Possible biochemical roles of oxalic acid as a low molecular weight compound involved in brown-rot and white-rot wood decays

Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes)

The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded program. Fruiting bodies reached the highest complexity levels in the Agaricomycetes; yet, the underlying genetics is currently poorly known. In this work, we functionally characterized a highly conserved gene termed snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologs of snb1 are present in almost all agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. snb1 deletion mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes, and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed differentially regulated genes and gene families that, based on wild-type RNA-Seq data, were upregulated early during development and showed tissue-specific expression, suggesting a potential role in differentiation. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying developmental patterning in the Agaricomycetes.

IMPORTANCE

Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures, with a spatially and temporally integrated developmental program that is, however, currently poorly known. In this study, we present a novel, conserved gene family, Snowball (snb), termed after the unique, differentiation-less fruiting body morphology of snb1 knockout strains in the model mushroom Coprinopsis cinerea. snb is a gene of unknown function that is highly conserved among agaricomycetes and encodes a protein of unknown function. A comparative transcriptomic analysis of the early developmental stages of differentiated wild-type and non-differentiated mutant fruiting bodies revealed conserved differentially expressed genes which may be related to tissue differentiation and developmental patterning fruiting body development.

Interaction of oxalate with β-glucan: Implications for the fungal extracellular matrix, and metabolite transport

β-glucan is the major component of the extracellular matrix (ECM) of many fungi, including wood degrading fungi. Many of these species also secrete oxalate into the ECM. Our research demonstrates that β-glucan forms a novel, previously unreported, hydrogel at room temperature with oxalate. Oxalate was found to alter the rheometric properties of the β-glucan hydrogels, and modeling showed that β-glucan hydrogen bonds with oxalate in a non-covalent matrix. Change of oxalate concentration also impacted the diffusion of a high-molecular-weight protein through the gels. This finding has relevance to the diffusion of extracellular enzymes into substrates and helps to explain why some types of wood-decay fungi rely on non-enzymatic degradation schemes for carbon cycling. Further, this research has potential impact on the diffusion of metabolites in association with pathogenic/biomedical fungi.

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

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

Rock phosphate solubilization by abiotic and fungal-produced oxalic acid: reaction parameters and bioleaching potential

Oxalic acid-producing fungi play an important role in biogeochemical transformations of rocks and minerals and possess biotechnological potential for extraction of valuable elements from primary or waste ores and other solid matrices. This research investigates the extraction of phosphate from rock phosphate (RP) by oxalic acid. Reaction parameters were derived using pure oxalic acid solutions to solubilize RP. It was found that the oxalic acid concentration was the main factor driving reaction kinetics. Excess oxalic acid could retard the reaction due to calcium oxalate encrustation on RP surfaces. However, complete P extraction was reached at stoichiometric proportions of apatite and oxalic acid. This reaction reached completion after 168 h, although most of the P (up to 75%) was released in less than 1 h. Most of the Ca released from the apatite formed sparingly soluble calcium oxalate minerals, with a predominance of whewellite over weddellite. Bioleaching of RP employing biomass-free spent culture filtrates containing oxalic acid (100 mM) produced by Aspergillus niger extracted ~ 74% of the P contained in the RP. These findings contribute to a better understanding of the reaction between apatite and oxalic acid and provide insights for potential applications of this process for biotechnological production of phosphate fertilizer.

Antifungal Effect of Copper Nanoparticles against Fusarium kuroshium, an Obligate Symbiont of Euwallacea kuroshio Ambrosia Beetle

Copper nanoparticles (Cu-NPs) have shown great antifungal activity against phytopathogenic fungi, making them a promising and affordable alternative to conventional fungicides. In this study, we evaluated the antifungal activity of Cu-NPs against Fusarium kuroshium, the causal agent of Fusarium dieback, and this might be the first study to do so. The Cu-NPs (at different concentrations) inhibited more than 80% of F. kuroshium growth and were even more efficient than a commercial fungicide used as a positive control (cupric hydroxide). Electron microscopy studies revealed dramatic damage caused by Cu-NPs, mainly in the hyphae surface and in the characteristic form of macroconidia. This damage was visible only 3 days post inoculation with used treatments. At a molecular level, the RNA-seq study suggested that this growth inhibition and colony morphology changes are a result of a reduced ergosterol biosynthesis caused by free cytosolic copper ions. Furthermore, transcriptional responses also revealed that the low- and high-affinity copper transporter modulation and the endosomal sorting complex required for transport (ESCRT) are only a few of the distinct detoxification mechanisms that, in its conjunction, F. kuroshium uses to counteract the toxicity caused by the reduced copper ion.

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.

