Intracellular pathways for lignin catabolism in white-rot fungi

Efficient catalytic degradation and detoxification of 6PPD-quinone by the multifunctional enzyme system of phanerochaete chrysosporium

The widespread environmental presence and toxicity of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-quinone, 6PPD-q), a rubber-derived pollutant, necessitates effective degradation strategies. This study demonstrates for the first time that Phanerochaete chrysosporium (P. chrysosporium) achieves a 99.06 % removal rate of 6PPD-q within 7 days through adsorption combined with enzyme catalysis. The breakdown of the quinone structure, primarily driven by lignin peroxidase isoenzymes, is accompanied by carbon chain shortening and structural simplification, which enhance the bioavailability of degradation products. These metabolites are assimilated and further mineralized by the P. chrysosporium metabolic system. Comprehensive toxicity assessments using zebrafish and Escherichia coli confirmed the biosafety of all degradation products. This study provides mechanistic insights into the fungal degradation of 6PPD-q and presents a sustainable approach for mitigating the environmental risks posed by other pollutants. Furthermore, a new generation of innovative bioremediation technologies can be developed by engineering fungi to regulate extracellular electric potential and enhance catalytic enzyme activity.

In planta production of the nylon precursor beta-ketoadipate

Beta-ketoadipate (βKA) is an intermediate of the βKA pathway involved in the degradation of aromatic compounds in several bacteria and fungi. Beta-ketoadipate also represents a promising chemical for the manufacturing of performance-advantaged nylons. We established a strategy for the in planta synthesis of βKA via manipulation of the shikimate pathway and the expression of bacterial enzymes from the βKA pathway. Using Nicotiana benthamiana as a transient expression system, we demonstrated the efficient conversion of protocatechuate (PCA) to βKA when plastid-targeted bacterial-derived PCA 3,4-dioxygenase (PcaHG) and 3-carboxy-cis,cis-muconate cycloisomerase (PcaB) were co-expressed with 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (AroG) and 3-dehydroshikimate dehydratase (QsuB). This metabolic pathway was reconstituted in Arabidopsis by introducing a construct (pAtβKA) with stacked pcaG, pcaH, and pcaB genes into a PCA-overproducing genetic background that expresses AroG and QsuB (referred as QsuB-2). The resulting QsuB-2 x pAtβKA stable lines displayed βKA titers as high as 0.25 % on a dry weight basis in stems, along with a drastic reduction in lignin content and improvement of biomass saccharification efficiency compared to wild-type controls, and without any significant reduction in biomass yields. Using biomass sorghum as a potential crop for large-scale βKA production, techno-economic analysis indicated that βKA accumulated at titers of 0.25 % and 4 % on a dry weight basis could be competitively priced in the range of $2.04-34.49/kg and $0.47-2.12/kg, respectively, depending on the selling price of the residual biomass recovered after βKA extraction. This study lays the foundation for a more environmentally-friendly synthesis of βKA using plants as production hosts.

Enzymatic cleavage of model lignin dimers depends on pH, enzyme, and bond type

Lignin is composed of phenylpropanoid monomers linked by ether and carbon-carbon bonds to form a complex heterogeneous structure. Bond-specific studies of lignin-modifying enzymes (LMEs; e.g., laccases and peroxidases) are limited by the polymerization of model lignin substrates and repolymerization of cleavage products. Here we present a high throughput platform to screen LME activities on four tagged model lignin compounds that represent the β-O-4', β-β', 5-5', and 4-O-5' linkages in lignin. We utilized nanostructure-initiator mass spectrometry (NIMS) and model lignin compounds with tags containing perfluorinated and cationic moieties, which effectively limit polymerization and condensation of the substrates and their degrading products. Sub-microliter sample droplets were printed on the NIMS chip with a novel robotics method. This rapid platform enabled characterization of LMEs across a range of pH 3-10 and relative quantification of modified (typically oxidized), cleaved, and polymerized products. All tested enzymes oxidized the four substrates and cleaved the β-O-4' and β-β' substrates to monomeric products. We discovered that the active pH range depended on both the substrate and the enzyme type. This has important applications for biomass conversion to biofuels and bioproducts, where the relative percentages of different bond types in lignin varies depending on feedstock and chemical pretreatment methods.

Cultivation methods and biology of Lentinula edodes

In this study, the biological applications of cultivation methods related to cultivar selection, vegetative growth, and reproductive development in Lentinula edodes cultivation are briefly reviewed to clarify the current situation and inform future developments. The current cultivars widely used in the main production areas are derived from wild strains distributed in northern Asia. The most effective techniques for cultivar identification are molecular markers identified in two nuclear genome datasets and one mitochondrial genome dataset. The current stage of cultivar breeding is at the junction of Breeding 3.0 (biological breeding) and Breeding 4.0 (intelligent breeding). Plant breeder's rights and patents have different emphases on new breeding variety protection, with the former being the most utilized globally. L. edodes is mostly produced on synthetic logs filled with sawdust substrates. Hardwood sawdust comprises approximately 80% of the substrates. The vegetative growth of L. edodes on synthetic logs involves two distinct stages of mycelial colonization and browning. Mycelia mainly perform glycolysis, tricarboxylic acid cycle, and respiratory metabolism reactions to produce energy and intermediates for synthesizing the structural components of hyphae in the vegetative colonization stage. Upon stimulation by physiological and environmental pressures after colonization, mycelia trigger gluconeogenesis, autophagy, and secondary metabolism, increase metabolic flux of pentose phosphate pathway, activate the glyoxylate cycle, and accumulate melanin on the surface of logs to ensure growth and survival. Sexually competent mycelia can form hyphal knots as a result of reprogrammed hyphal branching patterns after a period of vegetative growth (which varies by cultivar) and stimulation by specific environmental factors. Under a genetically encoded developmental program, hyphal knots undergo aggregation, tissue differentiation, primordium formation, meiosis in the hymenium, stipe elongation, basidiospore production and maturation, and cap expansion to form mature fruiting bodies. Growers can achieve good fruiting body shape and high yield by regulating the number of young fruiting bodies and adjusting specific environmental factors. KEY POINTS: • Cultivar selection becomes less with the increasing technological requirement of L. edodes cultivation. • L. edodes mycelia showed different biological events in the mycelial colonization and browning stages. • Specific cultivar breading may be the next milestone in L. edodes cultivation.

Metabolic profiling of two white-rot fungi during 4-hydroxybenzoate conversion reveals biotechnologically relevant biosynthetic pathways

White-rot fungi are efficient organisms for the mineralization of lignin and polysaccharides into CO2 and H2O. Despite their biotechnological potential, WRF metabolism remains underexplored. Building on recent findings regarding the utilization of lignin-related aromatic compounds as carbon sources by WRF, we aimed to gain further insights into these catabolic processes. For this purpose, Trametes versicolor and Gelatoporia subvermispora were incubated in varying conditions - in static and agitation modes and different antioxidant levels - during the conversion of 4-hydroxybenzoic acid (a lignin-related compound) and cellobiose. Their metabolic responses were assessed via transcriptomics, proteomics, lipidomics, metabolomics, and microscopy analyses. These analyses reveal the significant impact of cultivation conditions on sugar and aromatic catabolic pathways, as well as lipid composition of the fungal mycelia. Additionally, this study identifies biosynthetic pathways for the production of extracellular fatty acids and phenylpropanoids - both products with relevance in biotechnological applications - and provides insights into carbon fate in nature.

Advances in lignocellulosic feedstocks for bioenergy and bioproducts

Lignocellulose, an abundant renewable resource, presents a promising alternative for sustainable energy and industrial applications. However, large-scale adoption of lignocellulosic feedstocks faces considerable obstacles, including scalability, bioprocessing efficiency, and resilience to climate change. This Review examines current efforts and future opportunities for leveraging lignocellulosic feedstocks in bio-based energy and products, with a focus on enhancing conversion efficiency and scalability. It also explores emerging biotechnologies such as CRISPR-based genome editing informed by machine learning, aimed at improving feedstock traits and reducing the environmental impact of fossil fuel dependence.

