Biodegradation of lignin by white rot fungi

Development of functional consortia for the pretreatment of compostable lignocellulosic waste: A simple and effective solution to a large-scale problem

Microorganisms drive the degradation of organic matter thanks to their enzymatic versatility. However, the structure of lignocellulose poses a great challenge for the microbiota inhabiting a compost pile. Our purpose was to increase the biodegradability of vegetable waste in the early stages of the composting process by applying a microbial consortium with lignocelllulolytic capacity. For this, a previous screening was performed among the culturable microbiota from different composting processes to find inoculants with ligninocellulolytic activity. Selected strains were applied as a pure culture and as a microbial consortium. The starting material was composed of tomato plant and pruning remains mixed in a ratio (50:50 v/v), whose humidity was adjusted to around 65%. To determine the ability of both treatments to activate the biodegradation of the mixtures, moisture, organic matter, ash, C/N ratio, 4-day cumulative respirometric index (AT4) and degradation rates of cellulose, hemicellulose and lignin were evaluated. Subsequently, a real composting process was developed in which the performance of the microbial consortium was compared with the composting process without inoculum (control). According to our tests, three microbial strains (Bacillus safensis, Bacillus licheniformis and Fusarium oxysporum) were selected. The results showed that the application of the bacteria strains at low doses (104 CFU g-1 on the complete residual material of the pile) resulted in higher rates of lignocelullose degradation after 10 days of treatment compared to that observed after application of the fungus in pure culture or untreated controls. The implementation of the strategy described in this work resulted in obtaining compost with better agronomic quality than the uninoculated controls. Therefore, the application of this consortium could be considered as an interesting tool for bioactivation of lignocellulosic waste prior to the composting process.

Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation

SUMMARYFungi are ubiquitous and important biosphere inhabitants, and their abilities to decompose, degrade, and otherwise transform a massive range of organic and inorganic substances, including plant organic matter, rocks, and minerals, underpin their major significance as biodeteriogens in the built environment and of cultural heritage. Fungi are often the most obvious agents of cultural heritage biodeterioration with effects ranging from discoloration, staining, and biofouling to destruction of building components, historical artifacts, and artwork. Sporulation, morphological adaptations, and the explorative penetrative lifestyle of filamentous fungi enable efficient dispersal and colonization of solid substrates, while many species are able to withstand environmental stress factors such as desiccation, ultra-violet radiation, salinity, and potentially toxic organic and inorganic substances. Many can grow under nutrient-limited conditions, and many produce resistant cell forms that can survive through long periods of adverse conditions. The fungal lifestyle and chemoorganotrophic metabolism therefore enable adaptation and success in the frequently encountered extremophilic conditions that are associated with indoor and outdoor cultural heritage. Apart from free-living fungi, lichens are a fungal growth form and ubiquitous pioneer colonizers and biodeteriogens of outdoor materials, especially stone- and mineral-based building components. This article surveys the roles and significance of fungi in the biodeterioration of cultural heritage, with reference to the mechanisms involved and in relation to the range of substances encountered, as well as the methods by which fungal biodeterioration can be assessed and combated, and how certain fungal processes may be utilized in bioprotection.

Effect of heterogeneous fenton-like pretreatment on semi-permeable membrane-covered co-composting: Humification and microbial community succession

This study focused on the impacts of heterogeneous Fenton-like pretreatment on the humification and bacterial community during co-composting of wheat straw with cattle dung covered with a semi-permeable membrane. In this study, FeOCl and low concentration of H2O2 were used for pretreatment and composting, which lasted for 39 days. The results showed that the pretreatment promoted the humification process, with degree of polymerization and percentage of humic acid increasing by 53.2 % and 7.3 %, respectively. Furthermore, the diversity and structure of bacterial communities were altered by pretreatment. During the thermophilic phase, pretreatment considerably promoted the metabolism of carbohydrate. According to redundancy analysis, C/N, moisture and organic matter were the key environmental factors that dominated the microbial community. In summary, heterogeneous Fenton-like pretreatment provided a novel idea for improving the humic acid content and maturity of the compost pile.

An Artifact of Perfluoroalkyl Acid (PFAA) Removal Attributed to Sorption Processes in a Laccase Mediator System

Fungi and laccase mediator systems (LMSs) have a proven track record of oxidizing recalcitrant organic compounds. There has been considerable interest in applying LMSs to the treatment of perfluoroalkyl acids (PFAAs), a class of ubiquitous and persistent environmental contaminants. Some laboratory experiments have indicated modest losses of PFAAs over extended periods, but there have been no clear demonstrations of a transformation mechanism or the kinetics that would be needed for remediation applications. We set out to determine if this was a question of identifying and optimizing a rate-limiting step but discovered that observed losses of PFAAs were experimental artifacts. While unable to replicate the oxidation of PFAAs, we show that interactions of the PFAA compounds with laccase and laccase mediator mixtures could cause an artifact that mimics transformation (≲60%) of PFAAs. Furthermore, we employed a surrogate compound, carbamazepine (CBZ), and electron paramagnetic resonance spectroscopy to probe the formation of the radical species that had been proposed to be responsible for contaminant oxidation. We confirmed that under conditions where sufficient radical concentrations were produced to oxidize CBZ, no PFAA removal took place.

A Comparative Analysis of Biodegradation and Bioconversion of Lentinula edodes and Other Exotic Mushrooms

Mushrooms are capable of bioconverting organic residues into food. Understanding the relationship between high-quality yields and substrate biomass from these residues is critical for mushroom farms when choosing new strains. The objective of this exploratory study was, therefore, to analyze whether exotic mushrooms, namely, Pleurotus eryngii, Flammulina velutipes, and Agrocybe aegerita, could biologically convert the substrate into edible mushrooms as effectively as Lentinula edodes (baseline). Five experiments were carried out. Biological efficiency, biodegradability coefficient, mass balance and chemical characterization of the substrate were evaluated. Strategically hydrating the sawdust enabled L. edodes to achieve the greatest biodegradability and biological efficiency of 0.5 and 94.2 kg dt−1, respectively. The values for L. edodes on wheat straw without hydration were 0.2 and 68.8 kg dt−1, respectively. From 1000 kg of fresh substrate, P. eryngii produced 150.1 kg of edible mushrooms, making it technically competitive with L. edodes on wheat straw (195.9 kg). Hence, P. eryngii was the most reliable option for scaling among the exotic mushrooms. The analytical insights from our study provide further knowledge to advance the field’s prominence in high-throughput mushroom-producing systems, particularly for exotic mushrooms.