Preharvest Treatment with Oxalic Acid Improves Postharvest Storage of Lemon Fruit by Stimulation of the Antioxidant System and Phenolic Content

Lemon trees (Citrus limon (L.) Burm. F) were treated monthly with oxalic acid (OA) at 0.1, 0.5, and 1 mM from initial fruit growth on the tree until harvest in2019. The experiment was repeated in 2020, with the application of OA 1 mM (according to the best results of 2019). In both years, fruit from OA-treated trees and the controls were stored for 35 days at 10 °C. Results showed that all treatments reduced weight loss (WL) and maintained higher firmness, total soluble solids (TSS), and total acidity (TA) than in the controls. Meanwhile, colour (hue angle) did not show significant differences. The activity of antioxidant enzymes, catalase (CAT), ascorbate peroxidase (APX), and peroxidase (POD) in the flavedo of the fruit from the OA-treated trees was higher than in the controls at harvest and after 35 days of storage. Similarly, the total phenolic content (TPC) in the flavedo and juice of the fruit from the OA-treated trees were higher than in the controls. The increase in the activity of the antioxidant enzymes and TPC started with the first preharvest OA treatment and were maintained during fruit development on the tree until harvest. Preharvest OA treatments enhanced the antioxidant system of the lemon fruits, reducing the postharvest incidence of decay. Thus, OA could be a useful tool to increase the quality and functional properties of lemon fruits.

Simultaneous Determination of 13 Organic Acids in Liquid Culture Media of Edible Fungi Using High-Performance Liquid Chromatography

The study aimed at detecting 13 organic acids (oxalic acid, maleic acid, citric acid, tartaric acid, malic acid, quinic acid, succinic acid, fumaric acid, formic acid, acetic acid, propionic acid, isobutyric acid, and butyric acid) by establishing a high-performance liquid chromatography (HPLC). The analysis was performed using two sugar columns, i.e., SH1011 column and KC-811 column. The optimal conditions were as follows: 4 mmol/L HClO₄ solution as the eluent with UV-visible detector (210 nm), a flow rate of 1 mL/min at the temperature of 60°C, and the injection volume at 10 μL. The results showed that all the calibration curves had excellent linearity (R ² > 0.9991) within the test ranges. The RSD values of the thirteen analytes were lower than 2.94% at three levels, the recoveries were 91.9%-102.0%, the limit of detection (LOD) was between 0.05 and 10.63 μg/mL, and the quantification (LOQ) was between 0.10 and 19.53 μg/mL. Finally, the proposed methodology was successfully applied for the analysis of organic acids in the culture medium of edible fungi. In conclusion, the study findings proved that the method was sensitive, accurate, reproducible, and could be readily applied to analyze the organic acids in the samples.

Decomposition of spruce wood and release of volatile organic compounds depend on decay type, fungal interactions and enzyme production patterns

Effect of three wood-decaying fungi on decomposition of spruce wood was studied in solid-state cultivation conditions for a period of three months. Two white rot species (Trichaptum abietinum and Phlebia radiata) were challenged by a brown rot species (Fomitopsis pinicola) in varying combinations. Wood decomposition patterns as determined by mass loss, carbon to nitrogen ratio, accumulation of dissolved sugars and release of volatile organic compounds (VOCs) were observed to depend on both fungal combinations and growth time. Similar dependence of fungal species combination, either white or brown rot dominated, was observed for secreted enzyme activities on spruce wood. Fenton chemistry suggesting reduction of Fe³⁺ to Fe²⁺ was detected in the presence of F. pinicola, even in co-cultures, together with substantial degradation of wood carbohydrates and accumulation of oxalic acid. Significant correlation was perceived with two enzyme activity patterns (oxidoreductases produced by white rot fungi; hydrolytic enzymes produced by the brown rot fungus) and wood degradation efficiency. Moreover, emission of four signature VOCs clearly grouped the fungal combinations. Our results indicate that fungal decay type, either brown or white rot, determines the loss of wood mass and decomposition of polysaccharides as well as the pattern of VOCs released upon fungal growth on spruce wood.

Illustration of the Effects of Five Fungi on Acacia saligna Wood Organic Acids and Ultrastructure Alterations in Wood Cell Walls by HPLC and TEM Examinations

In the present study, Acacia saligna (Labill.) H.L.Wendl. wood blocks with dimensions of 0.5 × 1 × 2 cm were inoculated with five molds (Aspergillus niger, A. flavus, Alternaria tenuissima, Fusarium culmorum, and Trichoderma harzianum) and the changes in the organic acids (oxalic, citric, tartaric, succinic, glutaric, acetic, propionic, and butyric) of powdered wood were analyzed by HPLC. The effects of the five inoculated fungi on the alterations to the wood cell wall ultrastructures were examined by TEM. The wood became more acidic as it was inoculated with the studied fungi. From the HPLC analysis, the oxalic acid (293.34 µg/g o.d.) in the A. saligna, A. tenuissima (167.33 µg/g o.d.), and T. harzianum (245.01 µg/g o.d.) wood decreased, but it increased in the A. flavus (362.08 µg/g o.d.), A. niger (1202.53 µg/g o.d.), and F. culmorum (431.85 µg/g o.d.) inoculated wood. Citric acid was observed in the wood inoculated with A. flavus (110 µg/g o.d) and A. niger (2499.63 µg/g o.d). Tartaric (1150.98 µg/g o.d), acetic (2.04 µg/g o.d), and propionic (1.79 µg/g o.d) acids were found in the wood inoculated with A. niger. Butyric acid was found in small amounts. A loss of wood substances appeared as the electron-lucent increased in the middle lamella and the layers of the secondary wall. Within the secondary cell wall regions, checks and splits were also noted, which resulted from the effects of the acids on the carbohydrates, according to the fungus type and the acids. In conclusion, increasing the amount of organic acids in the wood samples through inoculation with fungi results in more degradations in the wood, especially in the wood inoculated with A. niger.