Revisiting alkali pretreatment to transform lignocellulose fermentation with integration of bioprocessible lignin

This study emphasized the synergistic production of bioprocessible lignin and carbohydrates during a sequential liquid hot water and alkali pretreatment of lignocellulose, facilitating their subsequent individual fermentation. Increasing the dose of alkaline lignin from 0 to 8 g/L inhibited cell growth in anaerobic digestion, with varying levels of inhibition observed in the following order: hydrolytic bacteria < acidogens < acetogens. Alkali pretreatment was adapted to maximize yields of bioprocessible lignin liquor without compromising utilization of the carbohydrates. Increasing the NaOH dose from 50 to 200 mg/g-feedstock monotonically improved lignin yields, but further increases in alkali loading led to a decline in lignin recovery. Volatile fatty acids production from anaerobic digestion of the carbohydrate moiety consistently increased with higher NaOH doses. The optimal conditions for maximizing lignin yields were determined to be 105 °C for 30 min, with NaOH loading in the range of 150-200 mg/g-feedstock, resulting in approximately 80 % lignin recovery, of which 35 % was biologically utilizable. Liquid hot water treatment prior to alkali pretreatment was confirmed as necessary to preserve carbohydrates of 0.1 g/g-feedstock at a low temperature of 70 °C. These findings are crucial for economically producing bioprocessible lignin without carbohydrate loss, a key step towards achieving full lignocellulose valorization.

Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium

Lignin, as the abundant carbon polymer, is essential for carbon cycle and biorefinery. Microorganisms interact to form communities for lignin biodegradation, yet it is a challenge to understand such complex interactions. Here, we develop a coastal lignin-degrading bacterial consortium (LD), through "top-down" enrichment. Sequencing and physiological analyses reveal that LD is dominated by the lignin degrader Pluralibacter gergoviae (>98%), with additional rare non-degraders. Interestingly, LD, cultured in lignin-MB medium, significantly enhances cell growth and lignin degradation as compared to P. gergoviae alone, implying a role of additional outliers. Using genome-scale metabolic models, metabolic profiling and culture experiments, modeling of inter-species interactions between P. gergoviae, Vibrio alginolyticus, Aeromonas hydrophila and Shewanella putrefaciens, unravels cross-feeding of amino acids, organic acids and alcohols between the degrader and non-degraders. Furthermore, the sub-population ratio is essential to enforce the synergy. Our study highlights the unrecognized role of outliers in lignin degradation.

Biochemical and structural characterization of enzymes in the 4-hydroxybenzoate catabolic pathway of lignin-degrading white-rot fungi

White-rot fungi (WRF) are the most efficient lignin-degrading organisms in nature. However, their capacity to use lignin-related aromatic compounds, such as 4-hydroxybenzoate, as carbon sources has only been described recently. Previously, the hydroxyquinol pathway was proposed for the bioconversion of these compounds in fungi, but gene- and structure-function relationships of the full enzymatic pathway remain uncharacterized in any single fungal species. Here, we characterize seven enzymes from two WRF, Trametes versicolor and Gelatoporia subvermispora, which constitute a four-enzyme cascade from 4-hydroxybenzoate to β-ketoadipate via the hydroxyquinol pathway. Furthermore, we solve the crystal structure of four of these enzymes and identify mechanistic differences with the closest bacterial and fungal structural homologs. Overall, this research expands our understanding of aromatic catabolism by WRF and establishes an alternative strategy for the conversion of lignin-related compounds to the valuable molecule β-ketoadipate, contributing to the development of biological processes for lignin valorization.

Metabolic mechanism of lignin-derived aromatics in white-rot fungi

White-rot fungi, such as Phanerochaete chrysosporium, play a crucial role in biodegrading lignocellulosic biomass including cellulose, hemicellulose, and lignin. These fungi utilise various extracellular and intracellular enzymes, such as lignin peroxidases, manganese peroxidases, versatile peroxidases, monooxygenases, and dioxygenases, to degrade lignin and lignin-derived aromatics, thereby significantly contributing to the global carbon cycle with potential applications in industrial bioprocessing and bioremediation. Although the metabolism of lignin fragments in P. chrysosporium has been studied extensively, the enzymes involved in fragment conversion remain largely unknown. This review provides an overview of the current knowledge regarding the metabolic pathways of lignin and its fragments by white-rot fungi. Recent studies have elucidated the intricate metabolic pathways and regulatory mechanisms of lignin-derived aromatic degradation by focusing on flavoprotein monooxygenases, intradiol dioxygenases, homogentisate dioxygenase-like proteins, and cytochrome P450 monooxygenases. Metabolic regulation of these enzymes demonstrates the adaptability of white-rot fungi in degrading lignin and lignin-derived aromatics. The interplay between the central metabolic pathways, haem biosynthesis, and haem-dependent NAD(P)H regeneration highlights the complexity of lignin degradation in white-rot fungi. These insights improve our understanding of fungal metabolism and pave the way for future studies aimed at leveraging these fungi for sustainable biotechnological applications. KEY POINTS: • White-rot fungi use enzymes to degrade lignin, and play a role in the carbon cycle. • Oxygenases are key enzymes for converting lignin-derived aromatics. • White-rot fungi adapt to metabolic changes by controlling the TCA/glyoxylate bicycle.

Intraspecies Variation Offers Potential to Improve White Rot Fungi for Increasing Degradability of Lignocellulose for Ruminants

The aim of fungal treatment of organic matter for ruminants is the improvement of its degradability. So far, such treatment appears to be time-consuming and improvement has been modest. In previous work, we observed within three white rot species that there is modest (Ceriporiopsis subvermispora) or low (Lentinula edodes and Pleurotus eryngii) variation in fiber degradation in wheat straw during seven weeks of incubation. By extending and re-examining the data from all three species, we see that strains of C. subvermispora show the largest variation and improvement in the degradability of treated wheat straw. In addition, C. subvermispora also generated the highest absolute amount of degradable organic matter, a parameter not calculated before, but is very relevant for the economic feasibility of fungal treatment. In estimating fungal growth, we found no good correlation between an increase in ergosterol and a decrease in plant biomass, indicating a variation within fungal species of the ergosterol/fungal biomass ratio and/or a variation in carbon use efficiency, which has also not been analyzed before. This work contributes to the knowledge of how fungi degrade lignocellulose and further specifies what can be targeted for breeding to make fungal pretreatment economically feasible for upgrading organic waste streams into ruminal feed.

Sustainable production of aromatic chemicals from lignin using enzymes and engineered microbes

Lignin is an aromatic biopolymer found in plant cell walls and is the most abundant source of renewable aromatic carbon in the biosphere. Hence there is considerable interest in the conversion of lignin, either derived from agricultural waste or produced as a byproduct of pulp/paper manufacture, into high-value chemicals. Although lignin is rather inert, due to the presence of ether C-O and C-C linkages, several microbes are able to degrade lignin. This review will introduce these microbes and the enzymes that they use to degrade lignin and will describe recent studies on metabolic engineering that can generate high-value chemicals from lignin bioconversion. Catabolic pathways for degradation of lignin fragments will be introduced, and case studies where these pathways have been engineered by gene knockout/insertion to generate bioproducts that are of interest as monomers for bioplastic synthesis or aroma chemicals will be described. Life cycle analysis of lignin bioconversion processes is discussed.

