Use of electron microscopy for aiding our understanding of wood biodegradation

Grapevine Wood-Degrading Activity of Fomitiporia mediterranea M. Fisch.: A Focus on the Enzymatic Pathway Regulation

Fomitiporia mediterranea is a Basidiomycetes fungus associated with some of the Esca complex diseases and responsible for decay in grapevine wood. Its role in the onset of foliar symptoms has recently been reconsidered, mainly after evidence showing a reduction in foliar symptom expression after removal of rotten wood. The study of its degradation pathways has already been approached by other authors, and with this study much information is consolidated. A microscopic observation of degraded wood provides a first approach to the characterization of F. mediterranea modalities of wood cellular structure degradation. The decay of grapevine wood was reproduced in vitro, and the measurement of each wood-forming polymer loss highlighted characteristics of F. mediterranea common to selective white rot and showed how fungal strain and vine variety are factors determining the wood degradation. All these observations were supported by the analysis of the laccase and manganese peroxidase enzyme activity, as well as by the expression of the genes coding 6 putative laccase isoforms and 3 manganese peroxidase isoforms, thereby highlighting substantial intraspecific variability.

Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes

Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.

Comparative Transcriptomics During Brown Rot Decay in Three Fungi Reveals Strain-Specific Degradative Strategies and Responses to Wood Acetylation

Brown rot fungi degrade wood in a two-step process in which enzymatic hydrolysis is preceded by an oxidative degradation phase. While a detailed understanding of the molecular processes during brown rot decay is mandatory for being able to better protect wooden products from this type of degradation, the underlying mechanisms are still not fully understood. This is particularly true for wood that has been treated to increase its resistance against rot. In the present study, the two degradation phases were separated to study the impact of wood acetylation on the behavior of three brown rot fungi commonly used in wood durability testing. Transcriptomic data from two strains of Rhodonia placenta (FPRL280 and MAD-698) and Gloeophyllum trabeum were recorded to elucidate differences between the respective decay strategies. Clear differences were found between the two decay stages in all fungi. Moreover, strategies varied not only between species but also between the two strains of the same species. The responses to wood acetylation showed that decay is generally delayed and that parts of the process are attenuated. By hierarchical clustering, we could localize several transcription factors within gene clusters that were heavily affected by acetylation, especially in G. trabeum. The results suggest that regulatory circuits evolve rapidly and are probably the major cause behind the different decay strategies as observed even between the two strains of R. placenta. Identifying key genes in these processes can help in decay detection and identification of the fungi by biomarker selection, and also be informative for other fields, such as fiber modification by biocatalysts and the generation of biochemical platform chemicals for biorefinery applications.

Gene Expression Analysis of Three Putative Copper-Transporting ATPases in Copper-Tolerant Fibroporia radiculosa

Copper tolerance of brown-rot basidiomycete decay fungi can lessen the efficacy of copper-containing wood preservatives for wood products in-service. The purpose of this study was to evaluate wood mass loss and differential expression of three genes that have putative annotations for copper-transporting ATPase pumps (FIBRA_00974, FIBRA_04716, and FIBRA_01430). Untreated southern pine (SP) and SP treated with three concentrations of ammoniacal copper citrate (CC, 0.6, 1.2, and 2.4%) were exposed to two copper-tolerant Fibroporia radiculosa isolates (FP-90848-T and L-9414-SP) and copper-sensitive Gloeophyllum trabeum isolate (MAD 617) in a 4-week-long standard decay test (AWPA E10-19). Decay of copper-treated wood was inhibited by G. trabeum (p = 0.001); however, there was no inhibition of decay with increasing copper concentrations by both F. radiculosa isolates. Initially, G. trabeum and one F. radiculosa isolate (L-9414-SP) highly upregulated FIBRA_00974 and FIBRA_04716 on copper-treated wood at week 1 (p = 0.005), but subsequent expression was either not detected or was similar to expression on untreated wood (p = 0.471). The other F. radiculosa isolate (FP-90848-T) downregulated FIBRA_00974 (p = 0.301) and FIBRA_04716 (p = 0.004) on copper-treated wood. FIBRA_01430 expression by G. trabeum was not detected, but was upregulated by both F. radiculosa FP-90848-T (p = 0.481) and L-9414-SP (p = 0.392). Results from this study suggest that all three test fungi utilized different mechanisms when decaying copper-treated wood. Additionally, results from this study do not provide support for the involvement of these putative gene annotations for copper-transporting ATPase pumps in the mechanism of copper-tolerance.

