Insights into lignin degradation and its potential industrial applications

Industrial applications of Phanerochaete chrysosporium lignin-degrading enzymes: current status, production challenges, and future directions

Phanerochaete chrysosporium (Pc) is a white-rot fungus recognized for its highly efficient lignin-degrading enzymes (LDEs), including lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase. These oxidative enzymes possess transformative capabilities across multiple industrial applications, such as biopulping, biofuel production, bioremediation and for the treatment of industrial wastewater. However, the commercial use of these enzymes is limited due to time-consuming scale-up procedures in native hosts, instability in industrial environments, and high production costs. The recent developments in recombinant expression systems, particularly those employing microbial and plant platforms provide promising opportunities to enhance enzyme yield, stability, and reduce the cost. Despite these advancements, significant challenges remain, which include the formation of inclusion bodies, the need for nutrient and co-factor supplementation, and the development of effective purification strategies. Modern advancements in protein engineering, such as site-directed mutation and in silico approaches, may hold significant promise in addressing the challenges posed by pH optimization, which is prominent in wild-type enzymes. This review examines the current industrial applications of P. chrysosporium ligninolytic enzymes, highlights production bottlenecks in several hosts, and discusses the strategies to enhance their commercial viability of these enzymes.

Structural and Biochemical Insights into Lignin-Oxidizing Activity of Bacterial Peroxidases against Soluble Substrates and Kraft Lignin

Great interest has recently been drawn to the production of value-added products from lignin; however, its recalcitrance and high chemical complexity have made this challenging. Dye-decolorizing peroxidases and catalase-peroxidases are among the enzymes that are recognized to play important roles in environmental lignin oxidation. However, bacterial lignin-oxidizing enzymes remain less characterized compared to related proteins from fungi. In this study, screening of 18 purified bacterial peroxidases against the general chromogenic substrate 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) (ABTS) revealed the presence of peroxidase activity in all proteins. Agarose plate-based screens with kraft lignin identified detectable and high lignin oxidation activity in 15 purified proteins. Crystal structures were determined for the DyP-type peroxidases FC2591 from Frankia casuarinae, PF3257 from Pseudomonas fluorescens, and PR9465 from Pseudomonas rhizosphaerae. The structures revealed the presence of hemes with bound oxygens coordinated by conserved His, Arg, and Asp residues as well as three molecular tunnels connecting the heme with the protein surface. Structure-based site-directed mutagenesis of FC2591 identified at least five active site residues as essential for oxidase activity against both ABTS and lignin, whereas the S370A mutant protein showed a three- to 4-fold activity increase with both substrates. HPLC analysis of reaction products of the wild-type FC2591 and S370A mutant proteins with the model lignin dimer guaiacylglycerol-β-guaiacyl ether and kraft lignin revealed the formation of products consistent with the radical coupling of the reaction intermediates. Thus, this study identified novel bacterial heme peroxidases with lignin oxidation activity and provided further insights into our understanding of these enzymes.

Cloning and expression of a short manganese peroxidase from Lentinus squarrosulus and its potential in enhancing the digestibility of crop residues

Tropical white-rot Lentinus squarrosulus is one of the most potent fungi in biodegradation of lignocellulosic biomass. Transcriptomic analyses of the fungus grown in submerged fermentation revealed that the fungus carries an exhaustive lignocellulose degrading system with laccases, high redox potential peroxidases, glycoside hydrolases and esterases. A novel gene encoding ligninolytic peroxidase with wide substrate specificity was selected for heterologous expression. Based on sequence analysis, this ligninolytic peroxidase was assigned as short-type manganese peroxidase (MnP) lacking the catalytic end tryptophan. cDNA encoding the mature protein was cloned in shuttle vector pPIC9K and successfully expressed in Pichia pastoris GS115. Optimum parameters for rMnP production were devised that yielded an extracellular enzyme concentration of 35 U/ml. Furthermore, application of this enzyme significantly increased the dry matter digestibility of straw by 53 % and 51 % with decrease in acid detergent lignin by 18 % and 17 % of finger millet and paddy straws respectively. Results elucidated the competence of this recombinant enzyme in enhancing the in vitro digestibility of crop residues thus suggesting its application potential in bioconversion of lignocellulosic crop residues into quality ruminant feed.

Combined induction by Cu(II) and veratrole enhances the degradation of high molecular weight polyaromatic hydrocarbons by Fusarium dlaminii ZH-H2

The effect of combined induction by Cu(II) and veratrole on the degradation of high molecular weight polyaromatic hydrocarbons (HMW-PAHs) by Fusarium sp. ZH-H2 was investigated. This strain was characterized as F. dlaminii. The combination treatment of Cu(II) with veratrole (CL) improved the degradation efficiency of a mixture of 10 HMW-PAHs by 16 % compared to the control without inducer (CK), by 5 % compared to single Cu(II) induction (C), and by 12 % compared to single veratrole induction (L). In particular, degradation of benzo(g,hi)perylene (BghiP) was improved by 36 % compared to CK and by 52 % compared to L. The CL combination treatment increased lignin peroxidase (LiP) activity by 162 % at day 5 of incubation compared to the control and by 277 % compared to C. Transcriptome analysis revealed that the expression of 910 Fusarium genes had changed as a result of the combination treatment, with 510 up-regulated genes and 443 down-regulated genes. The combined CL treatment not only significantly stimulated Lip activity, but also induced the expression of genes coding for non-ligninolytic enzymes, which contributed to the degradation of PAHs. These included cytochrome P450 monooxygenase (EC:1.-.-.-) and downstream PAH converting enzymes such as aldehyde dehydrogenase (EC:1.2.1.3), NADP-dependent ethanol dehydrogenase (EC:1.1.1.2), ethanol dehydrogenase (EC:1.1.1.156], tryptophan 2,3 dioxygenase (EC:1.13.11.52), gentisate 1,2-dioxygenase (EC:1.13.11.5), salicylate hydroxylase (EC:.14.13.1) β-hexokinase (EC:3.2.1.52), and glutathione transferase (EC: 2.5.1.18). Their increased expression enhanced the HMWPAHs degradation under induction of Cu(II) plus veratrole synergistically. These findings provide new insights in the combined use of these inducers for enhanced microbial remediation of HMW-PAHs in the environment.

Rumen-Targeted Mining of Enzymes for Bioenergy Production

Second-generation biofuel production, which aims to convert lignocellulose to liquid transportation fuels, could be transformative in worldwide energy portfolios. A bottleneck impeding its large-scale deployment is conversion of the target polysaccharides in lignocellulose to their unit sugars for microbial fermentation to the desired fuels. Cellulose and hemicellulose, the two major polysaccharides in lignocellulose, are complex in nature, and their interactions with pectin and lignin further increase their recalcitrance to depolymerization. This review focuses on the intricate linkages present in the feedstocks of interest and examines the potential of the enzymes evolved by microbes, in the microbe/ruminant symbiotic relationship, to depolymerize the target polysaccharides. We further provide insights to how a rational and more efficient assembly of rumen microbial enzymes can be reconstituted for lignocellulose degradation. We conclude by expounding on how gains in this area can impact the sustainability of both animal agriculture and the energy sector.