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.

Starch-degrading enzymes from the brown-rot fungus Fomitopsis palustris

Brown-rot fungi preferentially degrade softwood and cause severe breakdown of wooden structures. At the initial stage of the brown-rot decay, penetrating hyphae of the fungi are observed in ray parenchyma. Since starch grains are known to be present in the ray parenchyma of sapwood, investigation of the functions and roles of the starch-degrading enzymes is important to understand the initial stage of brown-rot decay. We purified and characterized two starch-degrading enzymes, an α-amylase (FpAmy13A) and a glucoamylase (FpGLA15A), from the brown-rot fungus, Fomitopsis palustris, and cloned the corresponding genes. The optimal temperature for both enzymes was 60 °C. FpAmy13A showed higher activity at a broad range of pH from 2.0 to 5.0, whereas FpGLA15A was most active at pH 5.0-6.0. Notable thermal stability was found for FpGLA15A. Approximately 25% of the activity remained even after treatment at 100 °C for 30 min in sodium phosphate buffer at pH 7.0. These different characteristics imply the different roles of these enzymes in the starch degradation of wood.

Aspergillus niger enhances oxalate production as a response to phosphate deficiency induced by aluminium(III)

This paper investigates Aspergillus niger's behaviour in the presence of mobile Al³⁺ species by evaluating the changes in oxalate exudation at various aluminium contents. When the fungus was exposed to Al³⁺, no significant changes in oxalate production were observed until 100 mg.L^-1 aluminium was reached resulting in oxalate production decrease by 18.2%. By stripping the culture medium completely of phosphate, even more prominent decrease by 34.8% and 67.1% at 10 and 100 mg.L^-1 aluminium was observed, respectively, indicating the phosphate's significance instead of Al³⁺ in oxalate production. Our results suggest that the low phosphate bioavailability, which most likely resulted from its interaction with Al³⁺, stimulated the overproduction of oxalate by A. niger. Furthermore, when the fungus was incubated in aluminium-free media supplemented with 0.1 mM of phosphate, oxalate production increased up to 281.5 μmol.g^-1, while at 1.85 mM of available phosphate only 80.7 μmol.g^-1 of oxalate was produced. This indicates that oxalic acid is produced by fungus not as a mean to detoxify aluminium, but as an attempt to gain access to additional phosphate.

Wood Modification by Furfuryl Alcohol Resulted in a Delayed Decomposition Response in Rhodonia (Postia) placenta

Fungi are important decomposers of woody biomass in natural habitats. Investigation of the mechanisms employed by decay fungi in their attempt to degrade wood is important for both the basic scientific understanding of ecology and carbon cycling in nature and for applied uses of woody materials. For wooden building materials, long service life and carbon storage are essential, but decay fungi are responsible for massive losses of wood in service. Thus, the optimization of durable wood products for the future is of major importance. In this study, we have investigated the fungal genetic response to furfurylated wood, a commercial environmentally benign wood modification approach that improves the service life of wood in outdoor applications. Our results show that there is a delayed wood decay by the fungus as a response to furfurylated wood, and new knowledge about the mechanisms behind the delay is provided.

The aim of this study was to investigate differential expression profiles of the brown rot fungus Rhodonia placenta (previously Postia placenta) harvested at several time points when grown on radiata pine (Pinus radiata) and radiata pine with three different levels of modification by furfuryl alcohol, an environmentally benign commercial wood protection system. The entire gene expression pattern of a decay fungus was followed in untreated and modified wood from initial to advanced stages of decay. The results support the current model of a two-step decay mechanism, with the expression of genes related to initial oxidative depolymerization, followed by an accumulation of transcripts of genes related to the hydrolysis of cell wall polysaccharides. When the wood decay process is finished, the fungus goes into starvation mode after five weeks when grown on unmodified radiata pine wood. The pattern of repression of oxidative processes and oxalic acid synthesis found in radiata pine at later stages of decay is not mirrored for the high-furfurylation treatment. The high treatment level provided a more unpredictable expression pattern throughout the incubation period. Furfurylation does not seem to directly influence the expression of core plant cell wall-hydrolyzing enzymes, as a delayed and prolonged, but similar, pattern was observed in the radiata pine and the modified experiments. This indicates that the fungus starts a common decay process in the modified wood but proceeds at a slower pace as access to the plant cell wall polysaccharides is restricted. This is further supported by the downregulation of hydrolytic enzymes for the high treatment level at the last harvest point (mass loss, 14%). Moreover, the mass loss does not increase during the last weeks. Collectively, this indicates a potential threshold for lower mass loss for the high-furfurylation treatment.

