Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review

New insights into Peniophora crassitunicata and its co-inoculation with commercial microbial inoculant accelerating lignocellulose degradation and compost maturation during orchard wastes composting

Lignocellulosic composting has been widely promoted in the utilization of agricultural wastes, while few focus on orchard lignocellulosic wastes in the fruit industry. Peniophora is a laccase hyper-producer highly efficient in lignin degradation, yet its application in lignocellulosic composting has not been investigated. Here, an aerobic composting experiment was conducted to investigate the effects of inoculation with Peniophora crassitunicata and a commercial microbial inoculant (mainly Bacillus and Aspergillus) on grape (Vitis Vinifera L.) orchard lignocellulosic wastes degradation and the underlying mechanisms. The inoculation with P. crassitunicata, both individually (H) and in combination with the commercial microbial inoculant (HS), enhanced lignocellulose degradation efficiency. Notably, the co-inoculation exhibited higher lignocellulose degradation ratios and higher lignocellulosic enzyme activities compared to other treatments. The compost piles with co-inoculation experienced a more rapid temperature rise, a longer duration (15 days) of high temperatures, lower pH, and lower electrical conductivity (EC). Firmicutes (e.g. Bacillus, Paenibacillus) and Ascomycota (e.g. Aspergillus) along with Bacteroidota, Actinobacteriota, and Basidiomycota (e.g. Peniophora) dominated the microbial community in compost; carbohydrate metabolism dominated microbial metabolic pathways at the thermophilic phase, highlighting an active microbial community. As compost processed, highly mature and non-toxic compost products were finally obtained for the co-inoculation, with a pH of 7.87, C/N ratio of 13.5, NH4+-N/NO3‾-N ratio of 0.21-0.41, EC of 0.90 mS cm-1, and germination index of 149 %. The co-inoculation of P. crassitunicata with the commercial microbial inoculant effectively accelerated lignocellulose degradation and compost maturation, producing a friendly and non-toxic organic fertilizer for agricultural applications and thereby providing a new strategy for orchard wastes management and agricultural applications.

Associations of indoor airborne microbiome with lung function: evidence from a randomized, double-blind, crossover study of microbial intervention

Microorganisms constitute an essential component of the indoor ecosystem and may pose potential health risks after inhalation. However, evidence regarding the impact of indoor airborne microbiome on general respiratory health is scarce. Additionally, while air purification has been shown to be an effective strategy for controlling culturable bioaerosols, its impact on indoor airborne microbiome remains unclear. To determine the impact of indoor airborne microbial exposure on lung function, and whether and how air purification can modify indoor airborne microbiome, we conducted a randomized, double-blind, crossover study employing air purification intervention among 68 healthy young adults in Beijing, China. Indoor airborne bacteria and fungi were characterized using amplicon sequencing technology and quantified by qPCR. Our results indicated positive associations between indoor airborne microbial α-diversity and lung function indices; however, adverse effects from total microbial load were observed. Males were more susceptible to microbial exposure than females. Beneficial effects from richness in Actinobacteria, Bacteroidia, Oxyphotobacteria, Bacilli, Clostridia, Alphaproteobacteria, Gammaproteobacteria, Dothideomycetes, and Sordariomycetes, and detrimental effects from five Proteobacteria genera, including Dechloromonas, Hydrogenophaga, Klebsiella, Pseudomonas, and Tolumonas, were also identified. Air purification contributed to decreased fungal diversity and total fungal load, but not the overall microbial community structure. Our study demonstrates the significant role of indoor airborne microbiome in regulating human respiratory health and provides inspiration for improving health through manipulation of indoor microbiome. Meanwhile, our study also underscores the importance of balancing the potential benefits from decreased microbial load and the underlying risks from reduced microbial diversity while applying environmental microbial interventions.