Multi-Enzymatic Synthesis of Lactobionic Acid Using Wood-Degrading Enzymes Produced by White Rot Fungi

Enzymes produced by white rot fungi are involved in the synthesis of secondary metabolites with valuable biotechnological properties. One of these metabolites is lactobionic acid (LBA). The aim of this study was to characterize a novel enzyme system consisting of a cellobiose dehydrogenase from Phlebia lindtneri (PlCDH), a laccase from Cerrena unicolor (CuLAC), a redox mediator (ABTS or DCPIP), and lactose as a substrate. We used quantitative (HPLC) and qualitative methods (TLC, FTIR) to characterise the obtained LBA. The free radical scavenging effect of the synthesised LBA was assessed with the DPPH method. Bactericidal properties were tested against Gram-negative and Gram-positive bacteria. We obtained LBA in all the systems tested; however, the study showed that the temperature of 50 °C with the addition of ABTS was the most advantageous condition for the synthesis of lactobionic acid. A mixture with 13 mM LBA synthesised at 50 °C with DCPIP showed the best antioxidant properties (40% higher compared with the commercial reagent). Furthermore, LBA had an inhibitory effect on all the bacteria tested, but the effect was better against Gram-negative bacteria with growth inhibition no lower than 70%. Summarizing the obtained data, lactobionic acid derived in a multienzymatic system is a compound with great biotechnological potential.

Click Synthesis of Triazole Polymers Based on Lignin-Derived Metabolic Intermediate and Their Strong Adhesive Properties to Cu Plate

2-Pyrone-4,6-dicarboxylic acid (PDC) is a chemically stable metabolic intermediate of lignin that can be produced on a large scale by transforming bacteria. Novel biomass-based polymers based on PDC were synthesized by Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and fully characterized by nuclear magnetic resonance, infrared spectroscopies, thermal analysis, and tensile lap shear strength measurements. The onset decomposition temperatures of these PDC-based polymers were all above 200 °C. In addition, the PDC-based polymers exhibited strong adhesive properties to various metal plates, with the highest adhesion to a copper plate of 5.73 MPa. Interestingly, this result was in contrast to our previous findings that PDC-based polymers weakly adhere to copper. Furthermore, when bifunctional alkyne and azide monomers were polymerized in situ under hot-press conditions for 1 h, the resulting PDC-based polymer displayed a similar adhesion to a copper plate of 4.18 MPa. The high affinity of the triazole ring to copper ions improved the adhesive ability and selectivity of the PDC-based polymers to copper while still maintaining the strong adhesive ability to other metals, which is conducive to enhancing the versatility of PDC-based polymers as adhesives.

Differential Activity of the Extracellular Phenoloxidases in Different Strains of the Phytopathogenic Fungus, Microdochium nivale

To cause plant diseases, phytopathogenic fungi use numerous extracellular enzymes, among which, the phenoloxidases (POs) seem underestimated for the pathogens of non-woody plants. Our study aimed to (1) compare extracellular PO activities (lignin peroxidase, Mn peroxidase, laccase, and tyrosinase) in differentially virulent strains (inhabiting winter rye in a single field) of the phytopathogenic species, Microdochium nivale; (2) check whether these activities are responsive to host plant metabolites; and (3) search for correlations between the activities, lignin-decomposing capacity, and virulence. All strains displayed all four enzymatic activities, but their levels and dynamics depended on the particular strain. The activities displayed the hallmarks of co-regulation and responsiveness to the host plant extract. No relationships between the virulence of strains and levels of their extracellular PO activities or lignin-degrading capacity were revealed. We consider that different strains may rely on different POs for plant colonization, and that different POs contribute to the “uniqueness” of the enzymatic cocktails that are delivered into host plant tissues by different virulent strains of M. nivale. Our study supports the hypothesis of the differential behavior of closely related M. nivale strains, and discusses an important role of POs in the interactions of phytopathogens with herbaceous plants.

From pomiculture waste to biotechnological raw material: efficient transformation using ligninosomes and cellulosomes from Pleurotus spp

The goal of this study was to determine the capacity of Pleurotus spp. lignocellulosome to transform frequent pomiculture residues (grapevine-, plum-, and raspberry sawdust) into raw materials for biotechnological processes. All three lignocellulosics induced the synthesis of ligninolytic and cellulolytic enzymes in the tested species. Laccase was dominant in the ligninolytic cocktail, with a maximum activity of 40,494.88 U L-1 observed after the cultivation of P. pulmonarius on grapevine sawdust. Grapevine sawdust also proved to be the optimal substrate for the synthesis of versatile peroxidases especially in P. eryngii (1010.10 U L-1), while raspberry sawdust favored the production of Mn-dependent peroxidase in P. pulmonarius (479.17 U L-1). P. pulmonarius was the dominant cellulolytic agent and raspberry sawdust was optimal for the synthesis of xylanases, and endo- and exo-cellulases (15,746.35 U L-1, 9741.56 U L-1, and 836.62 U L-1), while grapevine sawdust mostly induced β-glucosidase activity (166.11 U L-1). The degree of residues delignification was more substrate- than species-dependent, ranging between 6.44 and 23.72% after the fermentation of grapevine and raspberry sawdust with P. pulmonarius. On the other hand, the lowest level of cellulose consumption was also observed on raspberry sawdust after the cultivation of P. eryngii, which together with high delignification also induced the highest selectivity index (1.27). The obtained results show the exceptional lignocellulolytic potential of Pleurotus spp. enzyme cocktails which opens up many possibilities for their application in numerous biotechnological processes.