A Comprehensive Review of the Diversity of Fungal Secondary Metabolites and Their Emerging Applications in Healthcare and Environment

Fungi and their natural products, like secondary metabolites, have gained a huge demand in the last decade due to their increasing applications in healthcare, environmental cleanup, and biotechnology-based industries. The fungi produce these secondary metabolites (SMs) during the different phases of their growth, which are categorized into terpenoids, alkaloids, polyketides, and non-ribosomal peptides. These SMs exhibit significant biological activity, which contributes to the formulation of novel pharmaceuticals, biopesticides, and environmental bioremediation agents. Nowadays, these fungal-derived SMs are widely used in food and beverages, for fermentation, preservatives, protein sources, and in dairy industries. In healthcare, it is being used as an antimicrobial, anticancer, anti-inflammatory, and immunosuppressive drug. The usage of modern tools of biotechnology can achieve an increase in demand for these SMs and large-scale production. The present review comprehensively analyses the diversity of fungal SMs along with their emerging applications in healthcare, agriculture, environmental sustainability, and nutraceuticals. Here, the authors have reviewed the recent advancements in genetic engineering, metabolic pathway manipulation, and synthetic biology to improve the production and yield of these SMs. Advancement in fermentation techniques, bioprocessing, and co-cultivation approaches for large-scale production of SMs. Investigators further highlighted the importance of omics technologies in understanding the regulation and biosynthesis of SMs, which offers an understanding of novel applications in drug discovery and sustainable agriculture. Finally, the authors have addressed the potential for genetic manipulation and biotechnological innovations for further exploitation of fungal SMs for commercial and environmental benefits.

Pathway crosstalk between the central metabolic and heme biosynthetic pathways in Phanerochaete chrysosporium

A comprehensive analysis to survey heme-binding proteins produced by the white-rot fungus Phanerochaete chrysosporium was achieved using a biotinylated heme-streptavidin beads system. Mitochondrial citrate synthase (PcCS), glyceraldehyde 3-phosphate dehydrogenase (PcGAPDH), and 2-Cys thioredoxin peroxidase (mammalian HBP23 homolog) were identified as putative heme-binding proteins. Among these, PcCS and PcGAPDH were further characterized using heterologously expressed recombinant proteins. Difference spectra of PcCS titrated with hemin exhibited an increase in the Soret absorbance at 414 nm, suggesting that the axial ligand of the heme is a His residue. The activity of PcCS was strongly inhibited by hemin with Ki oxaloacetate of 8.7 μM and Ki acetyl-CoA of 5.8 μM. Since the final step of heme biosynthesis occurred at the mitochondrial inner membrane, the inhibition of PcCS by heme is thought to be a physiological event. The inhibitory mode of the heme was similar to that of CoA analogues, suggesting that heme binds to PcCS at His347 at the AcCoA-CoA binding site, which was supported by the homology model of PcCS. PcGAPDH was also inhibited by heme, with a lower concentration than that for PcCS. This might be caused by the different location of these enzymes. From the integration of these phenomena, it was concluded that metabolic regulations by heme in the central metabolic and heme synthetic pathways occurred in the mitochondria and cytosol. This novel pathway crosstalk between the central metabolic and heme biosynthetic pathways, via a heme molecule, is important in regulating the metabolic balance (heme synthesis, ATP synthesis, flux balance of the tricarboxylic acid (TCA) cycle and cellular redox balance (NADPH production) during fungal aromatic degradation. KEY POINTS: • A comprehensive survey of heme-binding proteins in P. chrysosporium was achieved. • Several heme-binding proteins including CS and GAPDH were identified. • A novel metabolic regulation by heme in the central metabolic pathways was found.

Oestrogen Detoxification Ability of White Rot Fungus Trametes hirsuta LE-BIN 072: Exoproteome and Transformation Product Profiling

White rot fungi, especially representatives of the genus Trametes spp. (Polyporaceae), are effective destructors of various xenobiotics, including oestrogens (phenol-like steroids), which are now widespread in the environment and pose a serious threat to the health of humans, animals and aquatic organisms. In this work, the ability of the white rot fungus Trametes hirsuta LE-BIN 072 to transform oestrone (E1) and 17β-oestradiol (E2), the main endocrine disruptors, was shown. More than 90% of the initial E1 and E2 were removed by the fungus during the first 24 h of transformation. The transformation process proceeded predominantly in the direction of the initial substrates' detoxification, with the radical oxidative coupling of E1 and E2 as well as their metabolites and the formation of less toxic dimers in various combinations. A number of minor metabolites, in particular, less toxic estriol (E3), were identified by HPLC-MS. The formation of E1 from E2 and vice versa were shown. The exoproteome of the white rot fungus during the transformation of oestrogens was studied in detail for the first time. The contribution of ligninolytic peroxidases (MnP5, MnP7 and VP2) to the process of the extracellular detoxification of oestrogens and their possible metabolites is highlighted. Thus, the studied strain appears to be a promising mycodetoxicant of phenol-like steroids in aquatic environments.

Selective Adsorption of Lignin Peroxidase on Lignin for Biocatalytic Conversion of Poplar Wood Biomass to Value-Added Chemicals

Lignin-first biorefineries aim to maximize the valorization of lignin by prioritizing its conversion over other biomass components. This study investigates the selective adsorption of lignin peroxidase (LiP) isozymes from white rot fungi Phanerochaete chrysosporium on lignin, aiming to enhance the biocatalytic conversion of poplar wood biomass into value-added chemicals. The research focuses on the adsorption characteristics of ten recombinant LiP isozymes, particularly PcLiP03, which exhibited the highest adsorption capacity on lignin and negligible adsorption on cellulose. Adsorption isotherms and structural analyses revealed that hydrophobic interactions significantly contribute to the selective adsorption of PcLiP03. Applying PcLiP03 in a continuous stirring cell system effectively converted lignin in unpretreated poplar wood to 2,6-dimethoxy-1,4-benzoquinone under ambient and mild conditions, highlighting its potential for selective lignin depolymerization in integrated biorefineries. This work underscores the importance of enzyme-substrate interactions and offers a promising approach for more efficient and sustainable biomass utilization.

Accessing monomers from lignin through carbon-carbon bond cleavage

Lignin, the heterogeneous aromatic macromolecule found in the cell walls of vascular plants, is an abundant feedstock for the production of biochemicals and biofuels. Many valorization schemes rely on lignin depolymerization, with decades of research focused on accessing monomers through C-O bond cleavage, given the abundance of β-O-4 bonds in lignin and the large number of available C-O bond cleavage strategies. Monomer yields are, however, invariably lower than desired, owing to the presence of recalcitrant C-C bonds whose selective cleavage remains a major challenge in catalysis. In this Review, we highlight lignin C-C cleavage reactions, including those of linkages arising from biosynthesis (β-1, β-5, β-β and 5-5) and industrial processing (5-CH2-5 and α-5). We examine multiple approaches to C-C cleavage, including homogeneous and heterogeneous catalysis, photocatalysis and biocatalysis, to identify promising strategies for further research and provide guidelines for definitive measurements of lignin C-C bond cleavage.

3D Printing of Wood Composites: State of the Art and Opportunities

With the production of wood waste constantly on the increase, questions relating to its recycling and reuse are becoming unavoidable. The reuse of wood and its derivatives can be achieved through the production of composite materials, using wood as a reinforcement or even as the main matrix of the material. Additive manufacturing (also known as 3D printing) is an emerging and very promising process, particularly with the use of bio-based and renewable materials such as wood or its industrial derivatives. The aim of this paper is to present an overview of additive manufacturing processes using wood as a raw material and including industrial solutions. After presenting wood and its waste products, all the additive manufacturing processes using wood or its industrial derivatives will be presented. Finally, for each 3D printing process, this review will consider the current state of research, the industrial solutions that may exist, as well as the main challenges and issues that still need to be overcome.