First evidence of microbial wood degradation in the coastal waters of the Antarctic

Wood submerged in saline and oxygenated marine waters worldwide is efficiently degraded by crustaceans and molluscs. Nevertheless, in the cold coastal waters of the Antarctic, these degraders seem to be absent and no evidence of other wood-degrading organisms has been reported so far. Here we examine long-term exposed anthropogenic wood material (Douglas Fir) collected at the seafloor close to McMurdo station, Antarctica. We used light and scanning electron microscopy and demonstrate that two types of specialized lignocellulolytic microbes—soft rot fungi and tunnelling bacteria—are active and degrade wood in this extreme environment. Fungal decay dominates and hyphae penetrate the outer 2–4 mm of the wood surface. Decay rates observed are about two orders of magnitude lower than normal. The fungi and bacteria, as well as their respective cavities and tunnels, are slightly smaller than normal, which might represent an adaptation to the extreme cold environment. Our results establish that there is ongoing wood degradation also in the Antarctic, albeit at a vastly reduced rate compared to warmer environments. Historical shipwrecks resting on the seafloor are most likely still in good condition, although surface details such as wood carvings, tool marks, and paint slowly disintegrate due to microbial decay.

Three-Dimensional Exploration of Soft-Rot Decayed Conifer and Angiosperm Wood by X-Ray Micro-Computed Tomography

X-ray micro-computed tomography (XμCT) was used to explore the decomposed structure of conifer and angiosperm wood after colonization by soft-rot fungi. The visualization of degradation features of soft-rot decay was challenging to achieve through XμCT. Difficulties in visualization emerged due to a decreased grayscale contrast (i.e. X-ray density) of the degraded wood. Nevertheless, we were able to image fungal-induced cell deformations in earlywood and cavities in the thick wall of latewood cells in three-dimensions (3D). Unlike the organic wood material, the higher X-ray density of inorganic deposits, identified as mainly calcium-based particles by energy-dispersive spectroscopy, allowed a facilitated 3D survey. The visualization of inorganic particles in 3D revealed a localized distribution in certain cells in conifer and angiosperm found mostly in earlywood.

Nitrogen-obtaining and -conserving strategies in xylotrophic basidiomycetes

Nitrogen in sufficient quantities is strictly necessary for all living organisms. In this study, the ability of some xylotrophic basidiomycetes to grow extremely long on a solid growth medium full of carbon nutrition but lacking a nitrogen source in its composition was discovered. The nitrogen oligotrophy of wood-decaying fungi is associated with their adaptation to live in a wood substrate, which is also deficient in nitrogen content. This nitrogen-depleted cultural growth is called "pseudo-foraging" and can be used as a simplified model of wood-decaying growth. Four main nitrogen-obtaining and -conserving strategies (nitrogen concentration, using alternative sources of nitrogen, economy of growth, and nutritional recycling), which are attributed to wood-colonizing xylotrophs in the literature, were revised studying the pseudo-foraging model. Based on the results, some aspects of the behavior of xylotrophs deep in undecomposed wood were predicted. For example, one of the results is that for pseudo-foraging xylotrophs, the main way to obtain nitrogen is its concentration in their mycelium from the nutrient medium in which nitrogen is contained in the impurities of the components of the medium. The result suggests that in bulk solid wood, the nitrogen concentration strategy also dominates the strategy of using diazotrophic and other alternative nitrogen. In addition, three individual unprecedented mechanisms, which supposedly help the xylotrophic fungi to colonize wood in nature (generation of fine mycelium, macrovesicular endocytosis, formation and conversion of super-elongated mitochondria), were investigated in the laboratory.