IMPORTANCE Fungi are important decomposers of woody biomass in natural habitats. Investigation of the mechanisms employed by decay fungi in their attempt to degrade wood is important for both the basic scientific understanding of ecology and carbon cycling in nature and for applied uses of woody materials. For wooden building materials, long service life and carbon storage are essential, but decay fungi are responsible for massive losses of wood in service. Thus, the optimization of durable wood products for the future is of major importance. In this study, we have investigated the fungal genetic response to furfurylated wood, a commercial environmentally benign wood modification approach that improves the service life of wood in outdoor applications. Our results show that there is a delayed wood decay by the fungus as a response to furfurylated wood, and new knowledge about the mechanisms behind the delay is provided.

Recent Advances in Applications of Acidophilic Fungi to Produce Chemicals

Processing of fossil fuels is the major environmental issue today. Biomass utilization for the production of chemicals presents an alternative to simple energy generation by burning. Lignocellulosic biomass (cellulose, hemicellulose and lignin) is abundant and has been used for variety of purposes. Among them, lignin polymer having phenyl-propanoid subunits linked together either through C-C bonds or ether linkages can produce chemicals. It can be depolymerized by fungi using their enzyme machinery (laccases and peroxidases). Both acetic acid and formic acid production by certain fungi contribute significantly to lignin depolymerization. Fungal natural organic acids production is thought to have many key roles in nature depending upon the type of fungi producing them. Biological conversion of lignocellulosic biomass is beneficial over physiochemical processes. Laccases, copper containing proteins oxidize a broad spectrum of inorganic as well as organic compounds but most specifically phenolic compounds by radical catalyzed mechanism. Similarly, lignin peroxidases (LiP), heme containing proteins perform a vital part in oxidizing a wide variety of aromatic compounds with H₂O₂. Lignin depolymerization yields value-added compounds, the important ones are aromatics and phenols as well as certain polymers like polyurethane and carbon fibers. Thus, this review will provide a concept that biological modifications of lignin using acidophilic fungi can generate certain value added and environmentally friendly chemicals.

Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution

Extensive research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.

A potential mechanism for degradation of 4,5-dichloro-2-(n-octyl)-3[2H]-isothiazolone (DCOIT) by brown-rot fungus Gloeophyllum trabeum

This study aims to investigate the biodegradation of 4,5-dichloro-2-(n-octyl)-3[2H]-isothiazolone (DCOIT) by a brown-rot fungus Gloeophyllum trabeum as well as the involved mechanism. In the present study, the retentions of DCOIT in treated Masson pine (Pinus massoniana) (MP) chips were determined periodically after incubation with G. trabeum. Then a Fenton-like reaction, known as the chelator-mediated Fenton (CMF) chemistry was used to degrade DCOIT that mimics the degradation pathway of DCOIT by typical brown-rot fungi, and the degradation intermediates were further analyzed. The results demonstrated that DCOIT was rapidly depleted in the early stages of incubation by G. trabeum. The CMF treatment was shown to oxidatively decompose DCOIT by producing reactive oxygen species. This evidence suggests that the CMF chemistry employed by brown-rot fungi contributes to the rapid depletion of DCOIT during G. trabeum exposure, although this does not rule out other possible mechanisms for the biodegradation of DCOIT. The new findings give new insights into the mechanism for the biodegradation of organic biocides, and potentially provide an efficient approach for the removal of organic pollutants in the contaminated water.

The (oxalato)aluminate complex as an antimicrobial substance protecting the "shiro" of Tricholoma matsutake from soil micro-organisms

Tricholoma matsutake, a basidiomycete, forms ectomycorrhizas with Pinus densiflora as the host tree. Its fruiting body, "matsutake" in Japanese, is an edible and highly prized mushroom, and it grows in a circle called a fairy ring. Beneath the fairy ring of T. matsutake, a whitish mycelium-soil aggregated zone, called "shiro" in Japanese, develops. The front of the shiro, an active mycorrhizal zone, functions to gather nutrients from the soil and roots to nourish the fairy ring. Bacteria and sporulating fungi decrease from the shiro front, whereas they increase inside and outside the shiro front. Ohara demonstrated that the shiro front exhibited antimicrobial activity, but the antimicrobial substance has remained unidentified for 50 years. We have identified the antimicrobial substance as the (oxalato)aluminate complex, known as a reaction product of oxalic acid and aluminum phosphate to release soluble phosphorus. The complex protects the shiro from micro-organisms, and contributes to its development.

A genomics-informed study of oxalate and cellulase regulation by brown rot wood-degrading fungi