New wheat straw fermentation feed: recombinant Schizosaccharomyces pombe efficient degradation of lignocellulose and increase feed protein

Wheat straw contains a high amount of lignin, hindering the action of cellulase and hemicellulase enzymes, leading to difficulties in nutrient absorption by animals from straw feed. However, currently, the biological treatment of straw relies primarily on fungal degradation and cannot be directly utilized for the preparation of livestock feed. This study focuses on enzymatic co-fermentation of wheat straw to produce high-protein, low-cellulose biological feed, integrating lignin degradation with feed manufacturing, thereby simplifying the feed production process. After the optimization using Box-Behnken Design for the feed formulation, with a glucose oxidase addition of 2.46%, laccase addition of 3.4%, and malonic acid addition of 0.6%, the wheat straw feed prepared in this experiment exhibited a true protein content of 9.35%. This represented a fourfold increase compared to the non-fermented state, and the lignocellulose degradation rate of wheat straw reached 45.42%. These results not only highlight the substantial enhancement in protein content but also underscore the significant advancement in lignocellulose breakdown. This formulation significantly enhanced the palatability and nutritional value of the straw feed, contributing to the industrial development of straw feed.

Characteristic study of Candida rugosa lipase immobilized on lignocellulosic wastes: effect of support material

For the first time is reported the comparison of solid biocatalysts derived from Candida rugosa lipase (CRL) immobilized on different lignocellulosic wastes (rice husk, brewer's spent grain, hemp tea waste, green tea waste, vine bark, and spent coffee grounds) focusing on the characterization of these materials and their impact on the lipase-support interaction. The wastes were subjected to meticulous characterization by ATR-FTIR, BET, and SEM analysis, besides lignin content and hydrophobicity determination. Investigating parameters influencing immobilization performance revealed the importance of morphology, textural properties, and hydrophobic interactions revealed the importance of morphology, textural properties and especially hydrophobic interactions which resulted in positive correlations between surface hydrophobicity and lipase immobilization efficiency. Hemp tea waste and spent coffee grounds demonstrated superior immobilization performances (7.20 U/g and 8.74 U/g immobilized activity, 102.3% and 33.5% efficiency, 13.4% and 15.4% recovery, respectively). Moreover, they demonstrated good temporal stability (100% and 92% residual activity after 120 days, respectively) and retained 100% of their immobilized activity after five reuses in the hydrolysis of p-nitrophenyl palmitate in hexane. In addition, the study of enzymatic desorption caused by ionic strength and detergent treatments indicated mixed hydrophobic and electrostatic interactions in rice husk, vine bark, and spent coffee grounds supports, while hemp tea waste and green tea waste were dominated by hydrophobic interactions.

Removal of the cytostatic drugs bleomycin and vincristine by white-rot fungi under various conditions, and determination of enzymes involved, degradation by-products, and toxicity

Anticancer drugs show recalcitrance to conventional wastewater treatments; thus, they are present in aquatic systems and pose an environmental threat. Fungi represent a promising biological alternative for wastewater treatments. Therefore, the goals of this work were to assess the potential of white-rot fungi (Fomes fomentarius (CB13), Hypholoma fasciculare (CB15), Phyllotopsis nidulans (CB14), Pleurotus ostreatus (BWPH), and Trametes versicolor (CB8)) for removing bleomycin and vincristine, and to investigate the impacts of various conditions (shaking, aeration, or biomass immobilization) on the process. The removal capacities were measured using Ultra-Performance Liquid Chromatography (UPLC) coupled with Mass Spectrometry (MS) and preceded by Solid Phase Extraction (SPE). We further identified major drugs degradation products; determined the fungi's main enzyme activity profiles (laccase, manganese and lignin peroxidases); and examined the toxicities of post-processed samples against Lemna minor, Daphnia magna and Pseudomonas putida. In just 2 days, all strains (except for P. nidulans) removed >90 % of vincristine, nearly completely eliminating the drug over time. Bleomycin content reduction occurred with T. versicolor or H. fasciculare, respectively reaching 55 % and 83 % drug elimination after 9 days. Oxygen was found to be crucial for cytostatics degradation, with their highest removal rates occurring in samples with air supply (aeration or agitation). Laccase was the only tested enzyme associated with cytostatics elimination. Drug biodegradation was followed by detoxification, demonstrating the utility of fungi in cytostatics removal.

Phytochemical and pharmacological investigation of the non-volatile compounds of Lepidium cartilagineum (J. C. Mayer) Thell. and determination of the essential oil composition of its flowers and fruits

Eighteen compounds, among them phenylpropanoids (1-2), neolignans (3-9), a megastigmane (10), a phenyl glucoside (11), flavonoids (12-14), and N-containing compounds (15-18) were isolated from the methanolic extract of the whole plant of L. cartilagineum. The structures of the compounds were determined by NMR and MS measurements. The composition of the essential oils prepared from the flowers and fruits of L. cartilagineum was investigated using GC and GC-MS measurements. The essential oils were rich in aliphatic aldehydes and hydrocarbons, but low in sulfur-containing compounds, e.g., isothiocyanates. The extracts prepared from the aerial parts and roots of the plant, the essential oil, and the isolated compounds (1-9) were tested for antiproliferative activity against COLO 205 and COLO 320 cell lines and antibacterial activity on Lactobacillus rhamnosus. Dehydrodiconiferyl alcohol γ'-methyl ether (5) possessed marked antiproliferative activity against both human tumor cell lines. Neither the extracts nor the compounds affected the growth of the bacteria and did not influence the biofilm formation of L. rhamnosus. Based on the results, it can be concluded that L. cartilagineum is non-toxic to the human gut microbiome forming L. rhamnosus.

Chemical Synthesis of Monolignols: Traditional Methods, Recent Advances, and Future Challenges in Sustainable Processes

Monolignols represent pivotal alcohol-based constituents in lignin synthesis, playing indispensable roles in plant growth and development with profound implications for industries reliant on wood and paper. Monolignols and their derivates have multiple applications in several industries. Monolignols exhibit antioxidant activity due to their ability to donate hydrogen atoms or electrons to neutralize free radicals, thus preventing oxidative stress and damage to cells. Characterized by their alcohol functionalities, monolignols present three main forms: p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol. In nature, particularly in plants, monolignols with geometry (E) predominate over their Z counterparts. The methods for obtaining the three canonical monolignols, two less-common monolignols, and a monolignol analogue are addressed to present an overview of these phenol-based compounds, particularly from a synthetic standpoint. A SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis is used to explain the advantages and disadvantages of synthesizing monolignols, key alcohol-containing raw materials with enormous significance in both plant biology and industrial applications, using bench chemical methods. The uniqueness of this work is that it provides an overview of the synthetic pathways of monolignols to assist researchers in pharmaceutical and biological fields in selecting an appropriate procedure for the preparation of their lignin models. Moreover, we aim to inspire scientists, particularly chemists, to develop more sustainable synthetic protocols for monolignols.