Closing the Carbon Loop in the Circular Plastics Economy

Today, plastics are ubiquitous in everyday life, problem solvers of modern technologies, and crucial for sustainable development. Yet the surge in global demand for plastics of the growing world population has triggered a tidal wave of plastic debris in the environment. Moving from a linear to a zero-waste and carbon-neutral circular plastic economy is vital for the future of the planet. Taming the plastic waste flood requires closing the carbon loop through plastic reuse, mechanical and molecular recycling, carbon capture, and use of the greenhouse gas carbon dioxide. In the quest for eco-friendly products, plastics do not need to be reinvented but tuned for reuse and recycling. Their full potential must be exploited regarding energy, resource, and eco efficiency, waste prevention, circular economy, climate change mitigation, and lowering environmental pollution. Biodegradation holds promise for composting and bio-feedstock recovery, but it is neither the Holy Grail of circular plastics economy nor a panacea for plastic littering. As an alternative to mechanical downcycling, molecular recycling enables both closed-loop recovery of virgin plastics and open-loop valorization, producing hydrogen, fuels, refinery feeds, lubricants, chemicals, and carbonaceous materials. Closing the carbon loop does not create a Perpetuum Mobile and requires renewable energy to achieve sustainability. This article is protected by copyright. All rights reserved.

Synergy between fungi and bacteria promotes polycyclic aromatic hydrocarbon cometabolism in lignin-amended soil

Lignin enhanced biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but collaboration among soil microorganisms during this process remains poorly understood. Here we explored the relations between microbial communities and PAH transformation in soil microcosms amended with lignin. Mineralization of the four-ring benzo(a)anthracene (BaA), which was selected as a model, was determined by using an isotope-labeled tracer. The eukaryotic inhibitor cycloheximide and redox mediator ABTS were used to validate the fungal role, while microbial communities were monitored by amplicon sequencing. The results demonstrated that lignin significantly promoted BaA mineralization to CO₂, which was inhibited and enhanced by cycloheximide and ABTS, respectively. Together with the increased abundance of Basidiomycota, these observations suggested an essential contribution of fungi to BaA biodegradation, which possibly through a ligninolytic enzyme-mediated pathway. The enrichment of Methylophilaceae and Sphingomonadaceae supported bacterial utilization of methyl and aryl groups derived from lignin, implicating cometabolic BaA degradation. Co-occurrence network analysis revealed increased interactions between fungi and bacteria, suggesting they played synergistic roles in the transformation of lignin and BaA. Collectively, these findings demonstrate the importance of synergy between fungi and bacteria in PAH transformation, and further suggest that the modulation of microbial interplay may ameliorate soil bioremediation with natural materials such as lignin.

Recent Advances in Synthesis and Degradation of Lignin and Lignin Nanoparticles and Their Emerging Applications in Nanotechnology

Lignin is an important commercially produced polymeric material. It is used extensively in both industrial and agricultural activities. Recently, it has drawn much attention from the scientific community. It is abundantly present in nature and has significant application in the production of biodegradable materials. Its wide usage includes drug delivery, polymers and several forms of emerging lignin nanoparticles. The synthesis of lignin nanoparticles is carried out in a controlled manner. The traditional manufacturing techniques are costly and often toxic and hazardous to the environment. This review article highlights simple, safe, climate-friendly and ecological approaches to the synthesis of lignin nanoparticles. The changeable, complex structure and recalcitrant nature of lignin makes it challenging to degrade. Researchers have discovered a small number of microorganisms that have developed enzymatic and non-enzymatic metabolic pathways to use lignin as a carbon source. These microbes show promising potential for the biodegradation of lignin. The degradation pathways of these microbes are also described, which makes the study of biological synthesis much easier. However, surface modification of lignin nanoparticles is something that is yet to be explored. This review elucidates the recent advances in the biodegradation of lignin in the ecological system. It includes the current approaches, methods for modification, new applications and research for the synthesis of lignin and lignin nanoparticles. Additionally, the intricacy of lignin’s structure, along with its chemical nature, is well-described. This article will help increase the understanding of the utilization of lignin as an economical and alternative-resource material. It will also aid in the minimization of solid waste arising from lignin.

Lignin degradation by microorganisms: A review

Lignin is an abundant plant-based biopolymer that has found applications in a variety of industries from construction to bioethanol production. This recalcitrant branched polymer is naturally degraded by many different species of microorganisms, including fungi and bacteria. These microbial lignin degradation mechanisms provide a host of possibilities to overcome the challenges of using harmful chemicals to degrade lignin biowaste in many industries. The classes and mechanisms of different microbial lignin degradation options available in nature form the primary focus of the present review. This review first discusses the chemical building blocks of lignin and the industrial sources and applications of this multifaceted polymer. The review further places emphasis on the degradation of lignin by natural means, discussing in detail the lignin degradation activities of various fungal and bacterial species. The lignin-degrading enzymes produced by various microbial species, specifically white-rot fungi, brown-rot fungi, and bacteria, are described. In the end, possible directions for future lignin biodegradation applications and research investigations have been provided.

Effects of lignocellulolytic enzymes on the fermentation profile, chemical composition, and in situ ruminal disappearance of whole-plant corn silage

The objective of this study was to examine the enzyme activities of an enzymatic complex produced by Pleurotus ostreatus in different pH and the effects of adding increased application rates of this enzymatic complex on the fermentation profile, chemical composition, and in situ ruminal disappearance of whole-plant corn silage (WPCS) at the onset of fermentation and 30 d after ensiling. The lignocellulolytic enzymatic complex was obtained through in vitro cultivation of P. ostreatus. In the first experiment, the activities of laccase, lignin peroxidase (LiP), manganese peroxidase, endo- and exo-glucanase, xylanase, and mannanase were determined at pH 3, 4, 5, and 6. In the second experiment, five application rates of enzymatic complex were tested in a randomized complete block design (0, 9, 18, 27, and 36 mg of lignocellulosic enzymes/kg of fresh whole-plant corn [WPC], corresponding to 0, 0.587, 1.156, 1.734, and 2.312 g of enzymatic complex/kg of fresh WPC, respectively). There were four replicates per treatment (vacuum-sealed bags) per opening time. Bags were opened 1, 2, 3, and 7 d after ensiling (onset of fermentation period) and 30 d after ensiling to evaluate the fermentation profile, chemical composition, and in situ dry matter and neutral fiber detergent disappearance of WPCS. Laccase had the greatest activity at pH 5 (P < 0.01), whereas manganese peroxidase and LiP had the greatest activity at pH 4 (P < 0.01; P < 0.01). There was no effect of the rate of application of enzymatic complex, at the onset of fermentation, on the fermentation profile (P > 0.21), and chemical composition (P > 0.36). The concentration of water-soluble carbohydrate quadratically decreased (P < 0.01) over the ensiling time at the onset of fermentation, leading to a quadratic increase of lactic acid (P = 0.02) and a linear increase of acetic acid (P = 0.02) throughout fermentation. Consequently, pH quadratically decreased (P < 0.01). Lignin concentration linearly decreased (P = 0.04) with the enzymatic complex application rates at 30 d of storage; however, other nutrients and fermentation profiles did not change (P > 0.11) with the enzymatic complex application rates. Addition of lignocellulolytic enzymatic complex from P. ostreatus cultivation to WPC at ensiling decreased WPCS lignin concentration 30 d after ensiling; however, it was not sufficient to improve in situ disappearance of fiber and dry matter.