Enterobacter spp. isolates from an underground coal mine reveal ligninolytic activity

Lignin, the second most abundant renewable carbon source on earth, holds significant potential for producing biobased specialty chemicals. However, its complex, highly branched structure, consisting of phenylpropanoic units and strong carbon-carbon and ether bonds, makes it highly resistant to depolymerisation. This recalcitrancy highlights the need to search for robust lignin-degrading microorganisms with potential for use as industrial strains. Bioprospecting for microorganisms from lignin-rich niches is an attractive approach among others. Here, we explored the ligninolytic potential of bacteria isolated from a lignin-rich underground coalmine, the Morupule Coal Mine, in Botswana. Using a culture-dependent approach, we screened for the presence of bacteria that could grow on 2.5% kraft lignin-supplemented media and identified them using 16 S rRNA sequencing. The potential ligninolytic isolates were evaluated for their ability to tolerate industry-associated stressors. We report the isolation of twelve isolates with ligninolytic abilities. Of these, 25% (3) isolates exhibited varying robust ligninolytic ability and tolerance to various industrial stressors. The molecular identification revealed that the isolates belonged to the Enterobacter genus. Two of three isolates had a 16 S rRNA sequence lower than the identity threshold indicating potentially novel species pending further taxonomic review. ATR-FTIR analysis revealed the ligninolytic properties of the isolates by demonstrating structural alterations in lignin, indicating potential KL degradation, while Py-GC/MS identified the resulting biochemicals. These isolates produced chemicals of diverse functional groups and monomers as revealed by both methods. The use of coalmine-associated ligninolytic bacteria in biorefineries has potential.

Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries

The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.

A Combination of Transcriptome and Enzyme Activity Analysis Unveils Key Genes and Patterns of Corncob Lignocellulose Degradation by Auricularia heimuer under Cultivation Conditions

The cultivation of Auricularia heimuer, a species of edible mushroom, heavily relies on the availability of wood resources serving as substrate for the growth of the species. To ensure the sustainable development of the A. heimuer industry and optimize the utilization of corncob as a substrate, this study sought to investigate the potential use of corncob as a substrate for the cultivation of A. heimuer. The purpose of this study was to explore the utilization of corncob lignocellulose by A. heimuer at the mycelium, primordium, and fruiting stages, by specifically examining the expression profiles of both carbohydrate-active enzymes (CAZymes) and the transcriptome of differentially expressed genes (DEGs) relevant to corncob biomass degradation. The results revealed 10,979, 10,630, and 11,061 DEGs at the mycelium, primordium, and fruiting stages, respectively, while 639 DGEs were identified as carbohydrate-active enzymes. Of particular interest were 46 differentially expressed CAZymes genes that were associated directly with lignocellulose degradation. Furthermore, the study found that A. heimuer exhibited adaptive changes that enabled it to effectively utilize the cellulose present in the corncob. These changes were observed primarily at the primordium and fruiting stages. Key genes involved in lignocellulose degradation were also identified, including g6952, g8349, g12487, and g2976 at the mycelium stage, g5775, g2857, g3018, and g11016 at the primordium stage, and g10290, g2857, g12385, g7656, and g8953 at the fruiting stage. This study found that lytic polysaccharide monooxygenase (LPMO) played a crucial role in the degradation of corncob cellulose, further highlighting the complexity of the molecular mechanisms involved in the degradation of lignocellulose biomass by A. heimuer. The study sheds light on the molecular mechanisms underlying the ability of A. heimuer to degrade corncob biomass, with implications for the efficient utilization of lignocellulose resources. The findings from this study may facilitate the development of innovative biotechnologies for the transformation of corncob biomass into useful products.

Modelling optimal ligninolytic activity during plant litter decomposition

A large fraction of plant litter comprises recalcitrant aromatic compounds (lignin and other phenolics). Quantifying the fate of aromatic compounds is difficult, because oxidative degradation of aromatic carbon (C) is a costly but necessary endeavor for microorganisms, and we do not know when gains from the decomposition of aromatic C outweigh energetic costs. To evaluate these tradeoffs, we developed a litter decomposition model in which the aromatic C decomposition rate is optimized dynamically to maximize microbial growth for the given costs of maintaining ligninolytic activity. We tested model performance against > 200 litter decomposition datasets collected from published literature and assessed the effects of climate and litter chemistry on litter decomposition. The model predicted a time-varying ligninolytic oxidation rate, which was used to calculate the lag time before the decomposition of aromatic C is initiated. Warmer conditions increased decomposition rates, shortened the lag time of aromatic C oxidation, and improved microbial C-use efficiency by decreasing the costs of oxidation. Moreover, a higher initial content of aromatic C promoted an earlier start of aromatic C decomposition under any climate. With this contribution, we highlight the application of eco-evolutionary approaches based on optimized microbial life strategies as an alternative parametrization scheme for litter decomposition models.

Two Zn2Cys6-type transcription factors respond to aromatic compounds and regulate the expression of laccases in the white-rot fungus Trametes hirsuta

White-rot fungi differentially express laccases when they encounter aromatic compounds. However, the underlying mechanisms are still being explored. Here, proteomics analysis revealed that in addition to increased laccase activity, proteins involved in sphingolipid metabolism and toluene degradation as well as some cytochrome P450s (CYP450s) were differentially expressed and significantly enriched during 48 h of o-toluidine exposure, in Trametes hirsuta AH28-2. Two Zn2Cys6-type transcription factors (TFs), TH8421 and TH4300, were upregulated. Bioinformatics docking and isothermal titration calorimetry assays showed that each of them could bind directly to o-toluidine and another aromatic monomer, guaiacol. Binding to aromatic compounds promoted the formation of TH8421/TH4300 heterodimers. TH8421 and TH4300 silencing in T. hirsuta AH28-2 led to decreased transcriptional levels and activities of LacA and LacB upon o-toluidine and guaiacol exposure. EMSA and ChIP-qPCR analysis further showed that TH8421 and TH4300 bound directly with the promoter regions of lacA and lacB containing CGG or CCG motifs. Furthermore, the two TFs were involved in direct and positive regulation of the transcription of some CYP450s. Together, TH8421 and TH4300, two key regulators found in T. hirsuta AH28-2, function as heterodimers to simultaneously trigger the expression of downstream laccases and intracellular enzymes. Monomeric aromatic compounds act as ligands to promote heterodimer formation and enhance the transcriptional activities of the two TFs.IMPORTANCEWhite-rot fungi differentially express laccase isoenzymes when exposed to aromatic compounds. Clarification of the molecular mechanisms underlying differential laccase expression is essential to elucidate how white-rot fungi respond to the environment. Our study shows that two Zn2Cys6-type transcription factors form heterodimers, interact with the promoters of laccase genes, and positively regulate laccase transcription in Trametes hirsuta AH28-2. Aromatic monomer addition induces faster heterodimer formation and rate of activity. These findings not only identify two new transcription factors involved in fungal laccase transcription but also deepen our understanding of the mechanisms underlying the response to aromatics exposure in white-rot fungi.

Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440

Biological conversion of lignin from biomass offers a promising strategy for sustainable production of fuels and chemicals. However, aromatic compounds derived from lignin commonly contain methoxy groups, and O-demethylation of these substrates is often a rate-limiting reaction that influences catabolic efficiency. Several enzyme families catalyze aromatic O-demethylation, but they are rarely compared in vivo to determine an optimal biocatalytic strategy. Here, two pathways for aromatic O-demethylation were compared in Pseudomonas putida KT2440. The native Rieske non-heme iron monooxygenase (VanAB) and, separately, a heterologous tetrahydrofolate-dependent demethylase (LigM) were constitutively expressed in P. putida, and the strains were optimized via adaptive laboratory evolution (ALE) with vanillate as a model substrate. All evolved strains displayed improved growth phenotypes, with the evolved strains harboring the native VanAB pathway exhibiting growth rates ∼1.8x faster than those harboring the heterologous LigM pathway. Enzyme kinetics and transcriptomics studies investigated the contribution of selected mutations toward enhanced utilization of vanillate. The VanAB-overexpressing strains contained the most impactful mutations, including those in VanB, the reductase for vanillate O-demethylase, PP_3494, a global regulator of vanillate catabolism, and fghA, involved in formaldehyde detoxification. These three mutations were combined into a single strain, which exhibited approximately 5x faster vanillate consumption than the wild-type strain in the first 8 h of cultivation. Overall, this study illuminates the details of vanillate catabolism in the context of two distinct enzymatic mechanisms, yielding a platform strain for efficient O-demethylation of lignin-related aromatic compounds to value-added products.

Disproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency

Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed carbon-use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in Pseudomonas putida, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our 13C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent 13C-metabolic flux analysis revealed a 3-fold lower investment of sugar carbons in CO2 efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis revealed enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO2-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained the substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided perspective for predicting the microbial conversion of accessible organic matter to CO2 efflux.

Airlift bioreactor-based strategies for prolonged semi-continuous cultivation of edible Agaricomycetes

Submerged cultivation of edible filamentous fungi (Agaricomycetes) in bioreactors enables maximum mass transfer of nutrients and has the potential to increase the volumetric productivity of fungal biomass compared to solid state cultivation. These aspects are paramount if one wants to increase the range of bioactives (e.g. glucans) in convenient time frames. In this study, Trametes versicolor (M9911) outperformed four other Agaricomycetes tested strains (during batch cultivations in an airlift bioreactor). This strain was therefore further tested in semi-continuous cultivation. Continuous and semi-continuous cultivations (driven by the dilution rate, D) are the preferred bioprocess strategies for biomass production. We examined the semi-continuous cultivation of T. versicolor at dilution rates between 0.02 and 0.1 h-1. A maximum volumetric productivity of 0.87 g/L/h was obtained with a D of 0.1 h-1 but with a lower total biomass production (cell dry weight, CDW 8.7 g/L) than the one obtained at lower dilution rates (12.3 g/L at D of 0.04 and vs 13.4 g/L, at a D of 0.02 h-1). However, growth at a D of 0.1 h-1 resulted in a very short fermentation (18 h) which terminated due to washout (the specific D exceeded the maximum growth rate of the fungal biomass). At a D of 0.04 h-1, a CDW of 12.3 g/L was achieved without compromising the total residence time (184 h) of the fermentation. While the D of 0.04 h-1 and 0.07 h-1 achieved comparable volumetric productivities (0.5 g/L/h), the total duration of the fermentation at D of 0.07 h-1 was only 85 h. The highest glucan content of cells (27.8 as percentage of CDW) was obtained at a D of 0.07 h-1, while the lowest glucan content was observed in T. versicolor cells grown at a D of 0.02 h-1. KEY POINTS: • The highest reported volumetric productivity for fungal biomass was 0.87 g/L/h. • Semi-continuous fermentation at D of 0.02 h-1 resulted in 13.4 g/L of fungal biomass. • Semi-continuous fermentation at D of 0.07 h-1 resulted in fungal biomass with 28% of total glucans.

Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates

Unlike 'white rot' (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, 'brown rot' (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R2 = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R2 = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities.

From 13C-lignin to 13C-mycelium: Agaricus bisporus uses polymeric lignin as a carbon source

Plant biomass conversion by saprotrophic fungi plays a pivotal role in terrestrial carbon (C) cycling. The general consensus is that fungi metabolize carbohydrates, while lignin is only degraded and mineralized to CO2. Recent research, however, demonstrated fungal conversion of 13C-monoaromatic compounds into proteinogenic amino acids. To unambiguously prove that polymeric lignin is not merely degraded, but also metabolized, carefully isolated 13C-labeled lignin served as substrate for Agaricus bisporus, the world's most consumed mushroom. The fungus formed a dense mycelial network, secreted lignin-active enzymes, depolymerized, and removed lignin. With a lignin carbon use efficiency of 0.14 (g/g) and fungal biomass enrichment in 13C, we demonstrate that A. bisporus assimilated and further metabolized lignin when offered as C-source. Amino acids were high in 13C-enrichment, while fungal-derived carbohydrates, fatty acids, and ergosterol showed traces of 13C. These results hint at lignin conversion via aromatic ring-cleaved intermediates to central metabolites, underlining lignin's metabolic value for fungi.

Fungal bioprocessing for circular bioeconomy: Exploring lignocellulosic waste valorization

The rising global demand for sustainable and eco-friendly practices has led to a burgeoning interest in circular bioeconomy, wherein waste materials are repurposed into valuable resources. Lignocellulosic waste, abundant in agricultural residues and forestry by-products, represents a significant untapped resource. This article explores the potential of fungal-mediated processes for the valorisation of lignocellulosic waste, highlighting their role in transforming these recalcitrant materials into bio-based products. The articles delve into the diverse enzymatic and metabolic capabilities of fungi, which enable them to efficiently degrade and metabolise lignocellulosic materials. The paper further highlights key fungal species and their mechanisms involved in the breakdown of complex biomass, emphasising the importance of understanding their intricate biochemical pathways for optimising waste conversion processes. The key insights of the article will significantly contribute to advancing the understanding of fungal biotechnology for circular bioeconomy applications, fostering a paradigm shift towards a more resource-efficient and environmentally friendly approach to waste management and bio-based product manufacturing.

Novel techniques for the mass production of nutritionally improved, fungus-treated lignocellulosic biomass for ruminant nutrition

BACKGROUND

Laboratory-scale experiments have shown that treatment with selective lignin-degrading white-rot fungi improves the nutritional value and ruminal degradability of lignocellulosic biomass (LCB). However, the lack of effective field-applicable pasteurization methods has long been recognized as a major obstacle for scaling up the technique for fungal treatment of large quantities of LCB for animal feeding. In this study, wheat straw (an LCB substrate) was subjected to four field-applicable pasteurization methods - hot-water, formaldehyde fumigation, steam, and hydrated lime - and cultured with Pleurotus ostreatus grain spawn for 10, 20, and 30 days under solid-state fermentation. Samples of untreated, pasteurized but non-inoculated and fungus-treated straws were analyzed for chemical composition, aflatoxin B1 (AFB1 ), and in vitro dry matter digestibility (IVDMD), in vitro total gas (IVGP), methane (CH4 ), and volatile fatty acid (VFA) production.

RESULTS

During the 30-day fungal treatment, steam and lime pasteurized straws had the greatest loss of lignin, resulting in marked improvements in crude protein (CP), IVDMD, IVGP, and total VFAs. Irrespective of the pasteurization method, the increase in IVDMD during fungal treatment was linearly (R2  = 0.77-0.92) related to lignin-loss in the substrate during fungal treatment. The CH4 production of the fungus-treated straw was not affected by the pasteurization methods. Aflatoxin B1 was within the safe level (<5 μg kg-1 ) in all pasteurized, fungus treated straws.

CONCLUSION

Steam and lime were promising field-applicable pasteurization techniques to produce nutritionally improved fungus-treated wheat straw to feed ruminants. Lime pasteurization was more economical and did not require expensive energy inputs. © 2023 Society of Chemical Industry.