Exploiting lignin-based nanomaterials for enhanced anticancer therapy: A comprehensive review and future direction

Lignin, a renewable and abundant natural polymer, has emerged as a promising candidate for anticancer therapy due to its unique properties and biocompatibility. This review provides a comprehensive overview of recent advancements in the utilization of lignin-based nanomaterials for enhancing anticancer drug delivery and therapeutic outcomes. A detailed examination of the literature reveals several synthesis methods, including nanoprecipitation, microemulsion, and solvent exchange, which produce lignin nanoparticles with improved drug solubility and bioavailability. The anticancer mechanisms of lignin nanoparticles, such as the generation of reactive oxygen species (ROS), induction of apoptosis, and enhanced cellular uptake, are also explored. Lignin nanoparticles loaded with drugs like curcumin, doxorubicin, camptothecin, and resveratrol have demonstrated the ability to improve drug efficacy, selectively target cancer cells, overcome multidrug resistance, and minimize toxicity in both in vitro and in vivo studies. These nanoparticles have shown significant potential in suppressing tumor growth, inducing cell death through apoptotic pathways, and enhancing the synergistic effects of combination therapies, such as chemo-phototherapy. Future research directions include optimizing lignin nanoparticle formulations for clinical applications, refining targeted delivery mechanisms to cancer cells, and conducting thorough biocompatibility and toxicity assessments. Overall, this review highlights the significant progress made in utilizing lignin-based nanomaterials for cancer therapy and outlines promising areas for further exploration in this rapidly evolving field.

Lignin valorization through the oxidative activity of β-etherases: Recent advances and perspectives

The increasing interest in lignin, a complex and abundant biopolymer, stems from its ability to produce environmentally beneficial biobased products. β-Etherases play a crucial role by breaking down the β-aryl ether bonds in lignin. This comprehensive review covers the latest advancements in β-etherase-mediated lignin valorization, focusing on substrate selectivity, enzymatic oxidative activity, and engineering methods. Research on the microbial origin, protein modification, and molecular structure determination of β-etherases has improved our understanding of their effectiveness. Furthermore, the use of these enzymes in biorefinery processes is promising for enhancing lignin breakdown and creating more valuable products. The review also discusses the challenges and future potential of β-etherases in advancing lignin valorization for biorefinery applications that are economically viable and environmentally sustainable.

Heterologous expression and characterization of a dye-decolorizing peroxidase from Ganoderma lucidum, and its application in decolorization and detoxifization of different types of dyes

Dye-decolorizing peroxidases (DyPs) belong to a novel superfamily of heme peroxidases that can oxidize recalcitrant compounds. In the current study, the GlDyP2 gene from Ganoderma lucidum was heterologously expressed in Escherichia coli, and the enzymatic properties of the recombinant GlDyP2 protein were investigated. The GlDyP2 protein could oxidize not only the typical peroxidase substrate ABTS but also two lignin substrates, namely guaiacol and 2,6-dimethoxy phenol (DMP). For the ABTS substrate, the optimum pH and temperature of GlDyP2 were 4.0 and 35 °C, respectively. The pH stability and thermal stability of GlDyP2 were also measured; the results showed that GlDyP2 could function normally in the acidic environment, with a T50 value of 51 °C. Moreover, compared to untreated controls, the activity of GlDyP2 was inhibited by 1.60 mM of Mg2+, Ni2+, Mn2+, and ethanol; 0.16 mM of Cu2+, Zn2+, methanol, isopropyl alcohol, and Na2EDTA·2H2O; and 0.016 mM of Fe2+ and SDS. The kinetic constants of recombinant GlDyP2 for oxidizing ABTS, Reactive Blue 19, guaiacol, and DMP were determined; the results showed that the recombination GlDyP2 exhibited the strongest affinity and the most remarkable catalytic efficiency towards guaiacol in the selected substrates. GlDyP2 also exhibited decolorization and detoxification capabilities towards several dyes, including Reactive Blue 19, Reactive Brilliant Blue X-BR, Reactive Black 5, Methyl Orange, Trypan Blue, and Malachite Green. In conclusion, GlDyP2 has good application potential for treating dye wastewater.

The Phylogeny and Metabolic Potentials of an Aromatics-Degrading Marivivens Bacterium Isolated from Intertidal Seawater in East China Sea

Lignocellulosic materials, made up of cellulose, hemicellulose, and lignin, constitute some of the most prevalent types of biopolymers in marine ecosystems. The degree to which marine microorganisms participate in the breakdown of lignin and their impact on the cycling of carbon in the oceans is not well understood. Strain LCG002, a novel Marivivens species isolated from Lu Chao Harbor's intertidal seawater, is distinguished by its ability to metabolize lignin and various aromatic compounds, including benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate and phenylacetate. It also demonstrates a broad range of carbon source utilization, including carbohydrates, amino acids and carboxylates. Furthermore, it can oxidize inorganic gases, such as hydrogen and carbon monoxide, providing alternative energy sources in diverse marine environments. Its diversity of nitrogen metabolism is supported by nitrate/nitrite, urea, ammonium, putrescine transporters, as well as assimilatory nitrate reductase. For sulfur assimilation, it employs various pathways to utilize organic and inorganic substrates, including the SOX system and DSMP utilization. Overall, LCG002's metabolic versatility and genetic profile contribute to its ecological significance in marine environments, particularly in the degradation of lignocellulosic material and aromatic monomers.

Utilization of plant-derived wastes as the potential biohydrogen source: a sustainable strategy for waste management

The sustainable economy has shown a renewed interest in acquiring access to the resources required to promote innovative practices that favor recycling and the reuse of existing, unconsidered things over newly produced ones. The production of biohydrogen through dark anaerobic fermentation of organic wastes is one of the intriguing possibilities for replacing fossil-based fuels through the circular economy. At present, plant-derived waste from the agro-based industry is the main global concern. When these wastes are improperly disposed of in landfills, they become the habitat for several pathogens. Additionally, it contaminates surface water as a result of runoff, and the leachate that is created from the waste enters groundwater and degrades its quality. However, cellulose and hemicellulose-rich plant wastes from agriculture fields and agro-based industries have been employed as the most efficient feedstock since carbohydrates are the primary substrate for the synthesis of biohydrogen. To produce biohydrogen from plant-derived wastes on a large scale, it is necessary to explore comprehensive knowledge of lab-scale parameters and pretreatment strategies. This paper summarizes the problems associated with the improper management of plant-derived wastes and discusses the recent developments in dark fermentation and substrate pretreatment techniques with the goal of gaining significant insight into the biohydrogen production process. It also highlights the utilization of anaerobic digestate, which is left over after biohydrogen gas as feedstock for the development of value-added products such as volatile fatty acids (VFA), biochar, and biofertilizer.