Wood-degrading fungi that selectively remove carbohydrates (brown rot) combine Fenton-based oxidation and enzymatic hydrolysis to degrade wood. These two steps are incompatible in close proximity. To explain this, brown rot fungi may stagger oxidative reactions ahead of hydrolysis, but the scale and environmental controls for such a mechanism have not been resolved in solid wood. Here, we focused on one reaction control parameter, oxalate. In coordination with Fe³⁺-reducing compounds (e.g., 2,5-dimethoxyhydroquinone), oxalate can either promote Fenton chemistry by mobilizing Fe³⁺ as mono-oxalates (facilitative) or inhibit Fenton chemistry (protective) by restricting reducibility and the formation of Fenton's reagent as Fe³⁺/Fe²-(oxalate)_2,3. Here, we sectioned wood wafers colonized directionally by Postia placenta and Gloeophyllum trabeum to map end-to-end the expression of oxalate synthesis genes and to overlay enzyme activities, metabolites, and wood modifications. Near advancing hyphal fronts, oxaloacetase expression was up upregulated for both fungi, while regulation patterns of paralogous of isocitrate lyases and glyoxylate dehydrogenases varied, suggesting different physiological roles. Oxalate decarboxylase (ODC) expression in G. trabeum was induced in more decayed wood behind the hyphal front, but was constitutively expressed in all P. placenta sections. Relative ODC activities increased and oxalate levels stabilized in more decayed wood behind the hyphal front. Endoglucanase (EG) activity, on the other hand, peaked for both fungi in later decay stages. These oxalate optimization patterns are in line with previous whole-block 'spiking' experiments tracking oxalate, but we provide here information on its genetic controls across a spatial gradient. As a complement, we also demonstrate in vitro the plausibility of a protective role for oxalate, to emphasize that these fungi might be optimizing oxalate at a given level to maximize Fenton reactions but to minimize oxidative damage.

Evaluation of Pb (II) biosorption utilizing sugarcane bagasse colonized by Basidiomycetes

The contamination of water resources by metallic ions is a serious risk to public health and the environment. Therefore, a great emphasis has been given to alternative biosorption methods that are based on the retention of aqueous-solution pollutants; in the last decades, several agricultural residues have been explored as low-cost adsorbent. In this study, the ability of Pb (II) biosorption using sugarcane bagasse modified by different fungal species was evaluated. The presence of carbonyl, hydroxyl, and carboxyl groups in the biosorbent was observed by spectroscopy in the infrared region. By scanning electron microscopy, changes in the morphology of modified material surfaces were observed. The highest adsorption capacity occurred at pH 5.0, while the shorter adsorbate-adsorbent equilibrium was at 20 min, and the system followed the pseudo-second-order model. The maximum biosorption in isotherms was found at 58.34 mg g(-1) for modified residue by Pleurotus ostreatus U2-11, and the system followed the Langmuir isotherm. The biosorption process was energetically spontaneous with low desorption values. This modification showed great potential for filters to remove Pb (II) and provide the preservation of water resources and animal health.

Oxalic acid: a signal molecule for fungus-feeding bacteria of the genus Collimonas?

Mycophagous (=fungus feeding) soil bacteria of the genus Collimonas have been shown to colonize and grow on hyphae of different fungal hosts as the only source of energy and carbon. The ability to exploit fungal nutrient resources might require a strategy for collimonads to sense fungi in the soil matrix. Oxalic acid is ubiquitously secreted by soil fungi, serving different purposes. In this study, we investigated the possibility that collimonads might use oxalic acid secretion to localize a fungal host and move towards it. We first confirmed earlier indications that collimonads have a very limited ability to use oxalic acid as growth substrate. In a second step, with using different assays, we show that oxalic acid triggers bacterial movement in such a way that accumulation of cells can be expected at micro-sites with high free oxalic acid concentrations. Based on these observations we propose that oxalic acid functions as a signal molecule to guide collimonads to hyphal tips, the mycelial zones that are most sensitive for mycophagous bacterial attack.

Oxalic acid and sclerotial differentiation of Polyporus umbellatus

The present investigation aimed to uncover the effects of exogenous oxalic acid during the sclerotial formation of Polyporus umbellatus, with an emphasis on determining the content of the endogenic oxalic acid in the fungus. To this end, the oxalic acid content of the vegetative mycelia, sclerotia, culture mediums and sclerotial exudate were measured using High Performance Liquid Chromatography (HPLC). Furthermore, the lipid peroxidation was estimated by detecting thiobarbituric bituric acid reactive substances (TBARS). The results showed that the exogenous oxalic acid caused a delay in sclerotial differentiation (of up to 9 or more days), suppressed the sclerotial biomass and decreased the lipid peroxidation significantly in a concentration-dependent manner. Oxalic acid was found at very low levels in the mycelia and the maltose medium, whereas it was found at high levels in the mycelia and sucrose medium. After sclerotial differentiation, oxalic acid accumulated at high levels in both the sclerotia and the sclerotial exudate. Oxalic acid was therefore found to inhibit P. umbellatus sclerotial formation.

Correlation between the production of exopolysaccharides and oxalic acid secretion by Ganoderma applanatum and Tyromyces palustris

The secretion of exopolysaccharides and oxalic acid in cultures of a white rot Ganoderma applanatum strain and a brown rot Tyromyces palustris strain were tested in terms of culture time, pH range, and temperature. The high yield of exopolysaccharides (EPS) required a moderate temperature of 28 °C for G. applanatum and 20 °C for T. palustris. G. applanatum and T. palustris accumulated more EPS when the concentration of the carbon source (maltose for G. applanatum and fructose for T. palustris) was 30 g/L. The results indicate that the production of oxalic acid by G. applanatum is correlated with the initial pH value of the culture medium and the concentration of oxalic acid increased to 1.66 ± 0.2 mM at the initial pH of 6.5 during the fungal growth. During the growth of T. palustris, the reduction of the initial pH value of the growing medium lowered the oxalic acid concentration from 7.7 ± 0.6 mM at pH 6.0 to 1.99 ± 0.2 mM at pH 3.5. T. palustris accumulated considerably more oxalic acid than G. applanatum and its presence did not affect significantly the production of exopolysaccharides. We also observed that the maximum amounts of exopolysaccharides secreted during cultivation of G. applanatum and T. palustris were 45.8 ± 1.2 and 19.1 ± 1.2 g/L, respectively.

RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger

Background

Filamentous fungi are well known for their ability to degrade lignocellulosic biomass and have a natural ability to convert certain products of biomass degradation, for example glucose, into various organic acids. Organic acids are suggested to give a competitive advantage to filamentous fungi over other organisms by decreasing the ambient pH. They also have an impact on the ecosystem by enhancing weathering and metal detoxification. Commercially, organic acids can be used as chemical intermediates or as synthons for the production of biodegradable polymers which could replace petroleum-based or synthetic chemicals. One of the advantages of filamentous fungi as biotechnological production platforms for synthetic biology is their ability to degrade vegetal biomass, which is a promising feedstock for the biotechnological production of organic acids. The Fungal Culture Collection of the International Centre of Microbial Resources (CIRM-CF), curated by our laboratory, contains more than 1600 strains of filamentous fungi, mainly Basidiomycetes and Ascomycetes. The natural biodiversity found in this collection is wide, with strains collected from around the world in different climatic conditions. This collection is mainly studied to unravel the arsenal of secreted lignocellulolytic enzymes available to the fungi in order to enhance biomass degradation. While the fungal biodiversity is a tremendous reservoir for “green” molecules production, its potentiality for organic acids production is not completely known.

Results

In this study, we screened 40 strains of Ascomycota and 26 strains of Basidiomycota, representing the distribution of fungal diversity of the CIRM-CF collection, in order to evaluate their potential for organic acid and ethanol production, in a glucose liquid medium. We observed that most of the filamentous fungi are able to grow and acidify the medium. We were also able to discriminate two groups of filamentous fungi considering their organic acid production at day 6 of incubation. This first group represented fungi co-producing a wide variety of organic acids and ethanol at concentrations up to 4 g.L⁻¹ and was composed of all the Aspergilli and only 3 other Ascomycota. The second group was composed of the remaining Ascomycota and all the Basidiomycota which produced mainly ethanol. Among the Basidiomycota, two strains produced oxalic acid and one strain produced gluconic and formic acid. Six strains of Aspergillus producing high concentrations of oxalic, citric and gluconic acids, and ethanol were selected for metabolism analysis.

Conclusion

These results illustrate the versatility in metabolites production among the fungal kingdom. Moreover, we found that some of the studied strains have good predispositions to produce valuable molecules. These strains could be of great interest in the study of metabolism and may represent new models for synthetic biology or consolidated bioprocessing of biomass.

Electronic supplementary material

The online version of this article (doi:10.1186/s40694-014-0001-z) contains supplementary material, which is available to authorized users.

Plant biomass degradation by fungi

Plant biomass degradation by fungi has implications for several fields of science. The enzyme systems employed by fungi for this are broadly used in various industrial sectors such as food & feed, pulp & paper, detergents, textile, wine, and more recently biofuels and biochemicals. In addition, the topic is highly relevant in the field of plant pathogenic fungi as they degrade plant biomass to either gain access to the plant or as carbon source, resulting in significant crop losses. Finally, fungi are the main degraders of plant biomass in nature and as such have an essential role in the global carbon cycle and ecology in general. In this review we provide a global view on the development of this research topic in saprobic ascomycetes and basidiomycetes and in plant pathogenic fungi and link this to the other papers of this special issue on plant biomass degradation by fungi.

Oxidation of aquatic pollutants by ferrous-oxalate complexes under dark aerobic conditions

This study evaluates the ability of Fe(II)-oxalate complexes for the generation of OH through oxygen reduction and the oxidative degradation of aquatic pollutants under dark aerobic conditions (i.e., with oxygen but without light). The degradation of 4-chlorophenol (4-CP) was rapid in the mixture of Fe(2+) and oxalate prepared using ultrapure water, but was absent without either Fe(2+) or oxalate. The formation of Fe(II)-oxalate complexes enables two-electron reduction of oxygen to generate H2O2 and subsequent production of OH. The significant inhibition of 4-CP degradation in the presence of H2O2 and OH scavenger confirms such mechanisms. The degradation experiments with varying [Fe(2+)], [oxalate], and initial pH demonstrated that the degradation rate depends on [Fe(II)(Ox)2(2-)], but the degree of degradation is primarily determined by [Fe(II)(Ox)2(2-)]+[Fe(II)(Ox)(0)]. Efficient degradation of diverse aquatic pollutants, especially phenolic pollutants, was observed in the Fe(II)-oxalate complexes system, wherein the oxidation efficacy was primarily correlated with the reaction rate constant between pollutant and OH. The effect of various organic ligands (oxalate, citrate, EDTA, malonate, and acetate) on the degradation kinetics of 4-CP was investigated. The highest efficiency of oxalate for the oxidative degradation is attributed to its high capability to enhance the reducing power and low reactivity with OH.