Microbial valorization of kraft black liquor for production of platform chemicals, biofuels, and value-added products: A critical review

The proper treatment and utilization of kraft black liquor, generated from the pulp and paper industry through the kraft pulping method, is required to reduce environmental impacts prior to the final disposal. It also improves the economic performance through the utilization of waste. Microbial valorization appears to demonstrates the dual benefits of waste management and resource recovery by providing an innovative solution to convert kraft black liquor into resource for reuse. A comprehensive review on the microbial valorization of kraft black liquor, describing the role in valorization and management, is still lacking in the literature, forming the rationale of this article. Thus, the present study reviews and systematically discusses the potential of utilizing microorganisms to valorize kraft black liquor as a sustainable feedstock to develop a numerous portfolio of platform chemicals, bioenergy, and other value-added products. This work contributes to sustainability and resource efficiency within the pulp and paper industry. The recent developments in utilization of synthetic biology tools and molecular techniques, including omics approaches for engineering novel microbial strains, for enhancing kraft black liquor valorization has been presented. This review explores how the better utilization of kraft black liquor in the pulp and paper industry contributes to achieving UN Sustainable Development Goals (SDGs), particularly clean water and sanitation (SDG 6) as well as the affordable and clean energy goal (SDG 7). The current review also addresses challenges related to toxicity, impurities, low productivity, and downstream processing that serve as obstacles to the progress of developing highly efficient bioproducts. The new directions for future research efforts to fill the critical knowledge gaps are proposed. This study concludes that by implementing microbial valorization techniques, the pulp and paper industry can transition from a linear to a circular bioeconomy and eco-friendly manage the kraft black liuor. This approach showed to be effective towards resource recovery, while simultaneously minimizing the environmental burden.

Lignocellulolytic Enzymes Production by Four Wild Filamentous Fungi for Olive Stones Valorization: Comparing Three Fermentation Regimens

Lignocellulolytic enzymes play a crucial role in efficiently converting lignocellulose into valuable platform molecules in various industries. However, they are limited by their production yields, costs, and stability. Consequently, their production by producers adapted to local environments and the choice of low-cost raw materials can address these limitations. Due to the large amounts of olive stones (OS) generated in Morocco which are still undervalued, Penicillium crustosum, Fusarium nygamai, Trichoderma capillare, and Aspergillus calidoustus, are cultivated under different fermentation techniques using this by-product as a local lignocellulosic substrate. Based on a multilevel factorial design, their potential to produce lignocellulolytic enzymes during 15 days of dark incubation was evaluated. The results revealed that P. crustosum expressed a maximum total cellulase activity of 10.9 IU/ml under sequential fermentation (SF) and 3.6 IU/ml of β-glucosidase activity under submerged fermentation (SmF). F. nygamai recorded the best laccase activity of 9 IU/ml under solid-state fermentation (SSF). Unlike T. capillare, SF was the inducive culture for the former activity with 7.6 IU/ml. A. calidoustus produced, respectively, 1,009 μg/ml of proteins and 11.5 IU/ml of endoglucanase activity as the best results achieved. Optimum cellulase production took place after the 5th day under SF, while ligninases occurred between the 9th and the 11th days under SSF. This study reports for the first time the lignocellulolytic activities of F. nygamai and A. calidoustus. Furthermore, it underlines the potential of the four fungi as biomass decomposers for environmentally-friendly applications, emphasizing the efficiency of OS as an inducing substrate for enzyme production.

Advances in succinic acid production: the enhancement of CO2 fixation for the carbon sequestration benefits

Succinic acid (SA), one of the 12 top platform chemicals produced from biomass, is a precursor of various high value-added derivatives. Specially, 1 mol CO2 is assimilated in 1 mol SA biosynthetic route under anaerobic conditions, which helps to achieve carbon reduction goals. In this review, methods for enhanced CO2 fixation in SA production and utilization of waste biomass for SA production are reviewed. Bioelectrochemical and bioreactor coupling systems constructed with off-gas reutilization to capture CO2 more efficiently were highlighted. In addition, the techno-economic analysis and carbon sequestration benefits for the synthesis of bio-based SA from CO2 and waste biomass are analyzed. Finally, a droplet microfluidics-based high-throughput screening technique applied to the future bioproduction of SA is proposed as a promising approach.