Detection and removal of poly and perfluoroalkyl polluting substances for sustainable environment

PFAs (poly and perfluoroalkyl compounds) are hazardous and bioaccumulative chemicals that do not readily biodegrade or neutralize under normal environmental conditions. They have various industrial, commercial, domestic and defence applications. According to the Organization for Economic Co-operation and Development, there are around 4700 PFAs registered to date. They are present in every stream of life, and they are often emerging and are even difficult to be detected by the standard chemical methods. This review aims to focus on the sources of various PFAs and the toxicities they impose on the environment and especially on humankind. Drinking water, food packaging, industrial areas and commercial household products are the primary PFAs sources. Some of the well-known treatment methods for remediation of PFAs presented in the literature are activated carbon, filtration, reverse osmosis, nano filtration, oxidation processes etc. The crucial stage of handling the PFAs occurs in determining and analysing the type of PFA and its remedy. This paper provides a state-of-the-art review of determination & tools, and techniques for remediation of PFAs in the environment. Improving new treatment methodologies that are economical and sustainable are essential for excluding the PFAs from the environment.

Linking Genes to Traits in Fungi

Fungi are mediators of the nitrogen and carbon cycles in terrestrial ecosystems. Examining how nitrogen uptake and organic matter decomposition potential differs in fungi can provide insight into the underlying mechanisms driving fungal ecological processes and ecosystem functioning. In this study, we assessed the frequency of genes encoding for specific enzymes that facilitate nitrogen uptake and organic matter decomposition in 879 fungal genomes with fungal taxa grouped into trait-based categories. Our linked gene-trait data approach revealed that gene frequencies vary across and within trait-based groups and that trait-based categories differ in trait space. We present two examples of how this linked gene-trait approach can be used to address ecological questions. First, we show that this type of approach can help us better understand, and potentially predict, how fungi will respond to environmental stress. Specifically, we found that trait-based categories with high nitrogen uptake gene frequency increased in relative abundance when exposed to high soil nitrogen enrichment. Second, by comparing frequencies of nitrogen uptake and organic matter decomposition genes, we found that most ectomycorrhizal fungi in our dataset have similar gene frequencies to brown rot fungi. This demonstrates that gene-trait data approaches can shed light on potential evolutionary trajectories of life history traits in fungi. We present a framework for exploring nitrogen uptake and organic matter decomposition gene frequencies in fungal trait-based groups and provide two concise examples on how to use our framework to address ecological questions from a mechanistic perspective.

Characteristics and functional bacteria in a microbial consortium for rice straw lignin-degrading

The degradation of lignin is the main rate-limiting step in the bio-pulping of rice straw. A lignin-degrading bacterial consortium LDC, which can efficiently degrade lignin of reed, was screened in the early stage of our laboratory work. In present study, 7-day incubation of LDC can degrade rice straw lignin by 31.18% in mineral salt medium. The communities' structure of different incubation phases varied greatly, in which high abundance (44.78%) of Anaerocolumna was first found. The expression levels of lignin degradation enzyme class II peroxidase (AA2), vanillyl alcohol oxidase (AA4) and 1,4-benzoquinone reductase (AA6) during peak phase (48 h) were significantly up-regulated than initial phase (24 h), increasing by 112%, 165% and 67%, respectively, and 42.86% AA2 was from Thaurea; 100% AA4 was from Clostridium; 62.5% AA6 was from Pseudomonas. These provide microbial resources and data support for the industrialization of rice straw bio-pulping.

Biotransformation of Lignin by an Artificial Heme Enzyme Designed in Myoglobin With a Covalently Linked Heme Group

The conversion of Kraft lignin in plant biomass into renewable chemicals, aiming at harvesting aromatic compounds, is a challenge process in biorefinery. Comparing to the traditional chemical methods, enzymatic catalysis provides a gentle way for the degradation of lignin. Alternative to natural enzymes, artificial enzymes have been received much attention for potential applications. We herein achieved the biodegradation of Kraft lignin using an artificial peroxidase rationally designed in myoglobin (Mb), F43Y/T67R Mb, with a covalently linked heme cofactor. The artificial enzyme of F43Y/T67R Mb has improved catalytic efficiencies at mild acidic pH for phenolic and aromatic amine substrates, including Kraft lignin and the model lignin dimer guaiacylglycerol-β-guaiacyl ether (GGE). We proposed a possible catalytic mechanism for the biotransformation of lignin catalyzed by the enzyme, based on the results of kinetic UV-Vis studies and UPLC-ESI-MS analysis, as well as molecular modeling studies. With the advantages of F43Y/T67R Mb, such as the high-yield by overexpression in E. coli cells and the enhanced protein stability, this study suggests that the artificial enzyme has potential applications in the biodegradation of lignin to provide sustainable bioresource.

Lignocellulosic Waste Pretreatment Solely via Biocatalysis as a Partial Simultaneous Lignino-Holocellulolysis Process

Human endeavors generate a significant quantity of bio-waste, even lignocellulosic waste, due to rapid industrialization and urbanization, and can cause pollution to aquatic ecosystems, and contribute to detrimental animal and human health because of the toxicity of consequent hydrolysis products. This paper contributes to a new understanding of the lignocellulosic waste bio-pretreatment process from a literature review, which can provide better biorefinery operational outcomes. The simultaneous partial biological lignin, cellulose and hemicellulose lysis, i.e., simultaneous semi-lignino-holocellulolysis, is aimed at suggesting that when ligninolysis ensues, holocellulolysis is simultaneously performed for milled lignocellulosic waste instead of having a sequential process of initial ligninolysis and subsequent holocellulolysis as is currently the norm. It is presumed that such a process can be solely performed by digestive enzyme cocktails from the monkey cups of species such as Nepenthes, white and brown rot fungi, and some plant exudates. From the literature review, it was evident that the pretreatment of milled lignocellulosic waste is largely incomplete, and ligninolysis including holocellulolysis ensues simultaneously when the waste is milled. It is further proposed that lignocellulosic waste pretreatment can be facilitated using an environmentally friendly approach solely using biological means. For such a process to be understood and applied on an industrial scale, an interdisciplinary approach using process engineering and microbiology techniques is required.

Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome

The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F. velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54-95 AAs, 145-188 GHs, 55-73 GTs, 6-19 PLs, 13-59 CEs, and 7-67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.

A novel high performance in-silico screened metagenome-derived alkali-thermostable endo-β-1,4-glucanase for lignocellulosic biomass hydrolysis in the harsh conditions

Background

Lignocellulosic biomass, is a great resource for the production of bio-energy and bio-based material since it is largely abundant, inexpensive and renewable. The requirement of new energy sources has led to a wide search for novel effective enzymes to improve the exploitation of lignocellulose, among which the importance of thermostable and halotolerant cellulase enzymes with high pH performance is significant.

Results

The primary aim of this study was to discover a novel alkali-thermostable endo-β-1,4-glucanase from the sheep rumen metagenome. At first, the multi-step in-silico screening approach was utilized to find primary candidate enzymes with superior properties. Among the computationally selected candidates, PersiCel4 was found and subjected to cloning, expression, and purification followed by functional and structural characterization. The enzymes’ kinetic parameters, including V_max, K_m, and specific activity, were calculated. The PersiCel4 demonstrated its optimum activity at pH 8.5 and a temperature of 85 °C and was able to retain more than 70% of its activity after 150 h of storage at 85 °C. Furthermore, this enzyme was able to maintain its catalytic activity in the presence of different concentrations of NaCl and several metal ions contains Mg²⁺, Mn²⁺, Cu²⁺, Fe²⁺ and Ca²⁺. Our results showed that treatment with MnCl₂ could enhance the enzyme’s activity by 78%. PersiCel4 was ultimately used for enzymatic hydrolysis of autoclave pretreated rice straw, the most abundant agricultural waste with rich cellulose content. In autoclave treated rice straw, enzymatic hydrolysis with the PersiCel4 increased the release of reducing sugar up to 260% after 72 h in the harsh condition (T = 85 °C, pH = 8.5).

Conclusion

Considering the urgent demand for stable cellulases that are operational on extreme temperature and pH conditions and due to several proposed distinctive characteristics of PersiCel4, it can be used in the harsh condition for bioconversion of lignocellulosic biomass.

Ionic Liquids as Antifungal Agents for Wood Preservation

Ionic liquids represent a class of highly versatile organic compounds used extensively in the last decade for lignocellulose biomass fractionation and dissolution, as well as property modifiers for wood materials. This review is dedicated to the use of ionic liquids as antifungal agents for wood preservation. Wood preservation against fungal attack represents a relatively new domain of application for ionic liquids, emerging in the late 1990s. Comparing to other application domains of ionic liquids, this particular one has been relatively little researched. Ionic liquids may be promising as wood preservatives due to their ability to swell wood, which translates into better penetration ability and fixation into the bulk of the wood material than other conventional antifungal agents, avoiding leaching over time. The antifungal character of ionic liquids depends on the nature of their alkyl-substituted cation, on the size and position of their substituents, and of their anion. It pertains to a large variety of wood-colonizing fungi, both Basidiomycetes and Fungiimperfecti.

KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept

The relatively poor simulation of the below-ground processes is a severe drawback for many ecosystem models, especially when predicting responses to climate change and management. For a meaningful estimation of ecosystem production and the cycling of water, energy, nutrients and carbon, the integration of soil processes and the exchanges at the surface is crucial. It is increasingly recognized that soil biota play an important role in soil organic carbon and nutrient cycling, shaping soil structure and hydrological properties through their activity, and in water and nutrient uptake by plants through mycorrhizal processes. In this article, we review the main soil biological actors (microbiota, fauna and roots) and their effects on soil functioning. We review to what extent they have been included in soil models and propose which of them could be included in ecosystem models. We show that the model representation of the soil food web, the impact of soil ecosystem engineers on soil structure and the related effects on hydrology and soil organic matter (SOM) stabilization are key issues in improving ecosystem-scale soil representation in models. Finally, we describe a new core model concept (KEYLINK) that integrates insights from SOM models, structural models and food web models to simulate the living soil at an ecosystem scale.

Application of enzymatic and bacterial biodelignification systems for enhanced breakdown of model lignocellulosic wastes

This paper explores the extent to which enzymatic and bacterial biodelignification systems can breakdown lignocellulose in model wastes to potentially enhance biogas generation. Two representative lignocellulosic wastes (newspaper and softwood) commonly found largely undegraded in old landfills were used. A fungal peroxidase (lignin peroxidase) enzyme and a recently isolated lignin-degrading bacterial strain (Agrobacterium sp.) were used. Tests were conducted in stirred bioreactors with methanogens from sewage sludge added to produce biogas from breakdown products. Addition of lignin peroxidase resulted in ~20% enhancement in cumulative methane produced in newspaper reactors. It had a negative effect on wood. Agrobacterium sp. strain enhanced biodegradation of both wood (~20% higher release of soluble organic carbon and enhanced breakdown) and newspaper (~2-fold biogas yield). The findings of this paper have important implications for enhanced breakdown in old landfills that are rich in these wastes, and anaerobic operations utilising lignocellulosic wastes for higher degradation efficiencies and biogas production.