Wild-growing lignicolous mushroom species as sources of novel agents with antioxidative and antibacterial potentials

Crude extracts of two edible and two medicinal lignicolous mushroom species: Meripilus giganteus, Agrocybe aegerita, Fomes fomentarius and Xylaria polymorpha, growing wild in Serbia, were analyzed for their antioxidative and antibacterial potentials. Free radical scavenging capacity (RSC) on DPPH(•) and (•)OH was evaluated both by spectrophotometer and by Electron Spin Resonance (ESR) spectroscopy against DPPH(•). The highest antioxidant and antibacterial bioactivity was obtained with F. fomentarius extracts (IC50 ≈ 10.7 µg/ml in DPPH(•) assay; 136.6 mg ascorbic acid equivalents (AAE)/g dry weight (d.w.) for ferric reducing antioxidant power FRAP). It also showed the highest total phenol (TP) (82.54 mg gallic acid equivalents (GAE)/g dry weight (d.w.)) and total flavonoid (TF) content (76.8 µg rutin equivalents (RE)/g dry weight (d.w.)). A. aegerita showed the best antioxidant activity (IC50 = 0.87 mg/ml) against DPPH(•) in ESR analysis. Total redox potential of extracts was in direct positive correlation with TP content (r(2 )= 0.98) and TF content (r(2 )= 0.58). GC/MS analysis detected major constituents of extracts, confirming the presence of the following organic and phenolic acids: fumaric, succinic, mallic, 4-hydroxy benzoic, gentisic, protocatechuic, vanillic, gallic and p-coumaric acid.

Biodegradation of chestnut shell and lignin-modifying enzymes production by the white-rot fungi Dichomitus squalens, Phlebia radiata

As a discarded lignocellulosic biomass, chestnut shell is of great potential economic value, thus a sustainable strategy is needed and valuable for utilization of this resource. Herein, the feasibility of biological processes of chestnut shell with Dichomitus squalens, Phlebia radiata and their co-cultivation for lignin-modifying enzymes (LMEs) production and biodegradation of this lignocellulosic biomass was investigated under submerged cultivation. The treatment with D. squalens alone at 12 days gained the highest laccase activity (9.42 ± 0.73 U mg(-1)). Combined with the data of laccase and manganese peroxidase, oxalate and H2O2 were found to participate in chestnut shell degradation, accompanied by a rapid consumption of reducing sugar. Furthermore, specific surface area of chestnut shell was increased by 77.6-114.1 % with the selected fungi, and total pore volume was improved by 90.2 % with D. squalens. Meanwhile, the surface morphology was observably modified by this fungus. Overall, D. squalens was considered as a suitable fungus for degradation of chestnut shell and laccase production. The presence of LMEs, H2O2 and oxalate provided more understanding for decomposition of chestnut shell by the white-rot fungi.

The pathogenic white-rot fungus Heterobasidion parviporum responds to spruce xylem defense by enhanced production of oxalic acid

Pathogen challenge of tree sapwood induces the formation of reaction zones with antimicrobial properties such as elevated pH and cation content. Many fungi lower substrate pH by secreting oxalic acid, its conjugate base oxalate being a reductant as well as a chelating agent for cations. To examine the role of oxalic acid in pathogenicity of white-rot fungi, we conducted spatial quantification of oxalate, transcript levels of related fungal genes, and element concentrations in heartwood of Norway spruce challenged naturally by Heterobasidion parviporum. In the pathogen-compromised reaction zone, upregulation of an oxaloacetase gene generating oxalic acid coincided with oxalate and cation accumulation and presence of calcium oxalate crystals. The colonized inner heartwood showed trace amounts of oxalate. Moreover, fungal exposure to the reaction zone under laboratory conditions induced oxaloacetase and oxalate accumulation, whereas heartwood induced a decarboxylase gene involved in degradation of oxalate. The excess level of cations in defense xylem inactivates pathogen-secreted oxalate through precipitation and, presumably, only after cation neutralization can oxalic acid participate in lignocellulose degradation. This necessitates enhanced production of oxalic acid by H. parviporum. This study is the first to determine the true influence of white-rot fungi on oxalate crystal formation in tree xylem.

Firing range soils yield a diverse array of fungal isolates capable of organic acid production and Pb mineral solubilization

Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil(-1). We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter(-1) (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health.