Valorization of crop residues and animal wastes: Anaerobic co-digestion technology

To switch the over-reliance on fossil-based resources, curb environmental quality deterioration, and promote the use of renewable fuels, much attention has recently been directed toward the implementation of sustainable and environmentally benign 'waste-to-energy' technology exploiting a clean, inexhaustible, carbon-neutral, and renewable energy source, namely agricultural biomass. From this perspective, anaerobic co-digestion (AcoD) technology emerges as a potent and plausible approach to attain sustainable energy development, foster environmental sustainability, and, most importantly, circumvent the key challenges associated with mono-digestion. This review article provides a comprehensive overview of AcoD as a biochemical valorization pathway of crop residues and livestock manure for biogas production. Furthermore, this manuscript aims to assess the different biotic and abiotic parameters affecting co-digestion efficiency and present recent advancements in pretreatment technologies designed to enhance feedstock biodegradability and conversion rate. It can be concluded that the substantial quantities of crop residues and animal waste generated annually from agricultural practices represent valuable bioenergy resources that can contribute to meeting global targets for affordable renewable energy. Nevertheless, extensive and multidisciplinary research is needed to evolve the industrial-scale implementation of AcoD technology of livestock waste and crop residues, particularly when a pretreatment phase is included, and bridge the gap between small-scale studies and real-world applications.

Current trends in textile wastewater treatment-bibliometric review

A bibliometric study using 1992 to 2021 database of the Science Citation Index Expanded was carried out to identify which are the current trends in textile wastewater treatment research. The study aimed to analyze the performance of scholarly scientific communications in terms of yearly publications/citations, total citations, scientific journals, and their categories in the Web of Sciences, top institutions/countries and research trends. The annual publication of scientific articles fluctuated in the first ten years, with a steady decrease for the last twenty years. An analysis of the most common terms used in the authors' keywords, publications' titles, and KeyWords Plus was carried out to predict future trends and current research priorities. Adsorbent nanomaterials would be the future of wastewater treatment for decoloration of the residual dyes in the wastewater. Membranes and electrolysis are important to demineralize textile effluent for reusing wastewater. Modern filtration techniques such as ultrafiltration and nanofiltration are advanced membrane filtration applications.

Robust Oxidase-Mimetic Supramolecular Nanocatalyst for Lignin Biodegradation

Enzymatic catalysis presents an eco-friendly, energy-efficient method for lignin degradation. However, challenges arise due to the inherent incompatibility between enzymes and native lignin. In this work, we introduce a supramolecular catalyst composed of fluorenyl-modified amino acids and Cu2+, designed based on the aromatic stacking of the fluorenyl group, which can operate in ionic liquid environments suitable for the dissolution of native lignin. Amino acids and halide anions of ionic liquids shape the copper site's coordination sphere, showcasing remarkable catechol oxidase-mimetic activity. The catalyst exhibits thermophilic property, and maintains oxidative activity up to 75 °C, which allows the catalyzed degradation of the as-dissolved native lignin with high efficiency even without assistance of the electron mediator. In contrast, at this condition, the native copper-dependent oxidase completely lost its activity. This catalyst with superior stability and activity offer promise for sustainable lignin valorization through biocatalytic routes compatible with ionic liquid pretreatment, addressing limitations in native enzymes for industrially relevant conditions.

Biodegradation strategies of veterinary medicines in the environment: Enzymatic degradation

One Health closely integrates healthy farming, human medicine, and environmental ecology. Due to the ecotoxicity and risk of transmission of drug resistance, veterinary medicines (VMs) are regarded as emerging environmental pollutants. To reduce or mitigate the environmental risk of VMs, developing friendly, safe, and effective removal technologies is an important means of environmental remediation for VMs. Many previous studies have proved that biodegradation has significant advantages in removing VMs, and biodegradation based on enzyme catalysis presents higher operability and specificity. This review focused on biodegradation strategies of environmental pollutants and reviewed the enzymatic degradation of VMs including antimicrobial drugs, insecticides, and disinfectants. We reviewed the sources and catalytic mechanisms of peroxidase, laccase, and organophosphorus hydrolases, and summarized the latest research status of immobilization methods and bioengineering techniques in improving the performance of degrading enzymes. The mechanism of enzymatic degradation for VMs was elucidated in the current research. Suggestions and prospects for researching and developing enzymatic degradation of VMs were also put forward. This review will offer new ideas for the biodegradation of VMs and have a guide significance for the risk mitigation and detoxification of VMs in the environment.

Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography

Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure-function relationship. We here used neutron and sub-ångström resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Å-resolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångström resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.

Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms

Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.

The etherase system of Novosphingobium sp. MBES04 functions as a sensor of lignin fragments through phenylpropanone production to induce specific transcriptional responses

The MBES04 strain of Novosphingobium accumulates phenylpropanone monomers as end-products of the etherase system, which specifically and reductively cleaves the β-O-4 ether bond (a major bond in lignin molecules). However, it does not utilise phenylpropanone monomers as an energy source. Here, we studied the response to the lignin-related perturbation to clarify the physiological significance of its etherase system. Transcriptome analysis revealed two gene clusters, each consisting of four tandemly linked genes, specifically induced by a lignin preparation extracted from hardwood (Eucalyptus globulus) and a β-O-4-type lignin model biaryl compound, but not by vanillin. The most strongly induced gene was a 2,4'-dihydroxyacetophenone dioxygenase-like protein, which leads to energy production through oxidative degradation. The other cluster was related to multidrug resistance. The former cluster was transcriptionally regulated by a common promoter, where a phenylpropanone monomer acted as one of the effectors responsible for gene induction. These results indicate that the physiological significance of the etherase system of the strain lies in its function as a sensor for lignin fragments. This may be a survival strategy to detect nutrients and gain tolerance to recalcitrant toxic compounds, while the strain preferentially utilises easily degradable aromatic compounds with lower energy demands for catabolism.

