphere samples collected at Caatinga, Atlantic and Amazon Forest. Laccase (Lac), lignin peroxidase (LiP), manganese peroxidase (MnP) and cellulase were evaluated for their efficiency. These enzymes have an essential role in lignin decomposition, through oxidation of phenolic and non-phenolic compounds, as well as enzymatic hydrolysis of vegetal biomass. In this sense, a total of 173 actinomycetes were investigated. Eleven (11) of them were selected by their enzymatic performance. The actinomycete AC166 displayed some activity in all analysed scenarios in terms of Lac, MnP and LiP activity, while AC171 was selected as the most promising strain, showing the following activities: 29.7 U.L-1 for Lac; 2.5 U.L-1 for LiP and 23 U.L-1 for MnP. Cellulolytic activities were evaluated at two pH conditions, 4.8 and 7.4, obtaining the following results: 25 U.L-1 and 71 U.L-1, respectively. Thermostability (4, 30 and 60 o C) and salinity concentrations (0 to 4 M) and pH variation (2.0 to 9.0) stabilities of the obtained LiP and Lac enzymatic extracts were also verified. The actinomycete strain AC171 displayed an adaptable response in distinct pH and salt profiles, indicating that bacterial LiP was some halophilic type. Additionally, the strain AC149 produced an alkali and extreme halophilic lignin peroxidase, which are promising profiles for their future application under lignocellulosic biomass at bioethanol biorefineries.

An overview on the current status and future prospects in Aspergillus cellulase production

Cellulase is a new research point besides glucoamylase, amylase, and protease in the enzyme industry. Cellulase can decompose lignocellulosic biomass into small-molecule sugars, which facilitates microbial utilization; thus, it has a vast market potential in the field of feed, food, energy, and chemistry. The Aspergillus was the first strain used in cellulase preparation because of its safety and non-toxicity, strong growth ability, and high enzyme yield. This review provides the latest research and advances on preparing cellulase from Aspergillus. The metabolic mechanisms of cellulase secretion by Aspergillus, the selection of fermentation substrates, the comparison of the fermentation modes, and the effect of fermentation conditions have been discussed in this review. Also, the subsequent separation and purification techniques of Aspergillus cellulase, including salting out, organic solvent precipitation, ultrafiltration, and chromatography, have been declared. Further, bottlenecks in Aspergillus cellulase preparation and corresponding feasible approaches, such as genetic engineering, mixed culture, and cellulase immobilization, have also been proposed in this review. This paper provides theoretical support for the efficient production and application of Aspergillus cellulase.

Enzymatic and biophysical characterization of a novel modular cellulosomal GH5 endoglucanase multifunctional from the anaerobic gut fungus Piromyces finnis

Cellulases from anaerobic fungi are enzymes less-studied biochemically and structurally than cellulases from bacteria and aerobic fungi. Currently, only thirteen GH5 cellulases from anaerobic fungi were biochemically characterized and two crystal structures were reported. In this context, here, we report the functional and biophysical characterization of a novel multi-modular cellulosomal GH5 endoglucanase from the anaerobic gut fungus Piromyces finnis (named here PfGH5). Multiple sequences alignments indicate that PfGH5 is composed of a GH5 catalytic domain and a CBM1 carbohydrate-binding module connected through a CBM10 dockerin module. Our results showed that PfGH5 is an endoglucanase from anaerobic fungus with a large spectrum of activity. PfGH5 exhibited preference for hydrolysis of oat β-glucan, followed by galactomannan, carboxymethyl cellulose, mannan, lichenan and barley β-glucan, therefore displaying multi-functionality. For oat β-glucan, PfGH5 reaches its optimum enzymatic activity at 40 °C and pH 5.5, with Km of 7.1 μM. Ion exchange chromatography analyzes revealed the production of oligosaccharides with a wide degree of polymerization indicated that PfGH5 has endoglucanase activity. The ability to bind and cleave different types of carbohydrates evidence the potential of PfGH5 for use in biotechnology and provide a useful basis for future investigation and application of new anaerobic fungi enzymes.

Identification of driving factors of lignocellulose degrading enzyme genes in different microbial communities during rice straw composting

The study aims to clarify the driving factors of lignocellulose degrading enzyme genes abundance during rice straw composting. Lignocellulose degrading strains b4 (Bacillus subtilis), z1 (Aspergillus fumigatus) were inoculated into pure culture, respectively. Meanwhile, three rice straw composting groups were set up, named CK (control), B4 (inoculating b4) and Z1 (inoculating z1). Results confirmed the composition of functional genes related to lignocellulose metabolism for strains. Lignocellulose degrading enzyme genes abundance was up-regulated by inoculation, which promoted the decomposition of lignocellulose. Modular microorganisms, such as Actinobacteria, Proteobacteria, Ascomycetes and Basidiomycetes, were identified as driving factors that affected lignocellulose degrading enzyme genes abundance. pH, organic matter and soluble sugar content affected lignocellulose degrading enzyme genes abundance by affecting modular microorganisms. In addition, a potential priming effect was put forward based on the driving factors. This study provided theoretical guidance for regulating the abundance of lignocellulose degrading enzyme genes to promote lignocellulose degradation.

Development of lignocellulosic biorefineries for the sustainable production of biofuels: Towards circular bioeconomy

The idea of environment friendly and affordable renewable energy resources has prompted the industry to focus on the set up of biorefineries for sustainable bioeconomy. Lignocellulosic biomass (LCB) is considered as an abundantly available renewable feedstock for the production of biofuels which can potentially reduce the dependence on petrochemical refineries. By utilizing various conversion technologies, an integrated biorefinery platform of LCB can be created, embracing the idea of the 'circular bioeconomy'. The development of effective pretreatment methods and biocatalytic systems by various bioengineering and machine learning approaches could reduce the bioprocessing costs, thereby making biomass-based biorefinery more sustainable. This review summarizes the development and advances in the lignocellulosic biorefineries from the LCB to the final product stage using various different state-of-the-art approaches for the progress of circular bioeconomy. The life cycle assessment which generates knowledge on the environmental impacts related to biofuel production chains is also summarized.