Initial Rhodonia placenta Gene Expression in Acetylated Wood: Group-Wise Upregulation of Non-Enzymatic Oxidative Wood Degradation Genes Depending on the Treatment Level

Acetylation has been shown to delay fungal decay, but the underlying mechanisms are poorly understood. Brown-rot fungi, such as Rhodonia placenta (Fr.) Niemelä, K.H. Larss. & Schigel, degrade wood in two steps, i.e., oxidative depolymerization followed by secretion of hydrolytic enzymes. Since separating the two degradation steps has been proven challenging, a new sample design was applied to the task. The aim of this study was to compare the expression of 10 genes during the initial decay phase in wood and wood acetylated to three different weight percentage gains (WPG). The results showed that not all genes thought to play a role in initiating brown-rot decay are upregulated. Furthermore, the results indicate that R. placenta upregulates an increasing number of genes involved in the oxidative degradation phase with increasing WPG.

Resistance of Injection Molded Wood-Polypropylene Composites against Basidiomycetes According to EN 15534-1: New Insights on the Test Procedure, Structural Alterations, and Impact of Wood Source

In this study, we investigated injection molded wood-polypropylene composites based on various wood sources and their decay resistance against white rot (Trametes versicolor) and brown rot (Coniophora puteana) in a laboratory test according to EN 15534-1:2014. The manufactured composites consisted of poplar (Populus spp.), willow (Salix spp.), European beech (Fagus sylvatica L.), Norway spruce (Picea abies (L.) H. Karst.), and a commercial wood source (Arbocel® C100), respectively. All formulations were compounded on a co-rotating twin screw extruder and subsequently injection molded to wood–PP specimens with a wood content of 60% or 70% by weight. It was found that the test procedure had a significant effect on the mechanical properties. Loss in mechanical properties was primarily caused by moisture and less by fungal decay. Moisture caused a loss in the modulus of rupture and modulus of elasticity of 34 to 45% and 29 to 73%, respectively. Mean mass and wood mass losses were up to a maximum of 3.7% and 5.3%, respectively. The high resistance against fungal decay was generally attributed to the encapsulation of wood by the polymer matrix caused by sample preparation, and enhanced by reduced moisture uptake during the preconditioning procedure. Notable differences with respect to the wood particle source and decay fungi were also observed. Structural characterization confirmed the decay pattern of the fungi such as void cavities close the surface and the deposition of calcium oxalates.

Tracking of Short Distance Transport Pathways in Biological Tissues by Ultra-Small Nanoparticles

In this work, ultra-small europium-doped HfO₂ nanoparticles were infiltrated into native wood and used as trackers for studying penetrability and diffusion pathways in the hierarchical wood structure. The high electron density, laser induced luminescence, and crystallinity of these particles allowed for a complementary detection of the particles in the cellular tissue. Confocal Raman microscopy and high-resolution synchrotron scanning wide-angle X-ray scattering (WAXS) measurements were used to detect the infiltrated particles in the native wood cell walls. This approach allows for simultaneously obtaining chemical information of the probed biological tissue and the spatial distribution of the integrated particles. The in-depth information about particle distribution in the complex wood structure can be used for revealing transport pathways in plant tissues, but also for gaining better understanding of modification treatments of plant scaffolds aiming at novel functionalized materials.

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.

Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system

BACKGROUND

The genome of Schizophyllum commune encodes a diverse repertoire of degradative enzymes for plant cell wall breakdown. Recent comparative genomics study suggests that this wood decayer likely has a mode of biodegradation distinct from the well-established white-rot/brown-rot models. However, much about the extracellular enzyme system secreted by S. commune during lignocellulose deconstruction remains unknown and the underlying mechanism is poorly understood. In this study, extracellular proteins of S. commune colonizing Jerusalem artichoke stalk were analyzed and compared with those of two white-rot fungi Phanerochaete chrysosporium and Ceriporiopsis subvermispora and a brown-rot fungus Gloeophyllum trabeum.

RESULTS

Under solid-state fermentation (SSF) conditions, S. commune displayed considerably higher levels of hydrolytic enzyme activities in comparison with those of P. chrysosporium, C. subvermispora and G. trabeum. During biodegradation process, this fungus modified the lignin polymer in a way which was consistent with a hydroxyl radical attack, similar to that of G. trabeum. The crude enzyme cocktail derived from S. commune demonstrated superior performance over a commercial enzyme preparation from Trichoderma longibrachiatum in the hydrolysis of pretreated lignocellulosic biomass at low enzyme loadings. Secretomic analysis revealed that compared with three other fungi, this species produced a higher diversity of carbohydrate-degrading enzymes, especially hemicellulases and pectinases acting on polysaccharide backbones and side chains, and a larger set of enzymes potentially supporting the generation of hydroxyl radicals. In addition, multiple non-hydrolytic proteins implicated in enhancing polysaccharide accessibility were identified in the S. commune secretome, including lytic polysaccharide monooxygenases (LPMOs) and expansin-like proteins.

CONCLUSIONS

Plant lignocellulose degradation by S. commune involves a hydroxyl radical-mediated mechanism for lignocellulose modification in parallel with the synergistic system of various polysaccharide-degrading enzymes. Furthermore, the complex enzyme system of S. commune holds significant potential for application in biomass saccharification. These discoveries will help unveil the diversity of natural lignocellulose-degrading mechanisms, and advance the design of more efficient enzyme mixtures for the deconstruction of lignocellulosic feedstocks.

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay

To degrade the polysaccharides, wood-decay fungi secrete a variety of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) classified into various sequence-based families of carbohydrate-active enzymes (CAZys) and their appended carbohydrate-binding modules (CBM). Oxidative enzymes, such as cellobiose dehydrogenase (CDH) and lytic polysaccharide monooxygenase (LPMO, formerly GH61), also have been implicated in cellulose degradation. To examine polysaccharide-degrading potential between white- and brown-rot fungi, we performed genomewide analysis of CAZys and these oxidative enzymes in 11 Polyporales, including recently sequenced monokaryotic strains of Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora. Furthermore, we conducted comparative secretome analysis of seven Polyporales grown on wood culture. As a result, it was found that genes encoding cellulases belonging to families GH6, GH7, GH9 and carbohydrate-binding module family CBM1 are lacking in genomes of brown-rot polyporales. In addition, the presence of CDH and the expansion of LPMO were observed only in white-rot genomes. Indeed, GH6, GH7, CDH and LPMO peptides were identified only in white-rot polypores. Genes encoding aldose 1-epimerase (ALE), previously detected with CDH and cellulases in the culture filtrates, also were identified in white-rot genomes, suggesting a physiological connection between ALE, CDH, cellulase and possibly LPMO. For hemicellulose degradation, genes and peptides corresponding to GH74 xyloglucanase, GH10 endo-xylanase, GH79 β-glucuronidase, CE1 acetyl xylan esterase and CE15 glucuronoyl methylesterase were significantly increased in white-rot genomes compared to brown-rot genomes. Overall, relative to brown-rot Polyporales, white-rot Polyporales maintain greater enzymatic diversity supporting lignocellulose attack.