Harnessing the potential of white rot fungi and ligninolytic enzymes for efficient textile dye degradation: A comprehensive review

The contamination of wastewater with textile dyes has emerged as a pressing environmental concern due to its persistent nature and harmful effects on ecosystems. Conventional dye treatment methods have proven inadequate in effectively breaking down complex dye molecules. However, a promising alternative for textile dye degradation lies in the utilization of white rot fungi, renowned for their remarkable lignin-degrading capabilities. This review provides a comprehensive analysis of the potential of white rot fungi in degrading textile dyes, with a particular focus on their ligninolytic enzymes, specifically examining the roles of lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase in the degradation of lignin and their applications in textile dye degradation. The primary objective of this paper is to elucidate the enzymatic mechanisms involved in dye degradation, with a spotlight on recent research advancements in this field. Additionally, the review explores factors influencing enzyme production, including culture conditions and genetic engineering approaches. The challenges associated with implementing white rot fungi and their ligninolytic enzymes in textile dye degradation processes are also thoroughly examined. Textile dye contamination poses a significant environmental threat due to its resistance to conventional treatment methods. White rot fungi, known for their ligninolytic capabilities, offer an innovative approach to address this issue. The review delves into the intricate mechanisms through which white rot fungi and their enzymes, including LiP, MnP, and laccase, break down complex dye molecules. These enzymes play a pivotal role in lignin degradation, a process that can be adapted for textile dye removal. The review also emphasizes recent developments in this field, shedding light on the latest findings and innovations. It discusses how culture conditions and genetic engineering techniques can influence the production of these crucial enzymes, potentially enhancing their efficiency in textile dye degradation. This highlights the potential for tailored enzyme production to address specific dye contaminants effectively. The paper also confronts the challenges associated with integrating white rot fungi and their ligninolytic enzymes into practical textile dye degradation processes. These challenges encompass issues like scalability, cost-effectiveness, and regulatory hurdles. By acknowledging these obstacles, the review aims to pave the way for practical and sustainable applications of white rot fungi in wastewater treatment. In conclusion, this comprehensive review offers valuable insights into how white rot fungi and their ligninolytic enzymes can provide a sustainable solution to the urgent problem of textile dye-contaminated wastewater. It underscores the enzymatic mechanisms at play, recent research breakthroughs, and the potential of genetic engineering to optimize enzyme production. By addressing the challenges of implementation, this review contributes to the ongoing efforts to mitigate the environmental impact of textile dye pollution. PRACTITIONER POINTS: Ligninolytic enzymes from white rot fungi, like LiP, MnP, and laccase, are crucial for degrading textile dyes. Different dyes and enzymatic mechanisms is vital for effective wastewater treatment. Combine white rot fungi-based strategies with mediator systems, co-culturing, or sequential treatment approaches to enhance overall degradation efficiency. Emphasize the broader environmental impact of textile dye pollution and position white rot fungi as a promising avenue for contributing to mitigation efforts. This aligns with the overarching goal of sustainable wastewater treatment practices and environmental conservation. Consider scalability, cost-effectiveness, and regulatory compliance to pave the way for sustainable applications that can effectively mitigate the environmental impact of textile dye pollution.

Production and characterization of novel thermostable CotA-laccase from Bacillus altitudinis SL7 and its application for lignin degradation

Laccases are multi-copper oxidases and found in ligninolytic bacteria catalyzing the oxidation of both phenolic and non-phenolic compounds, however its application in lignin degradation suffers due to low oxidation rate, which have intensified the search for new laccases. In the present study, spore coat A protein (CotA) encoding gene having laccase like activity from Bacillus altitudinis SL7 (CotA-SL7) was cloned and expressed in Escherichia coli. The purified CotA-SL7 was active at wide range of temperature and pH with optimum activity at 55 °C and pH 5.0. The kinetic parameters of CotA-SL7 was determined with Km, Vmax, and kcat values 0.4 mM, 2777 μmol/min/mg, and 5194 s-1, respectively. Molecular docking revealed the presence of Pro, Phe, Asp, Asn, His, and Ile residues at the active site taking part in the oxidation of ABTS. The purified CotA-SL7 reduced lignin contents by 31 % and changes in lignin structure were analyzed through fourier transformed infrared spectroscopy (FTIR), scanning electron microsscopy (SEM) and gas chromatography mass-spectrometry (GC-MS). The appearance of low molecular size compounds clearly indicates the cleavage of lignin polymer and opening of the benzene ring by purified CotA-SL7. Thus, high catalytic efficiency of CotA-SL7 makes it a suitable bio-catalyst for remediation of lignin contaminated wastewater from pulp and paper industries with clear insights into lignin degradation at molecular level.

Lignin Extraction by Using Two-Step Fractionation: A Review

Lignocellulosic biomass represents the most abundant renewable carbon source on earth and is already used for energy and biofuel production. The pivotal step in the conversion process involving lignocellulosic biomass is pretreatment, which aims to disrupt the lignocellulose matrix. For effective pretreatment, a comprehensive understanding of the intricate structure of lignocellulose and its compositional properties during component disintegration and subsequent conversion is essential. The presence of lignin-carbohydrate complexes and covalent interactions between them within the lignocellulosic matrix confers a distinctively labile nature to hemicellulose. Meanwhile, the recalcitrant characteristics of lignin pose challenges in the fractionation process, particularly during delignification. Delignification is a critical step that directly impacts the purity of lignin and facilitates the breakdown of bonds involving lignin and lignin-carbohydrate complexes surrounding cellulose. This article discusses a two-step fractionation approach for efficient lignin extraction, providing viable paths for lignin-based valorization described in the literature. This approach allows for the creation of individual process streams for each component, tailored to extract their corresponding compounds.

Combining computational tools and experimental studies towards endocrine disruptors mitigation: A review of biocatalytic and adsorptive processes

The endocrine disruptors (EDCs) are an important group of emerging contaminants, and their mitigation has been a huge challenge due to their chemistry complexity and variety of these compounds. The traditional treatments are inefficient to completely remove EDCs, and adsorptive processes are the major alternative investigated on their removal. Also, the use of EDCs degrading enzymes has been encouraged due to ecofriendly approach of biocatalytic processes. This paper highlights the occurrence, classification, and toxicity of EDCs with special focus in the use of enzyme-based and adsorptive technologies in the elimination of EDCs from ambiental matrices. Numerous prior reviews have focused on the discussions toward these technologies. However, the literature lacks theoretical discussions about important aspects of these methods such as the mechanisms of EDCs adsorption on the adsorbent surface or the interactions between degrading enzymes - EDCs. In this sense, theoretical calculations combined to experimental studies may help in the development of more efficient technologies to EDCs mitigation. In this review, we point out how computational tools such as molecular docking and molecular dynamics have to contribute to the design of new adsorbents and efficient catalytic processes towards endocrine disruptors mitigation.