Modification of post-industrial lignin by fungal strains of the genus Trichoderma isolated from different composting stages

One of the links in the environmental management chain is the environmentally friendly utilization of the emerging post-industrial waste and improvement of the methods of processing thereof. The aim and novelty of this research was to evaluate the potential of fungi to purify wastewater containing post-industrial lignin, i.e. waste originating from the pulp and paper industry. Trichoderma were dominant in the composts with different qualities and quantities of lignocellulosic compounds. The Trichoderma strains used in the research were isolated from two lignocellulosic composts at three different time points (from 10-, 20- and 30-week-old composting mass). Eighteen strains of the genus Trichoderma were tested for their ability to biodegrade 0.2% post-industrial lignin. It was evaluated by determination of decolorization, activities of ligninolytic enzymes, and concentration of phenolic compounds in the post-culture liquid. The Trichoderma strains isolated from 10-week-old compost I and 30-week-old compost II showed the highest decolorization activity and biotransformation of dark post-industrial lignin. All strains secreted horseradish-like peroxidase (HRP-like), superoxide dismutase-like (SOD-like), xylanase, and phenolic compounds. Strains isolated from 30-week-old compost I and from 10-week-old compost II released the greatest amounts of phenolic compounds into the culture liquid containing post-industrial lignin. The strains isolated from 10- and 20-week-old compost were characterized by high SOD-like and HRP-like activity, respectively. The concentration of phenolic compounds measured with HPLC in Trichoderma fungus culture VII from compost I corresponded with the decolorization degree and high HRP-like activity. The study results indicate that the genus Trichoderma with decolorization activity isolated from the first composting stages can be used in the biotransformation of post-industrial lignin waste.

Oxalate oxidase from Abortiporus biennis - protein localisation and gene sequence analysis

We have described for the first time the localisation of oxalate oxidase (OXO, EC 1.2.3.4) in Abortiporus biennis cells, using histochemical and immunochemical methods coupled with transmission electron microscopy. Rabbit anti-oxalate oxidase immunoglobulins with anti-rabbit secondary antibody conjugated with 10-nm gold particles were used. Moreover, the formation of electron dense precipitation of reaction of diaminobenzidine (DAB) with horseradish peroxidase (HRP) for histochemical localisation of the enzyme was found. OXO was localised close to the membranous structures of the cell membranes, in membranous vesicles located close to the outer cell membrane, and vacuolar membranes surrounding vacuoles. The positive immunoreaction to OXO was also intense in cell wall areas. Moreover, we proved that gene coding for OXO was expressed in the same cultures. Corresponding mRNA was isolated, full length cDNA was synthesized, cloned and sequenced. Two copies of cupin domains were found in the sequence of amino-acids conserved domain coding for the cupin enzyme. Comparison of the genomic DNA and cDNA sequences has revealed the presence of seventeen introns in the gene. The isoelectric point of the protein was estimated at pH 4.5 and several possible N-glycosylation sites were predicted.

Biotransformation and toxicity effect of monoanthraquinone dyes during Bjerkandera adusta CCBAS 930 cultures

The aim of this study was to evaluate of possibility of biotransformation and toxicity effect of monoanthraquinone dyes in cultures of Bjerkandera adusta CCBAS 930. Phenolic compounds, free radicals, phytotoxicity (Lepidium sativum L.), ecotoxicity (Vibrio fischeri) and cytotoxicity effect were evaluated to determine the toxicity of anthraquinone dyes before and after the treatment with B. adusta CCBAS 930. More than 80% of ABBB and AB129 was removed by biodegradation (decolorization) and biosorption, but biodegradation using oxidoreductases was the main dye removing mechanism. Secondary products toxic to plants and bacteria were formed in B. adusta strain CCBAS 930 cultures, despite efficient decolorization. ABBB and AB129 metabolites increased reactive oxygen species (ROS) production in human fibroblasts, but did not increase LDH release, did not affect the resazurine reduction assay and did not change caspase-9 or caspase-3 activity.

Genomic Insights into the Fungal Lignocellulolytic Machinery of Flammulina rossica

Next-generation sequencing (NGS) of the Flammulina rossica (wood-rotting basidiomycete) genome was performed to identify its carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) revealed a total length of 35,646,506 bp (49.79% GC content). In total, 12,588 gene models of F. rossica were predicted using an ab initio gene prediction tool (AUGUSTUS). Orthologous analysis with other fungal species revealed that 7433 groups contained at least one F. rossica gene. Additionally, 12,033 (95.6%) of 12,588 genes for F. rossica proteins had orthologs among the Dikarya, and F. rossica contained 12 species-specific genes. CAZyme annotation in the F. rossica genome revealed 511 genes predicted to encode CAZymes including 102 auxiliary activities, 236 glycoside hydrolases, 94 glycosyltransferases, 19 polysaccharide lyases, 56 carbohydrate esterases, and 21 carbohydrate binding-modules. Among the 511 genes, several genes were predicted to simultaneously encode two different CAZymes such as glycoside hydrolases (GH) as well as carbohydrate-binding module (CBM). The genome information of F. rossica offers opportunities to understand the wood-degrading machinery of this fungus and will be useful for biotechnological and industrial applications.

Pretreatment of Miscanthus with biomass-degrading bacteria for increasing delignification and enzymatic hydrolysability

Biomass recalcitrance is still a main challenge for the production of biofuels and high-value products. Here, an alternative Miscanthus pretreatment method by using lignin-degrading bacteria was developed. Six efficient Miscanthus-degrading bacteria were first cultured to produce laccase by using 0.5% Miscanthus biomass as carbon source. After 1-5 days of incubation, the maximum laccase activities induced by Miscanthus in the six strains were ranged from 103 to 8091 U l-1 . Then, the crude enzymes were directly diluted by equal volumes of citrate buffer and added Miscanthus biomass to a solid concentration at 4% (w/v). The results showed that all bacterial pretreatments significantly decreased the lignin content, especially in the presence of two laccase mediators (ABTS and HBT). The lignin removal directly correlated with increases in total sugar and glucose yields after enzymatic hydrolysis. When ABTS was used as a mediator, the best lignin-degrading bacteria (Pseudomonas sp. AS1) can remove up to 50.1% lignin of Miscanthus by obtaining 2.2-fold glucose yield, compared with that of untreated biomass. Therefore, this study provided an effective Miscanthus pretreatment method by using lignin-degrading bacteria, which may be potentially used in improving enzymatic hydrolysability of biomass.