Penetration capacity of the wood-decay fungus Physisporinus vitreus

Purpose

Bioincising is a biotechnological process for improving the permeability of refractory wood such as Norway spruce heartwood using the wood-decay fungus Physisporinus vitreus. The degradation of the bordered pit membranes by P. vitreus in its first stage of wood colonization enhances the uptake of preservatives and wood modification substances, whereas the strength of the material is not significantly reduced.

Methods

We propose to study bioincising by means of a mathematical model, because many factors affect the growth and effects of P. vitreus in Norway spruce in such a complex way that an evaluation of the optimal incubation conditions (i.e. water activity, temperature or pH) is very expensive or even not possible solely using laboratory experiments.

Results

Using a hyphal growth model we demonstrate here for the first time how to optimize bioincising by linking the microscopic growth behavior of P. vitreus with macroscopic system properties of the wood. Moreover, we propose universal measures of wood-decay fungi, i.e., penetration velocity, penetration work and penetration capacity, which may figure as measures for the efficiency of wood colonization. For example, our simulation shows that an increase of the hyphal growth rate (i.e. changing the incubation conditions) from 1 to 2 μm·d-1 results in an increase of the mycelium’s growth velocity from 0.8 to 1.75 μm·d-1 and an increase of the penetration capacity from 0.5 to 0.6 10-3·mm2·d-1 using a pit degradation rate of 2 μm·d-1.

Conclusions

Information about the penetration velocity, penetration work and penetration capacity is of significance for both its biotechnological use and the study of the colonization strategy of wood-decay fungi in general.

Transcriptional effect of a calmodulin inhibitor, W-7, on the ligninolytic enzyme genes in Phanerochaete chrysosporium

We investigated the effects of a calmodulin (CaM) inhibitor, W-7, on the expression of lignin peroxidase (LiP) and manganese peroxidase (MnP) genes in Phanerochaete chrysosporium to consider the role of cam gene, which was upregulated in parallel with the total activities of LiP and MnP in our previous transcriptomic analysis. The addition of 100 μM W-7 to the fungal cultures repressed the total activities of LiP and MnP, whereas the addition of 100 μM W-5, which is a control drug of W-7, retained approximately half of them, indicating that the effect of W-7 was attributable to CaM inhibition. Real-time reverse transcription polymerase chain reaction analysis revealed that most of lip and mnp isozyme genes predicted from whole-genome data were significantly inhibited by W-7 at the transcription level (P ≤ 0.05). These results suggest that CaM has an important role for the expression of isozyme genes of LiP and MnP at the transcription level.

Structural quantification of wood fibre surfaces--morphological effects of pulping and enzymatic treatment

Wood fibres have been utilized by our society as an important component of paper products and are presently gaining more interest as reinforcement in composite materials. During the last decades biochemical treatments have also found applications in the processing of wood fibres. The chemical, mechanical and biochemical treatments affect the morphology of the fibre wall structure at the micro- and nano-level. In this study, we present a modern approach where field-emission SEM (FE-SEM) and relevant computerized image analysis are applied to quantify the fibre wall characteristics. Details such as surface roughness and texture of the fibre walls are quantified objectively. Global polar plots are generated, which are considered to represent the fingerprint of a given pulp. The approach offers a novel perspective in the characterisation of surface structures, moving forward from performing subjective evaluations to performing objective quantifications of wood pulp fibre surfaces.

Biological treatment of the effluent from a bleached kraft pulp mill using basidiomycete and zygomycete fungi