Glycoside hydrolases in the biodegradation of lignocellulosic biomass

Lignocellulose is a plentiful and intricate biomass substance made up of cellulose, hemicellulose, and lignin. Cellulose and hemicellulose are polysaccharides characterized by different compositions and degrees of polymerization. As renewable resources, their applications are eco-friendly and can help reduce reliance on petrochemical resources. This review aims to illustrate cellulose, hemicellulose, and their structures and hydrolytic enzymes. To obtain desirable enzyme sources for the high hydrolysis of lignocellulose, highly stable, efficient and thermophilic enzyme sources, and new technologies, such as rational design and machine learning, have been introduced in detail. Generally, the efficient biodegradation of abundant natural biomass into fermentable sugars or other intermediates has great potential in practical applications.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03819-1.

Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass

Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.

Recent advances in the application of alcohols in extracting lignin with preserved β-O-4 content from lignocellulosic biomass

Utilizing lignocellulosic biomass wastes to produce bioproducts is essential to address the reliance on depleting fossil fuels. However, lignin is often treated as a low-value-added component in lignocellulosic wastes. Valorization of lignin into value-added products is crucial to improve the economic competitiveness of lignocellulosic biorefinery. Monomers obtained from lignin depolymerization could be upgraded into fuel-related products. However, lignins obtained from conventional methods are low in β-O-4 content and, therefore, unsuitable for monomer production. Recent literature has demonstrated that lignins extracted with alcohol-based solvents exhibit preserved structures with high β-O-4 content. This review discusses the recent advances in utilizing alcohols to extract β-O-4-rich lignin, where discussion based on different alcohol groups is considered. Emerging strategies in employing alcohols for β-O-4-rich lignin extraction, including alcohol-based deep eutectic solvent, flow-through fractionation, and microwave-assisted fractionation, are reviewed. Finally, strategies for recycling or utilizing the spent alcohol solvents are also discussed.

Response surface methodology for the mixed fungal fermentation of Codonopsis pilosula straw using Trichoderma reesei and Coprinus comatus

The objective of this study was to investigate the cellulose degradation rate (CDR) and lignin degradation rate (LDR) of Codonopsis pilosula straw (CPS) and the optimal fermentation parameters for mixed fungal fermentation. Single-factor tests were used to study the effects of the fungal ratio (Trichoderma reesei: Coprinus comatus), fungal inoculum, corn flour content, and fermentation time on the degradation rate of cellulose and lignin. Based on the results of this experiment, the optimal fermentation factors were identified, and the effects of various factors and their interactions on the degradation rates of cellulose and lignin were further evaluated using the response surface method. The quadratic polynomial mathematical model of degradation rates of the cellulose and lignin in CPS by mixed fungus fermentation was established using Design Expert software v8.0.6. Under the optimal parameters for fungal fermentation of CPS straw (fungal ratio 4:6, fungal inoculum 8%, corn flour content 10%, fermentation time of 15 d), the CDR and LDR reached 13.65% and 10.73%, respectively. Collectively, the mixed fungal fermentation of CPS resulted in decreased lignin and cellulose content, better retention of nutrients, and enhanced fermentation quality. The results of this study indicate that fermentation using Trichoderma reesei and Coprinus comatus is a productive method for straw degradation, providing a theoretical basis for the development of CPS as feed.

Insights into characteristics of white rot fungus during environmental plastics adhesion and degradation mechanism of plastics

Since the 1980s, plastic waste in the environment has been accumulating, and little is known about fungi biodegradation, especially in dry environments. Therefore, the research on plastic degradation technology is urgent. In this study, we demonstrated that Phanerochaete chrysosporium (P. chrysposporium), a typical species of white rot fungi, could react as a highly efficient biodegrader of polylactic acid (PLA), and 34.35 % of PLA degradation was obtained during 35-day incubation. A similar mass loss of 19.71 % could be achieved for polystyrene (PS) degradation. Here, we presented the visualization of the plastic deterioration process and their negative reciprocal on cell development, which may be caused by the challenge of using PS as a substrate. The RNA-seq analysis indicated that adaptations in energy metabolism and cellular defense were downregulated in the PS group, while lipid synthesis was upregulated in the PLA-treated group. Possible differentially expressed genes (DEG) of plastic degradation, such as hydrophobic proteins, lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac), Cytochrome P450 (CYP450), and genes involved in styrene or benzoic acid degradation pathways have been recorded, and we proposed a PS degradation pathway.

From trash to treasure: Sourcing high-value, sustainable cellulosic materials from living bioreactor waste streams

The appreciation of how conventional and fossil-based materials could be harmful to our planet is growing, especially when considering single-use and non-biodegradable plastics manufactured from fossil fuels. Accordingly, tackling climate change and plastic waste pollution entails a more responsible approach to sourcing raw materials and the adoption of less destructive end-of-life pathways. Livestock animals, in particular ruminants, process plant matter using a suite of mechanical, chemical and biological mechanisms through the act of digestion. The manure from these "living bioreactors" is ubiquitous and offers a largely untapped source of lignocellulosic biomass for the development of bio-based and biodegradable materials. In this review, we assess recent studies made into manure-based cellulose materials in terms of their material characteristics and implications for sustainability. Despite the surprisingly diverse body of research, it is apparent that progress towards the commercialisation of manure-derived cellulose materials is hindered by a lack of truly sustainable options and robust data to assess the performance against conventional materials alternatives. Nanocellulose, a natural biopolymer, has been successfully produced by living bioreactors and is presented as a candidate for future developments. Life cycle assessments from non-wood sources are however minimal, but there are some initial indications that manure-derived nanocellulose would offer environmental benefits over traditional wood-derived sources.

Designing Lignin-Based Biomaterials as Carriers of Bioactive Molecules

There is a need to develop circular and sustainable economies by utilizing sustainable, green, and renewable resources in high-tech industrial fields especially in the pharmaceutical industry. In the last decade, many derivatives of food and agricultural waste have gained considerable attention due to their abundance, renewability, biocompatibility, environmental amiability, and remarkable biological features. Particularly, lignin, which has been used as a low-grade burning fuel in the past, recently attracted a lot of attention for biomedical applications because of its antioxidant, anti-UV, and antimicrobial properties. Moreover, lignin has abundant phenolic, aliphatic hydroxyl groups, and other chemically reactive sites, making it a desirable biomaterial for drug delivery applications. In this review, we provide an overview of designing different forms of lignin-based biomaterials, including hydrogels, cryogels, electrospun scaffolds, and three-dimensional (3D) printed structures and how they have been used for bioactive compound delivery. We highlight various design criteria and parameters that influence the properties of each type of lignin-based biomaterial and corelate them to various drug delivery applications. In addition, we provide a critical analysis, including the advantages and challenges encountered by each biomaterial fabrication strategy. Finally, we highlight the prospects and future directions associated with the application of lignin-based biomaterials in the pharmaceutical field. We expect that this review will cover the most recent and important developments in this field and serve as a steppingstone for the next generation of pharmaceutical research.