Lignin-degrading enzyme production was enhanced by the novel transcription factor Ptf6 in synergistic microbial co-culture

Synergistic microbial co-culture has been an efficient and energy-saving strategy to produce lignin-degrading enzymes (LDEs), including laccase, manganese peroxidase, and versatile peroxidase. However, the regulatory mechanism of microbial co-culture is still unclear. Herein, the extracellular LDE activities of four white-rot fungi were significantly increased by 88-544% over monoculture levels when co-cultured with Rhodotorula mucilaginosa. Ptf6 was demonstrated from the 9 million Y1H clone library to be a shared GATA transcription factor in the four fungi, and could directly bind to the laccase gene promoter. Ptf6 exists in two alternatively spliced isoforms under monoculture, namely Ptf6-α (1078 amino acids) containing Cys2/Cys2-type zinc finger and Ptf6-β (963 amino acids) lacking the complete domain. Ptf6 responded to co-culture by up-regulation of both its own transcripts and the proportion of Ptf6-α. Ptf6-α positively activated the production of most LDE isoenzymes and bound to four GATA motifs on the LDEs' promoter with different affinities. Moreover, Ptf6-regulation mechanism can be applicable to a variety of microbial co-culture systems. This study lays a theoretical foundation for further improving LDEs production and providing an efficient way to enhance the effects of biological and enzymatic pretreatment for lignocellulosic biomass conversion.

Identification and characterization of methoxy- and dimethoxyhydroquinone 1,2-dioxygenase from Phanerochaete chrysosporium

White-rot fungi, such as Phanerochaete chrysosporium, are the most efficient degraders of lignin, a major component of plant biomass. Enzymes produced by these fungi, such as lignin peroxidases and manganese peroxidases, break down lignin polymers into various aromatic compounds based on guaiacyl, syringyl, and hydroxyphenyl units. These intermediates are further degraded, and the aromatic ring is cleaved by 1,2,4-trihydroxybenzene dioxygenases. This study aimed to characterize homogentisate dioxygenase (HGD)-like proteins from P. chrysosporium that are strongly induced by the G-unit fragment of vanillin. We overexpressed two homologous recombinant HGDs, PcHGD1 and PcHGD2, in Escherichia coli. Both PcHGD1 and PcHGD2 catalyzed the ring cleavage in methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ). The two enzymes had the highest catalytic efficiency (kcat/Km) for MHQ, and therefore, we named PcHGD1 and PcHGD2 as MHQ dioxygenases 1 and 2 (PcMHQD1 and PcMHQD2), respectively, from P. chrysosporium. This is the first study to identify and characterize MHQ and DMHQ dioxygenase activities in members of the HGD superfamily. These findings highlight the unique and broad substrate spectra of PcHGDs, rendering them attractive candidates for biotechnological applications.IMPORTANCEThis study aimed to elucidate the properties of enzymes responsible for degrading lignin, a dominant natural polymer in terrestrial lignocellulosic biomass. We focused on two homogentisate dioxygenase (HGD) homologs from the white-rot fungus, P. chrysosporium, and investigated their roles in the degradation of lignin-derived aromatic compounds. In the P. chrysosporium genome database, PcMHQD1 and PcMHQD2 were annotated as HGDs that could cleave the aromatic rings of methoxyhydroquinone (MHQ) and dimethoxyhydroquinone (DMHQ) with a preference for MHQ. These findings suggest that MHQD1 and/or MHQD2 play important roles in the degradation of lignin-derived aromatic compounds by P. chrysosporium. The preference of PcMHQDs for MHQ and DMHQ not only highlights their potential for biotechnological applications but also underscores their critical role in understanding lignin degradation by a representative of white-rot fungus, P. chrysosporium.

Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste

Complex polymers represent a challenge for remediating environmental pollution and an opportunity for microbial-catalysed conversion to generate valorized chemicals. Members of the genus Streptomyces are of interest because of their potential use in biotechnological applications. Their versatility makes them excellent sources of biocatalysts for environmentally responsible bioconversion, as they have a broad substrate range and are active over a wide range of pH and temperature. Most Streptomyces studies have focused on the isolation of strains, recombinant work and enzyme characterization for evaluating their potential for biotechnological application. This review discusses reports of Streptomyces-based technologies for use in the textile and pulp-milling industry and describes the challenges and recent advances aimed at achieving better biodegradation methods featuring these microbial catalysts. The principal points to be discussed are (1) Streptomyces' enzymes for use in dye decolorization and lignocellulosic biodegradation, (2) biotechnological processes for textile and pulp and paper waste treatment and (3) challenges and advances for textile and pulp and paper effluent treatment.

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichoderma's diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.

Synergistic lignin degradation between Phanerochaete chrysosporium and Fenton chemistry is mediated through iron cycling and ligninolytic enzyme induction

Removal of recalcitrant lignin from wastewater remains a critical bottleneck in multiple aspects relating to microbial carbon cycling ranging from incomplete treatment of biosolids during wastewater treatment to limited conversion of biomass feedstock to biofuels. Based on previous studies showing that the white rot fungus Phanerochaete chrysosporium and Fenton chemistry synergistically degrade lignin, we sought to determine optimum levels of Fenton addition and the mechanisms underlying this synergy. We tested the extent of degradation of lignin under different ratios of Fenton reagents and found that relatively low levels of H2O2 and Fe(II) enhanced fungal lignin degradation, achieving 80.4 ± 1.61 % lignin degradation at 1.5 mM H2O2 and 0.3 mM Fe(II). Using a combination of whole-transcriptome sequencing and iron speciation assays, we determined that at these concentrations, Fenton chemistry induced the upregulation of 80 differentially expressed genes in P. ch including several oxidative enzymes. This study underlines the importance of non-canonical, auxiliary lignin-degrading pathways in the synergy between white rot fungi and Fenton chemistry in lignin degradation. We also found that, relative to the abiotic control, P. ch. increases the availability of Fe(II) for the production of hydroxyl radicals in the Fenton reaction by recycling Fe(III) (p < 0.001), decreasing the Fe(II) inputs necessary for lignin degradation via the Fenton reaction.

Bio-mitigation of organic pollutants using horseradish peroxidase as a promising biocatalytic platform for environmental sustainability

A wide array of environmental pollutants is often generated and released into the ecosystem from industrial and human activities. Antibiotics, phenolic compounds, hydroquinone, industrial dyes, and Endocrine-Disrupting Chemicals (EDCs) are prevalent pollutants in water matrices. To promote environmental sustainability and minimize the impact of these pollutants, it is essential to eliminate such contaminants. Although there are multiple methods for pollutants removal, many of them are inefficient and environmentally unfriendly. Horseradish peroxidase (HRP) has been widely explored for its ability to oxidize the aforementioned pollutants, both alone and in combination with other peroxidases, and in an immobilized way. Numerous positive attributes make HRP an excellent biocatalyst in the biodegradation of diverse environmentally hazardous pollutants. In the present review, we underlined the major advancements in the HRP for environmental research. Numerous immobilization and combinational studies have been reviewed and summarized to comprehend the degradability, fate, and biotransformation of pollutants. In addition, a possible deployment of emerging computational methodologies for improved catalysis has been highlighted, along with future outlook and concluding remarks.

Characterization and nutritional valorization of agricultural waste corncobs from Italian maize landraces through the growth of medicinal mushrooms

The research investigates the potential use of maize cobs (or corncobs) from five genotypes, including the B73 inbred line and four locally cultivated landraces from Northern Italy, as substrate for implementing Solid State fermentation processes with four Medicinal Mushrooms (MMs). The corncobs were characterized based on their proximate composition, lignin, phenolics content (both free and bound), and total antioxidant capacity. Among the MMs tested, Pleurotus ostreatus and Ganoderma annularis demonstrated the most robust performance. Their growth was parametrized using Image Analysis technique, and chemical composition of culture samples was characterized compared to that of corncobs alone. In all culture samples, the growth of MMs led to a significant reduction (averaging 40%) in the total phenolics contents compared to that measured in corncobs alone. However, the high content of free phenolics in the cobs negatively impacted the growth of P. ostreatus. The final MM-corncob matrix exhibited reduced levels of free sugars and starch (≤ 2.2% DW, as a sum) and increased levels of proteins (up to 5.9% DW) and soluble dietary fiber (up to 5.0% DW), with a notable trend toward higher levels of β-glucan compared to corncobs alone. This research paves the way for the use of this matrix as an active ingredient to enhance the nutritional value of food preparations.