Copper promotes E. coli laccase-mediated TNT biotransformation and alters the toxicity of TNT metabolites toward Tigriopus japonicus

Although laccase is involved in the biotransformation of 2,4,6-trinitrotoluene (TNT), little is known regarding the effect of E. coli laccase on TNT biotransformation. In this study, E. coli K12 served as the parental strain to construct a laccase deletion strain and two laccase-overexpressing strains. These E. coli strains were used to investigate the effect of laccase together with copper ions on the efficiency of TNT biotransformation, the variety of TNT biotransformation products generated and the toxicity of the TNT metabolites. The results showed that the laccase level was not relevant to TNT biotransformation in the soluble fraction of the culture medium. Conversely, TNT metabolites varied in the insoluble fraction analyzed by thin-layer chromatography (TLC). The insoluble fraction from the laccase-null strain showed fewer and relatively fainter spots than those detected in the wild-type and laccase-overexpressing strains, indicating that laccase expression levels were interrelated determinants of the varieties and amounts of TNT metabolites produced. In addition, the aquatic invertebrate Tigriopus japonicus was used to assess the toxicity of the TNT metabolites. The toxicity of the TNT metabolite mixture increased when the intracellular laccase level in strains increased or when purified E. coli recombinant Laccase (rLaccase) was added to the culture medium. Thus, our results suggest that laccase activity must be considered when performing microbial TNT remediation.

Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database

Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.

Synthesis of Structurally Precise Polysiloxanes via the Piers⁻Rubinsztajn Reaction

Silicone materials are widely used, from daily life to the military industry. With the advancement of science and technology and the increasing demands of industry, the requirement for high-performance precise structural silicone materials has increased. Therefore, the most important aspect in this field is finding a breakthrough in the synthetic methods. In this review, the latest research developments in controllable morphological structure and composite structure optimized synthesis of silicone materials using the Piers⁻Rubinsztajn (PR) reaction are summarized. The advantages of the PR reaction compared with traditional synthetic routes to silicone materials are presented. The highly controllable spatial structure of silicone materials and the structural combination of biomass or inorganic materials with silicone materials results in an improvement in performance or function. The morphological control of more complex silicone materials and the synthesis of non-traditional silicone materials with composite structures through the PR reaction will be the main research directions for the development of silicone materials in the future.

Delamination of plastic-coated waste paper by enzymes of the white rot fungus Dichomitus squalens

Many paper products are coated with plastic to improve their quality and stability. However, this limits recycling and recovery options and the plastic-coated waste paper is mostly disposed in landfills. Such practices are uneconomical and contrary to sustainable waste management. In this work enzymes of the white rot fungus Dichomitus squalens were investigated for possible delamination of plastic-coated waste paper. Enzymes were found capable to release the polyethylene foil from plastic-coated paper which resulted in 88.6-91.5% mass loss. The delamination rate, however, was depended on the ratio between plastic-coated paper and volume of enzyme filtrate. Results of a consequent experiment showed that enzymes are also efficient when plastic-coated paper is treated in a sequencing batch reactor resulting in 88.2-90.6% mass loss. The system was fully functional up to the 5th cycle; afterwards, the delamination rate reduced due to high thickness of the waste paper sludge. The enzyme activity, however, was still very high; with the laccase activity at the end of the experiment above 900 U/L and manganese peroxidase above 250 U/L. Our results demonstrated, that plastic-coated waste paper has the potential to be efficiently recovered instead of being disposed in landfills.

Pretreatment of Lignocellulosic Materials as Substrates for Fermentation Processes

Lignocellulosic biomass is an abundant and renewable resource that potentially contains large amounts of energy. It is an interesting alternative for fossil fuels, allowing the production of biofuels and other organic compounds. In this paper, a review devoted to the processing of lignocellulosic materials as substrates for fermentation processes is presented. The review focuses on physical, chemical, physicochemical, enzymatic, and microbiologic methods of biomass pretreatment. In addition to the evaluation of the mentioned methods, the aim of the paper is to understand the possibilities of the biomass pretreatment and their influence on the efficiency of biofuels and organic compounds production. The effects of different pretreatment methods on the lignocellulosic biomass structure are described along with a discussion of the benefits and drawbacks of each method, including the potential generation of inhibitory compounds for enzymatic hydrolysis, the effect on cellulose digestibility, the generation of compounds that are toxic for the environment, and energy and economic demand. The results of the investigations imply that only the stepwise pretreatment procedure may ensure effective fermentation of the lignocellulosic biomass. Pretreatment step is still a challenge for obtaining cost-effective and competitive technology for large-scale conversion of lignocellulosic biomass into fermentable sugars with low inhibitory concentration.

Characterization and use of a bacterial lignin peroxidase with an improved manganese-oxidative activity

Peroxidases are well-known biocatalysts produced by all organisms, especially microorganisms, and used in a number of biotechnological applications. The enzyme DypB from the lignin-degrading bacterium Rhodococcus jostii was recently shown to degrade solvent-obtained fractions of a Kraft lignin. In order to promote the practical use, the N246A variant of DypB, named Rh_DypB, was overexpressed in E. coli using a designed synthetic gene: by employing optimized conditions, the enzyme was fully produced as folded holoenzyme, thus avoiding the need for a further time-consuming and expensive reconstitution step. By a single chromatographic purification step, > 100 mg enzyme/L fermentation broth with a > 90% purity was produced. Rh_DypB shows a classical peroxidase activity which is significantly increased by adding Mn²⁺ ions: kinetic parameters for H₂O₂, Mn²⁺, ABTS, and 2,6-DMP were determined. The recombinant enzyme shows a good thermostability (melting temperature of 63-65 °C), is stable at pH 6-7, and maintains a large part of the starting activity following incubation for 24 h at 25-37 °C. Rh_DypB activity is not affected by 1 M NaCl, 10% DMSO, and 5% Tween-80, i.e., compounds used for dye decolorization or lignin-solubilization processes. The enzyme shows broad dye-decolorization activity, especially in the presence of Mn²⁺, oxidizes various aromatic monomers from lignin, and cleaves the guaiacylglycerol-β-guaiacyl ether (GGE), i.e., the Cα-Cβ bond of the dimeric lignin model molecule of β-O-4 linkages. Under optimized conditions, 2 mM GGE was fully cleaved by recombinant Rh_DypB, generating guaiacol in only 10 min, at a rate of 12.5 μmol/min mg enzyme.

Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica

Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.