Enzymolysis kinetics of corn straw by impeded Michaelis model and Box-Behnken design

Enzymatic hydrolysis is an essential step in the lignocellulosic biorefining process. In this paper, Box-Behnken was used to optimize the enzymatic hydrolysis process of corn stalk, and the promotion effect of three typical surfactants on the enzymatic hydrolysis process was investigated. The experimental results showed that the total reducing sugar yield reached 67.6% under the best-predicted conditions. When the concentration of Tween 80 is 0.1%, it could be increased to 80.2%. In addition, the Impeded Michaels Model (IMM) is introduced in this study to describe the enzymatic hydrolysis process of corn stalks. Finally, the initial contact coefficient between the enzyme and cellulose (Kobs,0) and the gradual loss coefficient of enzyme activity (ki) caused by reaction obstruction were obtained by fitting data, which successfully verified the rationality of the model.

Proteomic analyses of Bacteroides ovatus and Bifidobacterium longum in xylan bidirectional culture shows sugar cross-feeding interactions

The intestinal microbiome is a community of anaerobic microorganisms whose activities significantly impact human health. Its composition can be modulated by consuming foods rich in dietary fiber, such as xylan, a complex polysaccharide that can be considered an emerging prebiotic. In this work, we evaluated how certain gut bacteria acted as primary degraders, fermenting dietary fibers, and releasing metabolites that other bacteria can further use. Different bacterial strains of Lactobacillus, Bifidobacterium, and Bacteroides were evaluated for their ability to consume xylan and interact with one another. Results from unidirectional assays gave indications of possible cross-feeding between bacteria using xylan as a carbon source. Bidirectional assays showed that Bifidobacterium longum PT4 increased its growth in the presence of Bacteroides ovatus HM222. Proteomic analyses indicated that B. ovatus HM222 synthesizes enzymes facilitating xylan degradation, such as β-xylanase, arabinosidase, L-arabinose isomerase, and xylosidase. Interestingly, the relative abundance of these proteins remains largely unaffected in the presence of Bifidobacterium longum PT4. In the presence of B. ovatus, B. longum PT4 increased the production of enzymes such as α-L-arabinosidase, L-arabinose isomerase, xylulose kinase, xylose isomerase, and sugar transporters. These results show an example of positive interaction between bacteria mediated by xylan consumption. Bacteroides degraded this substrate to release xylooligosaccharides, or monosaccharides (xylose, arabinose), which might support the growth of secondary degraders such as B. longum.

Co-production process optimization and carbon footprint analysis of biohydrogen and biofertilizer from corncob by photo-fermentation

In this study, corncob was taken as substrate, the co-production process of biohydrogen and biofertilizer by photo-fermentation was investigated and its carbon footprint analysis was conducted to evaluate the carbon transfer pathway. Biohydrogen was produced by photo-fermentation, and the hydrogen producing residues were immobilized by sodium alginate. Cumulative hydrogen yield (CHY) and nitrogen release ability (NRA) was taken as references, and the effect of substrate particle size on the co-production process was evaluated. Results showed that due to the porous adsorption properties, corncob size of 120 mesh was the optimal one. Under that condition, the highest CHY and NRA were 71.16 mL/g TS and 68.76%, respectively. The carbon footprint analysis indicted that 7.9% carbon element was released as carbon dioxide, 78.3% carbon element was immobilized in the biofertilizer, and 13.8% carbon element was lost. This work is significant of the biomass utilization and clean energy production.

Protein Profiling of Psittacanthus calyculatus during Mesquite Infection

Psittacanthus calyculatus is a hemiparasite mistletoe that represents an ecological problem due to the impacts caused to various tree species of ecological and commercial interest. Although the life cycle for the Psittacanthus genus is well established in the literature, the development stages and molecular mechanism implicated in P. calyculatus host infection are poorly understood. In this study, we used a manageable infestation of P. laevigata with P. calyculatus to clearly trace the infection, which allowed us to describe five phenological infective stages of mistletoe on host tree branches: mature seed (T1), holdfast formation (T2), haustorium activation (T3), haustorium penetration (T4), and haustorium connection (T5) with the host tree. Proteomic analyses revealed proteins with a different accumulation and cellular processes in infective stages. Activities of the cell wall-degrading enzymes cellulase and β-1,4-glucosidase were primarily active in haustorium development (T3), while xylanase, endo-glucanase, and peptidase were highly active in the haustorium penetration (T4) and xylem connection (T5). Patterns of auxins and cytokinin showed spatial concentrations in infective stages and moreover were involved in haustorium development. These results are the first evidence of proteins, cell wall-degrading enzymes, and phytohormones that are involved in early infection for the Psittacanthus genus, and thus represent a general infection mechanism for other mistletoe species. These results could help to understand the molecular dialogue in the establishment of P. calyculatus parasitism.