Diverse Xylaria in the Ecuadorian Amazon and their mode of wood degradation

BACKGROUND

Xylaria is a diverse and ecologically important genus in the Ascomycota. This paper describes the xylariaceous fungi present in an Ecuadorian Amazon Rainforest and investigates the decay potential of selected Xylaria species. Fungi were collected at Yasuní National Park, Ecuador during two collection trips to a single hectare plot divided into a 10-m by 10-m grid, providing 121 collection points. All Xylaria fruiting bodies found within a 1.2-m radius of each grid point were collected. Dried fruiting bodies were used for culturing and the internal transcribed spacer region was sequenced to identify Xylaria samples to species level. Agar microcosms were used to assess the decay potential of three selected species, two unknown species referred to as Xylaria 1 and Xylaria 2 and Xylaria curta, on four different types of wood from trees growing in Ecuador including balsa (Ochroma pyramidale), melina (Gmelina arborea), saman (Samanea saman), and moral (Chlorophora tinctoria). ANOVA and post-hoc comparisons were used to test for differences in biomass lost between wood blocks inoculated with Xylaria and uninoculated control blocks. Scanning electron micrographs of transverse sections of each wood and assay fungus were used to assess the type of degradation present.

RESULTS

210 Xylaria collections were sequenced, with 106 collections belonging to 60 taxa that were unknown species, all with less than 97% match to NCBI reference sequences. Xylaria with sequence matches of 97% or greater included X. aff. comosa (28 isolates), X. cuneata (9 isolates) X. curta and X. oligotoma (7 isolates), and X. apiculta (6 isolates)., All Xylaria species tested were able to cause type 1 or type 2 soft rot degradation in the four wood types and significant biomass loss was observed compared to the uninoculated controls. Balsa and melina woods had the greatest amount of biomass loss, with as much as 60% and 25% lost, respectively, compared to the controls.

CONCLUSIONS

Xylaria species were found in extraordinary abundance in the Ecuadorian rainforest studied. Our study demonstrated that the Xylaria species tested can cause a soft rot type of wood decay and with the significant amount of biomass loss that occurred within a short incubation time, it indicates these fungi likely play a significant role in nutrient cycling in the Amazonian rainforest.

Distinct laccase expression and activity profiles of Trametes versicolor facilitate degradation of benzo[a]pyrene

A Trametes versicolor isolate from the Changbai Mountain showed promising activity in degrading benzo[a]pyrene (BaP), which is a high molecular weight (HMW) polycyclic aromatic hydrocarbon (PAH) compound. It was hypothesized that the T. versicolor isolate encode BaP-degrading enzymes, among which laccase is mostly sought after due to significant commercial potential. Genome of the T. versicolor isolate was sequenced and assembled, and seven laccase homologues were identified (TvLac1-7) as candidate genes potentially contributing to BaP degradation. In order to further identify the BaP responsive laccases, time-course transcriptomic and proteomic analyses were conducted in parallel on the T. versicolor isolate upon BaP treatment. Homologous laccases showed distinct expression patterns. Most strikingly, TvLac5 was rapidly induced in the secreted proteomes (secretomes), while TvLac2 was repressed. Recombinant laccase expression and biochemical characterization further showed corresponding enzymatic activity profiles, where TvLac5 was 21-fold more effective in BaP degradation compared to TvLac2. Moreover, TvLac5 also showed 3.6-fold higher BaP degrading activity compared to a commercial laccase product of T. versicolor origin. Therefore, TvLac5 was concluded to be a BaP-responsive enzyme from T. versicolor showing effective BaP degradation activity.

Ergosterol and Its Metabolites Induce Ligninolytic Activity in the Lignin-Degrading Fungus Phanerochaete sordida YK-624

White-rot fungi are the most important group of lignin biodegraders. Phanerochaete sordida YK-624 has higher ligninolytic activity than that of model white-rot fungi. However, the underlying mechanism responsible for lignin degradation by white-rot fungi remains unknown, and the induced compounds isolated from white-rot fungi for lignin degradation have never been studied. In the present study, we tried to screen ligninolytic-inducing compounds produced by P. sordida YK-624. After large-scale incubation of P. sordida YK-624, the culture and mycelium were separated by filtration. After the separation and purification, purified compounds were analyzed by high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance. The sterilized unbleached hardwood kraft pulp was used for the initial evaluation of ligninolytic activity. Ergosterol was isolated and identified and it induced the lignin-degrading activity of this fungus. Moreover, we investigated ergosterol metabolites from P. sordida YK-624, and the ergosterol metabolites ergosta-4,7,22-triene-3,6-dione and ergosta-4,6,8(14),22-tetraen-3-one were identified and then chemically synthesized. These compounds significantly improved the lignin-degrading activity of the fungus. This is the first report on the ligninolytic-inducing compounds produced by white-rot fungi.

Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates

Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.

Exoproteomic Study and Transcriptional Responses of Laccase and Ligninolytic Peroxidase Genes of White-Rot Fungus Trametes hirsuta LE-BIN 072 Grown in the Presence of Monolignol-Related Phenolic Compounds

Being an abundant renewable source of aromatic compounds, lignin is an important component of future bio-based economy. Currently, biotechnological processing of lignin through low molecular weight compounds is one of the conceptually promising ways for its valorization. To obtain lignin fragments suitable for further inclusion into microbial metabolism, it is proposed to use a ligninolytic system of white-rot fungi, which mainly comprises laccases and peroxidases. However, laccase and peroxidase genes are almost always represented by many non-allelic copies that form multigene families within the genome of white-rot fungi, and the contributions of exact family members to the overall process of lignin degradation has not yet been determined. In this article, the response of the Trametes hirsuta LE-BIN 072 ligninolytic system to the presence of various monolignol-related phenolic compounds (veratryl alcohol, p-coumaric acid, vanillic acid, and syringic acid) in culture media was monitored at the level of gene transcription and protein secretion. By showing which isozymes contribute to the overall functioning of the ligninolytic system of the T. hirsuta LE-BIN 072, the data obtained in this study will greatly contribute to the possible application of this fungus and its ligninolytic enzymes in lignin depolymerization processes.

Mechanistic Insights into the Biodegradation of Carbon Dots by Fungal Laccase

While carbon dots (CDs) have the potential to support the agricultural revolution, it remains obscure about their environmental fate and bioavailability by plants. Fungal laccase-mediated biotransformation of carbon nanomaterials has received little attention despite its known capacity to eliminate recalcitrant contaminants. Herein, we presented the initial investigation into the transformation of CDs by fungal laccase. The degradation rates of CDs were determined to be first-order in both substrate and enzyme. Computational docking studies showed that CDs preferentially bonded to the pocket of laccase on the basal plane rather than the edge through hydrogen bonds and hydrophobic interactions. Electrospray ionization-Fourier transform-ion cyclotron resonance mass spectrometry (ESI-FT-ICR MS) and other characterizations revealed that the phenolic/amino lignins and tannins portions in CDs are susceptible to laccase transformation, resulting in graphitic structure damage and smaller-sized fragments. By using the 13C stable isotope labeling technique, we quantified the uptake and translocation of 13C-CDs by mung bean plants. 13C-CDs (10 mg L-1) accumulated in the root, stem, and leaf were estimated to be 291, 239, and 152 μg g-1 at day 5. We also evidenced that laccase treatment alters the particle size and surface chemistry of CDs, which could facilitate the uptake of CDs by plants and reduce their nanotoxicity to plants.