Immobilization of ligninolytic enzymes from white-rot fungi in cross-linked aggregates

Ligninolytic enzymes from white-rot fungi are widely used in biotechnological processes. However, the application of these enzymes as free enzymes is limited due to their instability and lack of reusability. Enzyme stabilization is therefore a major challenge in biocatalytic process research, and immobilization methods are desirable. Using cross-linked enzyme aggregates (CLEAs) such as magnetic CLEAs, porous-CLEAs and combi-CLEAs is a promising technique for overcoming these issues. Cross-linking methods can stabilize and immobilize enzymes by interconnecting enzyme molecules via multiple bonds using cross-linking agents such as glutaraldehyde. The high catalyst density and microporous assembly of CLEAs guarantee high catalyst activity, which, together with their long shelf life, operational stability, and reusability, provide a cost-efficient alternative to matrix-assisted immobilization approaches. Here, we review current progress in ligninolytic enzyme immobilization and provide a comprehensive review of CLEAs. Moreover, we summarize the use of these CLEAs for biocatalysis processes, bioremediation such as dye decolourization, wastewater treatment or pharmaceutically active compound elimination.

Can white-rot fungi be a real wastewater treatment alternative for organic micropollutants removal? A review

Micropollutants are a diverse group of compounds that are detected at trace concentrations and may have a negative effect on the environment and/or human health. Most of them are unregulated contaminants, although they have raised a concern in the scientific and global community and future regulation might be written in the near future. Several approaches have been tested to remove micropollutants from wastewater streams. In this manuscript, a focus is placed in reactor biological treatments that use white-rot fungi. A critical review of white-rot fungal-based technologies for micropollutant removal from wastewater has been conducted, several capabilities and limitations of such approaches have been identified and a range of solutions to overcome most of the limitations have been reviewed and/or proposed. Overall, this review argues that white-rot fungal reactors could be an efficient technology to remove micropollutants from specific wastewater streams.

Decolorization of remazol brilliant blue R with laccase from Lentinus crinitus grown in agro-industrial by-products

Lentinus crinitus is a white-rot fungus that produces laccase, an enzyme used for dye decolorization. Enzyme production depends on cultivation conditions, mainly agro-industrial by-products. We aimed to produce laccase from Lentinus crinitus with agro-industrial by-products for dye decolorization. Culture medium had coffee husk (CH) or citric pulp pellet (CP) and different nitrogen sources (urea, yeast extract, ammonium sulfate and sodium nitrate) at concentrations of 0, 0.7, 1.4, 2.8, 5.6 and 11.2 g/L. Enzymatic extract was used in the decolorization of remazol brilliant blue R. CH medium promoted greater laccase production than CP in all evaluated conditions. Urea provided the greatest laccase production for CH (37280 U/L) as well as for CP (34107 U/L). In CH medium, laccase activity was suppressed when carbon-to-nitrogen ratio changed from 4.5 to 1.56, but the other nitrogen concentrations did not affect laccase activity. For CP medium, reduction in carbon-to-nitrogen ratio from 6 to 1.76 increased laccase activity in 17%. The peak of laccase activity in CH medium occurred on the 11th day (41246 U/L) and in CP medium on the 12th day (32660 U/L). The maximum decolorization within 24 h was observed with CP enzymatic extract (74%) and with CH extract (76%).

Structural and functional characterisation of multi-copper oxidase CueO from lignin-degrading bacterium Ochrobactrum sp. reveal its activity towards lignin model compounds and lignosulfonate

The identification of enzymes responsible for oxidation of lignin in lignin-degrading bacteria is of interest for biotechnological valorization of lignin to renewable chemical products. The genome sequences of two lignin-degrading bacteria, Ochrobactrum sp., and Paenibacillus sp., contain no B-type DyP peroxidases implicated in lignin degradation in other bacteria, but contain putative multicopper oxidase genes. Multi-copper oxidase CueO from Ochrobactrum sp. was expressed and reconstituted as a recombinant laccase-like enzyme, and kinetically characterized. Ochrobactrum CueO shows activity for oxidation of β-aryl ether and biphenyl lignin dimer model compounds, generating oxidized dimeric products, and shows activity for oxidation of Ca-lignosulfonate, generating vanillic acid as a low molecular weight product. The crystal structure of Ochrobactrum CueO (OcCueO) has been determined at 1.1 Å resolution (PDB: 6EVG), showing a four-coordinate mononuclear type I copper center with ligands His495, His434 and Cys490 with Met500 as an axial ligand, similar to that of Escherichia coli CueO and bacterial azurin proteins, whereas fungal laccase enzymes contain a three-coordinate type I copper metal center. A trinuclear type 2/3 copper cluster was modeled into the active site, showing similar structure to E. coli CueO and fungal laccases, and three solvent channels leading to the active site. Site-directed mutagenesis was carried out on amino acid residues found in the solvent channels, indicating the importance for residues Asp102, Gly103, Arg221, Arg223, and Asp462 for catalytic activity. The work identifies a new bacterial multicopper enzyme with activity for lignin oxidation, and implicates a role for bacterial laccase-like multicopper oxidases in some lignin-degrading bacteria.

DATABASE

Structural data are available in the PDB under the accession number 6EVG.

Toward engineering E. coli with an autoregulatory system for lignin valorization

Efficient lignin valorization could add more than 10-fold the value gained from burning it for energy and is critical for economic viability of future biorefineries. However, lignin-derived aromatics from biomass pretreatment are known to be potent fermentation inhibitors in microbial production of fuels and other value-added chemicals. In addition, isopropyl-β-d-1-thiogalactopyranoside and other inducers are routinely added into fermentation broth to induce the expression of pathway enzymes, which further adds to the overall process cost. An autoregulatory system that can diminish the aromatics' toxicity as well as be substrate-inducible can be the key for successful integration of lignin valorization into future lignocellulosic biorefineries. Toward that goal, in this study an autoregulatory system is demonstrated that alleviates the toxicity issue and eliminates the cost of an external inducer. Specifically, this system is composed of a catechol biosynthesis pathway coexpressed with an active aromatic transporter CouP under induction by a vanillin self-inducible promoter, ADH7, to effectively convert the lignin-derived aromatics into value-added chemicals using Escherichia coli as a host. The constructed autoregulatory system can efficiently transport vanillin across the cell membrane and convert it to catechol. Compared with the system without CouP expression, the expression of catechol biosynthesis pathway with transporter CouP significantly improved the catechol yields about 30% and 40% under promoter pTrc and ADH7, respectively. This study demonstrated an aromatic-induced autoregulatory system that enabled conversion of lignin-derived aromatics into catechol without the addition of any costly, external inducers, providing a promising and economically viable route for lignin valorization.