Criteria for Assessing Sustainability of Lignocellulosic Wastes: Applied to the Cellulose Nanofibril Packaging Production in the UK

Extensive use of petrochemical plastic packaging leads to the greenhouse gas emission and contamination to soil and oceans, posing major threats to the ecosystem. The packaging needs, hence, are shifting to bioplastics with natural degradability. Lignocellulose, the biomass from forest and agriculture, can produce cellulose nanofibrils (CNF), a biodegradable material with acceptable functional properties, that can make packaging among other products. Compared to primary sources, CNF extracted from lignocellulosic wastes reduces the feedstock cost without causing an extension to agriculture and associated emissions. Most of these low value feedstocks go to alternative applications, making their use in CNF packaging competitive. To transfer the waste materials from current practices to the packaging production, it is imperative to assess their sustainability, encompassing environmental and economic impacts along with the feedstock physical and chemical properties. A combined overview of these criteria is absent in the literature. This study consolidates thirteen attributes, delineating sustainability of lignocellulosic wastes for commercial CNF packaging production. These criteria data are gathered for the UK waste streams, and transformed into a quantitative matrix, evaluating the waste feedstock sustainability for CNF packaging production. The presented approach can be adopted to decision scenarios in bioplastics packaging conversion and waste management.

Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase

pH buffer plays versatile roles in both biology and chemistry. In this study, we unravel the critical role of pH buffer in accelerating degradation of the lignin substrate in lignin peroxidase (LiP) using QM/MM MD simulations and the nonadiabatic electron transfer (ET) and proton-coupled electron transfer (PCET) theories. As a key enzyme involved in lignin degradation, LiP accomplishes the oxidation of lignin via two consecutive ET reactions and the subsequent C-C cleavage of the lignin cation radical. The first one involves ET from Trp171 to the active species of Compound I, while the second one involves ET from the lignin substrate to the Trp171 radical. Differing from the common view that pH = 3 may enhance the oxidizing power of Cpd I via protonation of the protein environment, our study shows that the intrinsic electric fields have minor effects on the first ET step. Instead, our study shows that the pH buffer of tartaric acid plays key roles during the second ET step. Our study shows that the pH buffer of tartaric acid can form a strong H-bond with Glu250, which can prevent the proton transfer from the Trp171-H^•+ cation radical to Glu250, thereby stabilizing the Trp171-H^•+ cation radical for the lignin oxidation. In addition, the pH buffer of tartaric acid can enhance the oxidizing power of the Trp171-H^•+ cation radical via both the protonation of the proximal Asp264 and the second-sphere H-bond with Glu250. Such synergistic effects of pH buffer facilitate the thermodynamics of the second ET step and reduce the overall barrier of lignin degradation by ∼4.3 kcal/mol, which corresponds to a rate acceleration of 10³-fold that agrees with experiments. These findings not only expand our understanding on pH-dependent redox reactions in both biology and chemistry but also provide valuable insights into tryptophan-mediated biological ET reactions.

Characterization of Fungal Foams from Edible Mushrooms Using Different Agricultural Wastes as Substrates for Packaging Material

Agricultural wastes and leaves, which are classified as lignocellulosic biomass, have been used as substrates in the production of fungal foams due to the significant growth of the mushroom industry in recent years. Foam derived from fungi can be utilized in a variety of industrial applications, including the production of packaging materials. Here, white oyster mushrooms (Pleurotus florida) and yellow oyster mushrooms (Pleurotus citrinopileatus) were cultivated on rice husk, sawdust, sugarcane bagasse, and teak leaves. Fungal foams were produced after 30 days of incubation, which were then analyzed using scanning electron microscopy (SEM), thermal analysis (TGA), and chemical structure using Fourier-transform infrared spectroscopy. Mechanical testing examined the material's hardness, resilience, and springiness, and water absorption tests were used to determine the durability of the fungal foams. Our findings demonstrated that fungal foams made from rice husk and teak leaves in both mycelium species showed better mechanical properties, thermal stability, and minimal water absorption compared to the other substrates, and can thus have great potential as efficient packaging materials.

Trait biases in microbial reference genomes

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.

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

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

Efficient Azo Dye Biodecolorization System Using Lignin-Co-Cultured White-Rot Fungus

The extensive use of azo dyes by the global textile industry induces significant environmental and human health hazards, which makes efficient remediation crucial but also challenging. Improving dye removal efficiency will benefit the development of bioremediation techniques for textile effluents. In this study, an efficient system for azo dye (Direct Red 5B, DR5B) biodecolorization is reported, which uses the white-rot fungus Ganoderma lucidum EN2 and alkali lignin. This study suggests that the decolorization of DR5B could be effectively enhanced (from 40.34% to 95.16%) within 48 h in the presence of alkali lignin. The dye adsorption test further confirmed that the alkali-lignin-enhanced decolorization of DR5B was essentially due to biodegradation rather than physical adsorption, evaluating the role of alkali lignin in the dye biodegradation system. Moreover, the gas chromatography/mass spectrometry analysis and DR5B decolorization experiments also indicated that alkali lignin carried an excellent potential for promoting dye decolorization and displayed a significant role in improving the activity of lignin-modifying enzymes. This was mainly because of the laccase-mediator system, which was established by the induced laccase activity and lignin-derived small aromatic compounds.

Bioethanol Production from Lignocellulosic Biomass-Challenges and Solutions

Regarding the limited resources for fossil fuels and increasing global energy demands, greenhouse gas emissions, and climate change, there is a need to find alternative energy sources that are sustainable, environmentally friendly, renewable, and economically viable. In the last several decades, interest in second-generation bioethanol production from non-food lignocellulosic biomass in the form of organic residues rapidly increased because of its abundance, renewability, and low cost. Bioethanol production fits into the strategy of a circular economy and zero waste plans, and using ethanol as an alternative fuel gives the world economy a chance to become independent of the petrochemical industry, providing energy security and environmental safety. However, the conversion of biomass into ethanol is a challenging and multi-stage process because of the variation in the biochemical composition of biomass and the recalcitrance of lignin, the aromatic component of lignocellulose. Therefore, the commercial production of cellulosic ethanol has not yet become well-received commercially, being hampered by high research and production costs, and substantial effort is needed to make it more widespread and profitable. This review summarises the state of the art in bioethanol production from lignocellulosic biomass, highlights the most challenging steps of the process, including pretreatment stages required to fragment biomass components and further enzymatic hydrolysis and fermentation, presents the most recent technological advances to overcome the challenges and high costs, and discusses future perspectives of second-generation biorefineries.

Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics

Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.