Oxidation-driven lignin removal by Agaricus bisporus from wheat straw-based compost at industrial scale

Fungi are main lignin degraders and the edible white button mushroom, Agaricus bisporus, inhabits lignocellulose-rich environments. Previous research hinted at delignification when A. bisporus colonized pre-composted wheat straw-based substrate in an industrial setting, assumed to aid subsequent release of monosaccharides from (hemi-)cellulose to form fruiting bodies. Yet, structural changes and specific quantification of lignin throughout A. bisporus mycelial growth remain largely unresolved. To elucidate A. bisporus routes of delignification, at six timepoints throughout mycelial growth (15 days), substrate was collected, fractionated, and analyzed by quantitative pyrolysis-GC-MS, 2D-HSQC NMR, and SEC. Lignin decrease was highest between day 6 and day 10 and reached in total 42 % (w/w). The substantial delignification was accompanied by extensive structural changes of residual lignin, including increased syringyl to guaiacyl (S/G) ratios, accumulated oxidized moieties, and depleted intact interunit linkages. Hydroxypropiovanillone and hydroxypropiosyringone (HPV/S) subunits accumulated, which are indicative for β-|O-4' ether cleavage and imply a laccase-driven ligninolysis. We provide compelling evidence that A. bisporus is capable of extensive lignin removal, have obtained insights into mechanisms at play and susceptibilities of various substructures, thus we were contributing to understanding fungal lignin conversion.

Wood decay fungi show enhanced biodeterioration of low-density polyethylene in the absence of wood in culture media

The involvement of microorganisms in low-density polyethylene (LDPE) degradation is widely studied across the globe. Even though soil, landfills, and garbage dumps are reported to be promising niches for such organisms, recently the involvement of wood decay fungi in polyethylene degradation is highlighted. In light of this, 50 fungal samples isolated from decaying hardwoods were assessed for their wood degradation ability and for their depolymerization enzymatic activities. For the LDPE deterioration assay, 22 fungal isolates having wood decay ability and de-polymerization enzymatic activities were selected. Fungal cultures with LDPE sheets (2 cm x 10 cm x 37.5 μm) were incubated in the presence and in the absence of wood as the carbon source (C) for 45 days. Degradation was measured by weight loss, changes in tensile properties, reduction in contact angle, changes of functional groups in Fourier-transform infrared spectroscopy, Scanning electron microscopic imaging, and CO2 evolution by strum test. Among the isolates incubated in the absence of wood, Phlebiopsis flavidoalba out-performed the other fungal species showing the highest percentage of weight reduction (23.68 ± 0.34%), and the lowest contact angle (64.28° ± 5.01). Biodegradation of LDPE by P. flavidoalba was further supported by 46.79 ± 0.67% of the mass loss, and 3.07 ± 0.13% of CO2 emission (mg/L) in the strum test. The most striking feature of the experiment was that all the isolates showed elevated degradation of LDPE in the absence of wood than that in the presence of wood. It is clear that in the absence of a preferred C source, wood decay fungi thrive to utilize any available C source (LDPE in this case) showing the metabolic adaptability of fungi to survive under stressful conditions. A potential mechanism for LDPE degradation is also proposed.

The secretome of Agaricus bisporus: Temporal dynamics of plant polysaccharides and lignin degradation

Despite substantial lignocellulose conversion during mycelial growth, previous transcriptome and proteome studies have not yet revealed how secretomes from the edible mushroom Agaricus bisporus develop and whether they modify lignin models in vitro. To clarify these aspects, A. bisporus secretomes collected throughout a 15-day industrial substrate production and from axenic lab-cultures were subjected to proteomics, and tested on polysaccharides and lignin models. Secretomes (day 6-15) comprised A. bisporus endo-acting and substituent-removing glycoside hydrolases, whereas β-xylosidase and glucosidase activities gradually decreased. Laccases appeared from day 6 onwards. From day 10 onwards, many oxidoreductases were found, with numerous multicopper oxidases (MCO), aryl alcohol oxidases (AAO), glyoxal oxidases (GLOX), a manganese peroxidase (MnP), and unspecific peroxygenases (UPO). Secretomes modified dimeric lignin models, thereby catalyzing syringylglycerol-β-guaiacyl ether (SBG) cleavage, guaiacylglycerol-β-guaiacyl ether (GBG) polymerization, and non-phenolic veratrylglycerol-β-guaiacyl ether (VBG) oxidation. We explored A. bisporus secretomes and insights obtained can help to better understand biomass valorization.

Multi-stage nuclear transcriptomic insights of morphogenesis and biparental role changes in Lentinula edodes

Based on six offspring with different mitochondrial (M) and parental nuclear (N) genotypes, the multi-stage morphological characteristics and nuclear transcriptomes of Lentinula edodes were compared to investigate morphogenesis mechanisms during cultivation, the key reason for cultivar resistance to genotype changes, and regulation related to biparental role changes. Six offspring had specific transcriptomic data and morphological characteristics that were mainly regulated by the two parental nuclei, followed by the cytoplasm, at different growth stages. Importing a wild N genotype easily leads to failure or instability of fruiting; however, importing wild M genotypes may improve cultivars. Major facilitator superfamily (MFS) transporter genes encoding specific metabolites in spawns may play crucial roles in fruiting body formation. Pellets from submerged cultivation and spawns from sawdust substrate cultivation showed different carbon metabolic pathways, especially in secondary metabolism, degradation of lignin, cellulose and hemicellulose, and plasma membrane transport (mainly MFS). When the stage of small young pileus (SYP) was formed on the surface of the bag, the spawns inside were mainly involved in nutrient accumulation. Just broken pileus (JBP) showed a different expression of plasma membrane transporter genes related to intracellular material transport compared to SYP and showed different ribosomal proteins and cytochrome P450 functioning in protein biosynthesis and metabolism than near spreading pileus (NSP). Biparental roles mainly regulate offspring metabolism, growth, and morphogenesis by differentially expressing specific genes during different vegetative growth stages. Additionally, some genes encoding glycine-rich RNA-binding proteins, F-box, and folliculin-interacting protein repeat-containing proteins may be related to multi-stage morphogenesis. KEY POINTS: • Replacement of nuclear genotype is not suitable for cultivar breeding of L. edodes. • Some genes show a biparental role-divergent expression at mycelial growth stage. • Transcriptomic changes of some sawdust substrate cultivation stages have been elucidated.

Advances in microbial pretreatment for biorefining of perennial grasses

Perennial grasses are potentially abundant sources of biomass for biorefineries, which can produce high yields with low input requirements, and many added environmental benefits. However, perennial grasses are highly recalcitrant to biodegradation and may require pretreatment before undergoing many biorefining pathways. Microbial pretreatment uses the ability of microorganisms or their enzymes to deconstruct plant biomass and enhance its biodegradability. This process can enhance the enzymatic digestibility of perennial grasses, enabling saccharification with cellulolytic enzymes to produce fermentable sugars and derived fermentation products. Similarly, microbial pretreatment can increase the methanation rate when the grasses are used to produce biogas through anaerobic digestion. Microorganisms can also increase the digestibility of the grasses to improve their quality as animal feed, enhance the properties of grass pellets, and improve biomass thermochemical conversion. Metabolites produced by fungi or bacteria during microbial pretreatment, such as ligninolytic and cellulolytic enzymes, can be further recovered as added-value products. Additionally, the action of the microorganisms can release chemicals with commercialization potential, such as hydroxycinnamic acids and oligosaccharides, from the grasses. This review explores the recent advances and remaining challenges in using microbial pretreatment for perennial grasses with the goal of obtaining added-value products through biorefining. It emphasizes recent trends in microbial pretreatment such as the use of microorganisms as part of microbial consortia or in unsterilized systems, the use and development of microorganisms and consortia capable of performing more than one biorefining step, and the use of cell-free systems based on microbial enzymes. KEY POINTS: • Microorganisms or enzymes can reduce the recalcitrance of grasses for biorefining • Microbial pretreatment effectiveness depends on the grass-microbe interaction • Microbial pretreatment can generate value added co-products to enhance feasibility.

Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology

Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational framework, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.