Oxalic acid degradation in wood-rotting fungi. Searching for a new source of oxalate oxidase

Oxalate oxidase (EC 1.2.3.4) is an oxalate-decomposing enzyme predominantly found in plants but also described in basidiomycete fungi. In this study, we investigated 23 fungi to determine their capability of oxalic acid degradation. After analyzing their secretomes for the products of the oxalic acid-degrading enzyme activity, three groups were distinguished among the fungi studied. The first group comprised nine fungi classified as oxalate oxidase producers, as their secretome pattern revealed an increase in the hydrogen peroxide concentration, no formic acid, and a reduction in the oxalic acid content. The second group of fungi comprised eight fungi described as oxalate decarboxylase producers characterized by an increase in the formic acid level associated with a decrease in the oxalate content in their secretomes. In the secretomes of the third group of six fungi, no increase in formic acid or hydrogen peroxide contents was observed but a decline in the oxalate level was found. The intracellular activity of OXO in the mycelia of Schizophyllum commune, Trametes hirsuta, Gloeophyllum trabeum, Abortiporus biennis, Cerrena unicolor, Ceriosporopsis mediosetigera, Trametes sanguinea, Ceriporiopsis subvermispora, and Laetiporus sulphureus was confirmed by a spectrophotometric assay.

Lignocellulose dissociation with biological pretreatment towards the biochemical platform: A review

Lignocellulose utilization has been gaining great attention worldwide due to its abundance, accessibility, renewability and recyclability. Destruction and dissociation of the cross-linked, hierarchical structure within cellulose hemicellulose and lignin is the key procedure during chemical utilization of lignocellulose. Of the pretreatments, biological treatment, which can effectively target the complex structures, is attractive due to its mild reaction conditions and environmentally friendly characteristics. Herein, we report a comprehensive review of the current biological pretreatments for lignocellulose dissociation and their corresponding degradation mechanisms. Firstly, we analyze the layered, hierarchical structure of cell wall, and the cross-linked network between cellulose, hemicellulose and lignin, then highlight that the cracking of β-aryl ether is considered the key to lignin degradation because of its dominant position. Secondly, we explore the effect of biological pretreatments, such as fungi, bacteria, microbial consortium, and enzymes, on substrate structure and degradation efficiency. Additionally, combining biological pretreatment with other methods (chemical methods and catalytic materials) may reduce the time necessary for the whole process, which also help to strengthen the lignocellulose dissociation efficiency. Thirdly, we summarize the related applications of lignocellulose, such as fuel production, chemicals platform, and bio-pulping, which could effectively alleviate the energy pressure through bioconversion into high value-added products. Based on reviewing of current progress of lignocellulose pretreatment, the challenges and future prospects are emphasized. Genetic engineering and other technologies to modify strains or enzymes for improved biotransformation efficiency will be the focus of future research.

Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering

Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed.

The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts

In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.

Role of ascomycete and basidiomycete fungi in meeting established and emerging sustainability opportunities: a review

Fungal biomass is the future's feedstock. Non-septate Ascomycetes and septate Basidiomycetes, famously known as mushrooms, are sources of fungal biomass. Fungal biomass, which on averagely comprises about 34% protein and 45% carbohydrate, can be cultivated in bioreactors to produce affordable, safe, nontoxic, and consistent biomass quality. Fungal-based technologies are seen as attractive, safer alternatives, either substituting or complementing the existing standard technology. Water and wastewater treatment, food and feed, green technology, innovative designs in buildings, enzyme technology, potential health benefits, and wealth production are the key sectors that successfully reported high-efficiency performances of fungal applications. This paper reviews the latest technical know-how, methods, and performance of fungal adaptation in those sectors. Excellent performance was reported indicating high potential for fungi utilization, particularly in the sectors, yet to be utilized and improved on the existing fungal-based applications. The expansion of fungal biomass in the industrial-scale application for the sustainability of earth and human well-being is in line with the United Nations' Sustainable Development Goals.

Thermophilic Geobacillus WSUCF1 Secretome for Saccharification of Ammonia Fiber Expansion and Extractive Ammonia Pretreated Corn Stover

A thermophilic Geobacillus bacterial strain, WSUCF1 contains different carbohydrate-active enzymes (CAZymes) capable of hydrolyzing hemicellulose in lignocellulosic biomass. We used proteomic, genomic, and bioinformatic tools, and genomic data to analyze the relative abundance of cellulolytic, hemicellulolytic, and lignin modifying enzymes present in the secretomes. Results showed that CAZyme profiles of secretomes varied based on the substrate type and complexity, composition, and pretreatment conditions. The enzyme activity of secretomes also changed depending on the substrate used. The secretomes were used in combination with commercial and purified enzymes to carry out saccharification of ammonia fiber expansion (AFEX)-pretreated corn stover and extractive ammonia (EA)-pretreated corn stover. When WSUCF1 bacterial secretome produced at different conditions was combined with a small percentage of commercial enzymes, we observed efficient saccharification of EA-CS, and the results were comparable to using a commercial enzyme cocktail (87% glucan and 70% xylan conversion). It also opens the possibility of producing CAZymes in a biorefinery using inexpensive substrates, such as AFEX-pretreated corn stover and Avicel, and eliminates expensive enzyme processing steps that are used in enzyme manufacturing. Implementing in-house enzyme production is expected to significantly reduce the cost of enzymes and biofuel processing cost.