Characterizing corn-straw-degrading actinomycetes and evaluating application efficiency in straw-returning experiments

Corn straw is an abundant lignocellulose resource and by-product of agricultural production. With the continuous increase in agricultural development, the output of corn straw is also increasing significantly. However, the inappropriate disposal of straw results in wasting of resources, and also causes a serious ecological crisis. Screening microorganisms with the capacity to degrade straw and understanding their mechanism of action is an efficient approach to solve such problems. For this purpose, our research group isolated three actinomycete strains with efficient lignocellulose degradation ability from soil in the cold region of China: Streptomyces sp. G1T, Streptomyces sp. G2T and Streptomyces sp. G3T. Their microbial properties and taxonomic status were assessed to improve our understanding of these strains. The three strains showed typical characteristics of the genus Streptomyces, and likely represent three different species. Genome functional annotation indicated that most of their genes were related to functions like carbohydrate transport and metabolism. In addition, a similar phenomenon also appeared in the COG and CAZyme analyses, with a large number of genes encoding carbohydrate-related hydrolases, such as cellulase, glycosidase and endoglucanase, which could effectively destroy the structure of lignocellulose in corn straw. This unambiguously demonstrated the potential of the three microorganisms to hydrolyze macromolecular polysaccharides at the molecular level. In addition, in the straw-returning test, the decomposing consortium composed of the three Streptomyces isolates (G123) effectively destroyed the recalcitrant bonds between the various components of straw, and significantly reduced the content of active components in corn straw. Furthermore, microbial diversity analysis indicated that the relative abundance of Proteobacteria, reportedly associated with soil antibiotic resistance and antibiotic degradation, was significantly improved with straw returning at both tested time points. The microbial diversity of each treatment was also dramatically changed by supplementing with G123. Taken together, G123 has important biological potential and should be further studied, which will provide new insights and strategies for appropriate treatment of corn straw.

Microalgae Harvesting after Tertiary Wastewater Treatment with White-Rot Fungi

Tertiary wastewater treatment with microalgae incorporates environmental sustainability with future technologies and high exploitation costs. Despite the apparent ecological benefits of microalgae-assisted wastewater treatment/biomass-based resource production, technological improvements are still essential to compete with other technologies. Bio-flocculation instead of mechanical harvesting has been demonstrated as an alternative cost-effective approach. So far, mostly filamentous fungi of genus Aspergillus have been used for this purpose. Within this study, we demonstrate a novel approach of using white-rot fungi, with especially high potential of algae-Irpex lacteus complex that demonstrates efficiency with various microalgae species at a broad range of temperatures (5-20 °C) and various pH levels. Harvesting of microalgae from primary and secondary wastewater resulted in 73-93% removal efficiencies within the first 24 h and up to 95% after 48 h. The apparent reuse potential of the algae-I. lacteus pellets further complements the reduced operating costs and environmental sustainability of bio-flocculation technology.

Valorisation Potential of Invasive Acacia dealbata, A. longifolia and A. melanoxylon from Land Clearings

Acacia spp. are invasive in Southern Europe, and their high propagation rates produce excessive biomass, exacerbating wildfire risk. However, lignocellulosic biomass from Acacia spp. may be utilised for diverse biorefinery applications. In this study, attenuated total reflectance Fourier transform infrared spectroscopy (FTIR-ATR), high-performance anion-exchange chromatography pulsed amperometric detection (HPAEC-PAD) and lignin content determinations were used for a comparative compositional characterisation of A. dealbata, A. longifolia and A. melanoxylon. Additionally, biomass was treated with three white-rot fungi species (Ganoderma lucidum, Pleurotus ostreatus and Trametes versicolor), which preferentially degrade lignin. Our results showed that the pre-treatments do not significantly alter neutral sugar composition while reducing lignin content. Sugar release from enzymatic saccharification was enhanced, in some cases possibly due to a synergy between white-rot fungi and mild alkali pretreatments. For example, in A. dealbata stems treated with alkali and P. ostreatus, saccharification yield was 702.3 nmol mg^-1, which is higher than the samples treated only with alkali (608.1 nmol mg^-1), and 2.9-fold higher than the non-pretreated controls (243.9 nmol mg^-1). By characterising biomass and pretreatments, generated data creates value for unused biomass resources, contributing to the implementation of sustainable biorefining systems. In due course, the generated value will lead to economic incentives for landowners to cut back invasive Acacia spp. more frequently, thus reducing excess biomass, which exacerbates wildfire risk.

Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review

Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.

Does Tyrosine Protect S. coelicolor Laccase from Oxidative Degradation or Act as an Extended Catalytic Site?

We have investigated the roles of tyrosine (Tyr) and tryptophan (Trp) residues in the four-electron reduction of oxygen catalyzed by Streptomyces coelicolor laccase (SLAC). During normal enzymatic turnover in laccases, reducing equivalents are delivered to a type 1 Cu center (CuT1) and then are transferred over 13 Å to a trinuclear Cu site (TNC: (CuT3)2CuT2) where O2 reduction occurs. The TNC in SLAC is surrounded by a large cluster of Tyr and Trp residues that can provide reducing equivalents when the normal flow of electrons is disrupted. Prior studies by Canters and co-workers [J. Am. Chem. Soc. 2009, 131 (33), 11680-11682] have shown that when O2 reacts with a reduced SLAC variant lacking the CuT1 center, a Tyr108• radical near the TNC forms rapidly. We have found that the Tyr108• radical is reduced 10 times faster than CuT12+ by excess ascorbate, possibly because of radical transfer along Tyr/Trp chains.

Valorization of Lignin and Its Derivatives Using Yeast

As the third most plentiful biopolymer after other lignocellulosic derivates such as cellulose and hemicellulose, lignin carries abundant potential as a substitute for petroleum-based products. However, the efficient, practical, value-added product valorization of lignin remains quite challenging. Although several studies have reviewed the valorization of lignin by microorganisms, this present review covers recent studies on the valorization of lignin by employing yeast to obtain products such as single-cell oils (SCOs), enzymes, and other chemical compounds. The use of yeasts has been found to be suitable for the biological conversion of lignin and might provide new insights for future research to develop a yeast strain for lignin to produce other valuable chemical compounds.

Recent Advancements and Challenges in Lignin Valorization: Green Routes towards Sustainable Bioproducts

The aromatic hetero-polymer lignin is industrially processed in the paper/pulp and lignocellulose biorefinery, acting as a major energy source. It has been proven to be a natural resource for useful bioproducts; however, its depolymerization and conversion into high-value-added chemicals is the major challenge due to the complicated structure and heterogeneity. Conversely, the various pre-treatments techniques and valorization strategies offers a potential solution for developing a biomass-based biorefinery. Thus, the current review focus on the new isolation techniques for lignin, various pre-treatment approaches and biocatalytic methods for the synthesis of sustainable value-added products. Meanwhile, the challenges and prospective for the green synthesis of various biomolecules via utilizing the complicated hetero-polymer lignin are also discussed.