A bacterial-fungal metaproteomic analysis enlightens an intriguing multicomponent interaction in the rhizosphere of Lactuca sativa

Fusarium oxysporum MSA 35 [wild-type (WT) strain] is an antagonistic isolate that protects plants against pathogenic Fusaria. This strain lives in association with ectosymbiotic bacteria. When cured of the prokaryotic symbionts [cured (CU) form], the fungus is pathogenic, causing wilt symptoms similar to those of F. oxysporum f.sp. lactucae. The aim of this study was to understand if and how the host plant Lactuca sativa contributes to the expression of the antagonistic/pathogenic behaviors of MSA 35 strains. A time-course comparative analysis of the proteomic profiles of WT and CU strains was performed. Fungal proteins expressed during the early stages of plant-fungus interaction were involved in stress defense, energy metabolism, and virulence and were equally induced in both strains. In the late phase of the interkingdom interaction, only CU strain continued the production of virulence- and energy-related proteins. The expression analysis of lettuce genes coding for proteins involved in resistance-related processes corroborated proteomic data by showing that, at the beginning of the interaction, both fungi are perceived by the plant as pathogen. On the contrary, after 8 days, only the CU strain is able to induce plant gene expression. For the first time, it was demonstrated that an antagonistic F. oxysporum behaves initially as pathogen, showing an interesting similarity with other beneficial organisms such as mychorrizae.

Role of laccase and low molecular weight metabolites from Trametes versicolor in dye decolorization

The studies regarding decolorization of dyes by laccase may not only inform about the possible application of this enzyme for environmental purposes, but also may provide important information about its reaction mechanism and the influence of several factors that could be involved. In this paper, decolorization of crystal violet and phenol red was carried out with different fractions of extracellular liquids from Trametes versicolor cultures, in order to describe the role of laccase in this reaction. Moreover, the possible role of the low molecular weight metabolites (LMWMs) also produced by the fungus was evaluated. The results confirm the existence of a nonenzymatic decolorization factor, since the nonprotein fraction of the extracellular liquids from cultures of T. versicolor has shown decolorization capability. Several experiments were performed in order to identify the main compounds related to this ability, which are probably low molecular weight peroxide compounds.

Oxalic acid, versatile peroxidase secretion and chelating ability of Bjerkandera fumosa in rich and limited culture conditions

Efficient ligninolytic systems of wood-degrading fungi include not only oxidizing enzymes, but also low-molecular-weight effectors. The ability of Bjerkandera fumosa to secrete oxalic acid and versatile peroxidase (VP) in nitrogen-rich and nitrogen-limited media was studied. Higher activity of VP was determined in the nitrogen-limited media but greater concentration of oxalic acid was observed in the cultures of B. fumosa without nitrogen limitation. Ferric ions chelating ability of Bjerkandera fumosa studied in ferric ions limited media was correlated with the increased level of oxalic acid. The presence of hydroxamate-type siderophores in B. fumosa media were also detected. Oxalate decarboxylase was found to be responsible for regulation of oxalic acid concentration in the tested B. fumosa cultures.

Response surface optimization of oxalic acid pretreatment of yellow poplar (Liriodendron tulipifera) for production of glucose and xylose monosaccarides

The primary goal of this study was to determine the optimal condition to obtain fermentable monosaccharides (xylose and glucose) from hydrolysates of yellow poplar (Liriodendron tulipifera) by oxalic acid pretreatment as a potential bio-ethanol source. Based on 2(3) factorial design, fifteen operations were performed by varying on acid loading, reaction time and temperature, and the components of the solid and liquid fractions were analyzed. The sugar concentration (g/L) in hydrolysates and xylose solubilization (%) were applied to response surface methodology. The optimal condition for producing sugars was 151 °C, 0.042 g/g (weight of oxalic acid/dry matter), 13 min with predicted yield of 37.4 g/L, and for the xylose solubilization was 158 °C, 0.037 g/g, 13 min yielding 72.0% of the predicted value. Severe conditions generated inhibitors. By measuring the concentrations, the possibility utilizing hydrolysates for fermentation were estimated.

Oxalate efflux transporter from the brown rot fungus Fomitopsis palustris

An oxalate-fermenting brown rot fungus, Fomitopsis palustris, secretes large amounts of oxalic acid during wood decay. Secretion of oxalic acid is indispensable for the degradation of wood cell walls, but almost nothing is known about the transport mechanism by which oxalic acid is secreted from F. palustris hyphal cells. We characterized the mechanism for oxalate transport using membrane vesicles of F. palustris. Oxalate transport in F. palustris was ATP dependent and was strongly inhibited by several inhibitors, such as valinomycin and NH(4)(+), suggesting the presence of a secondary oxalate transporter in this fungus. We then isolated a cDNA, FpOAR (Fomitopsis palustris oxalic acid resistance), from F. palustris by functional screening of yeast transformants with cDNAs grown on oxalic acid-containing plates. FpOAR is predicted to be a membrane protein that possesses six transmembrane domains but shows no similarity with known oxalate transporters. The yeast transformant possessing FpOAR (FpOAR-transformant) acquired resistance to oxalic acid and contained less oxalate than the control transformant. Biochemical analyses using membrane vesicles of the FpOAR-transformant showed that the oxalate transport property of FpOAR was consistent with that observed in membrane vesicles of F. palustris. The quantity of FpOAR transcripts was correlated with increasing oxalic acid accumulation in the culture medium and was induced when exogenous oxalate was added to the medium. These results strongly suggest that FpOAR plays an important role in wood decay by acting as a secondary transporter responsible for secretion of oxalate by F. palustris.