Enzymes and enzymatic mechanisms in enzymatic degradation of lignocellulosic biomass: A mini-review

Enzymatic hydrolysis is the key step limiting the efficiency of the biorefinery of lignocellulosic biomass. Enzymes involved in enzymatic hydrolysis and their interactions with biomass should be comprehended to form the basis for looking for strategies to improve process efficiency. This article updates the contemporary research on the properties of key enzymes in the lignocellulose biorefinery and their interactions with biomass, adsorption, and hydrolysis. The advanced analytical techniques to track the interactions for exploiting mechanisms are discussed. The challenges and prospects for future research are outlined.

Recent progress in key lignocellulosic enzymes: Enzyme discovery, molecular modifications, production, and enzymatic biomass saccharification

Lignocellulose, the most prevalent biomass on earth, can be enzymatically converted into carbohydrates for bioethanol production and other uses. Among lignocellulosic enzymes, endoglucanase, xylanase, and laccase are the key enzymes, owing to their ability to disrupt the main structure of lignocellulose. Recently, new discovery methods have been established to obtain key lignocellulosic enzymes with excellent enzymatic properties. Molecular modification of enzymes to modulate their thermostability, catalytic activity, and substrate specificity has been performed with protein engineering technology. In addition, the enzyme expression has been effectively improved through expression element screening and host modification, as well as fermentation optimization. Immobilization of enzymes, use of surfactants, synergistic degradation, and optimization of reaction conditions have addressed the inefficiency of enzymatic saccharification. In this review, recent advances in key lignocellulosic enzymes are summarized, along with future prospects for the development of super-engineered strains and integrative technologies for enzymatic biomass saccharification.

Inhibitor formation and detoxification during lignocellulose biorefinery: A review

For lignocellulose biorefinery, pretreatment is needed to maximize the cellulose accessibility, frequently generating excess inhibitory substances to decline the efficiency of the subsequent fermentation processes. This mini-review updates the current research efforts to detoxify the adverse impacts of generated inhibitors on the performance of biomass biorefinery. The lignocellulose pretreatment processes are first reviewed. The generation of inhibitors, furans, furfural, phenols, formic acid, and acetic acid, from the lignocellulose, with their action mechanisms, are listed. Then the detoxification processes are reviewed, from which the biological detoxification processes are noted as promising and worth further study. The challenges and prospects for applying biological detoxification in lignocellulose biorefinery are outlined. Integrated studies considering the entire biorefinery should be performed on a case-by-case basis.

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.

Exploring the potential of a newly constructed manganese peroxidase-producing yeast consortium for tolerating lignin degradation inhibitors while simultaneously decolorizing and detoxifying textile azo dye wastewater

MnP-YC4, a newly constructed manganese peroxidase-producing yeast consortium, has been developed to withstand lignin degradation inhibitors while degrading and detoxifying azo dye. MnP-YC4 tolerance to major biomass-derived inhibitors was promising. MnP induced by lignin was found to be highly related to dye decolorization by MnP-YC4. Simulated azo dye-containing wastewater supplemented with a lignin co-substrate (3,5-Dimethoxy-4-hydroxybenzaldehyde) decolorized up to 100, 91, and 76% at final concentrations of 20, 40, and 60%, respectively. MnP-YC4 effectively decolorized the real textile wastewater sample, reaching up to 91.4%, and the COD value decreased significantly during the decolorization, reaching 7160 mg/l within 7 days. A possible dye biodegradation pathway was proposed based on the degradation products identified by UV-vis, FTIR, GC/MS, and HPLC techniques, beginning with azo bond cleavage and eventually mineralized to CO₂ and H₂O. When compared to the phytotoxic original dye, the phytotoxicity of MnP-YC4 treated dye-containing wastewater samples confirmed the nontoxic nature.