Three white-rot fungi (Pleurotus sajor caju, Trametes versicolor and Phanerochaete chrysosporium) and one soft-rot fungi (Rhizopus oryzae) species confirmed their potential for future applications in the biological treatment of effluents derived from the secondary treatment of a bleached kraft pulp mill processing Eucalyptus globulus. Among the four species P. sajor caju and R. oryzae were the most effective in the biodegradation of organic compounds present in the effluent, being responsible for the reduction of relative absorbance (25-46% at 250 nm and 72-74% at 465 nm) and of chemical oxygen demand levels (74 to 81%) after 10 days of incubation. Laccase (Lac), lignin (Lip) and manganese peroxidases (MnP) expression varied among fungal species, where Lac and LiP activities were correlated with the degradation of organic compounds in the effluent treated with P. sajor caju. The first two axes of a principal component analysis explained 88.9% of the total variation among sub-samples treated with the four fungus species, after different incubation periods. All the variables measured contributed positively to the first component except for the MnP enzyme activity which was the only variable contributing negatively to the first component. Absorbances at 465 nm, LiP and Lac enzyme activities were the variables with more weight on the second component. P. sajor caju revealed to be the only species able to perform the biological treatment without promoting an increment in the toxicity of the effluent to the Vibrio fischeri, as it was assessed by the Microtox assay. The opposite was recorded for the treatments with the other three species of fungus. EC(50-5 min) values ranging between 28 and 57% (effluent concentrations) were recorded even after 10 to 13 days of treatment with P. chrysosporium, R. oryzae or with T. versicolor.

Characteristics of Gloeophyllum trabeum alcohol oxidase, an extracellular source of H2O2 in brown rot decay of wood

A novel alcohol oxidase (AOX) has been purified from mycelial pellets of the wood-degrading basidiomycete Gloeophyllum trabeum and characterized as a homooctameric nonglycosylated protein with native and subunit molecular masses of 628 and 72.4 kDa, containing noncovalently bonded flavin adenine dinucleotide. The isolated AOX cDNA contained an open reading frame of 1,953 bp translating into a polypeptide of 651 amino acids displaying 51 to 53% identity with other published fungal AOX amino acid sequences. The enzyme catalyzed the oxidation of short-chain primary aliphatic alcohols with a preference for methanol (K(m) = 2.3 mM, k(cat) = 15.6 s(-1)). Using polyclonal antibodies and immunofluorescence staining, AOX was localized on liquid culture hyphae and extracellular slime in sections from degraded wood and on cotton fibers. Transmission electron microscopy immunogold labeling localized the enzyme in the hyphal periplasmic space and wall and on extracellular tripartite membranes and slime, while there was no labeling of hyphal peroxisomes. AOX was further shown to be associated with membranous or slime structures secreted by hyphae in wood fiber lumina and within the secondary cell walls of degraded wood fibers. The differences in AOX targeting compared to the known yeast peroxisomal localization were traced to a unique C-terminal sequence of the G. trabeum oxidase, which is apparently responsible for the protein's different translocation. The extracellular distribution and the enzyme's abundance and preference for methanol, potentially available from the demethylation of lignin, all point to a possible role for AOX as a major source of H(2)O(2), a component of Fenton's reagent implicated in the generally accepted mechanisms for brown rot through the production of highly destructive hydroxyl radicals.

Estimation of bound and free fractions of lignocellulose-degrading enzymes of wood-rotting fungi Pleurotus ostreatus, Trametes versicolor and Piptoporus betulinus

Liquid cultures with cellulose and solid state fermentation cultures on wheat straw of the white-rot fungi Pleurotus ostreatus and Trametes versicolor and the brown-rot fungus Piptoporus betulinus were assayed for the free and solid fraction-bound activity of lignocellulose-degrading enzymes. The majority of the ligninolytic enzymes laccase and Mn peroxidase was detected in the free fraction of P. ostreatus and T. versicolor. The endocleaving enzymes endo-1,4-beta-glucanase, endo-1,4-beta-mannanase and endo-1,4-beta-xylanase were detected almost exclusively in the free fraction, while significant amounts of 1,4-beta-glucosidase, cellobiohydrolase, 1,4-beta-xylosidase and 1,4-beta-mannosidase were present in the bound fraction depending on the mode of cultivation and the species. The bound enzymes accounted for 66% of the total activity in P. ostreatus straw cultures, 35% in T. versicolor and only 8% in P. betulinus. The enzymes also showed significant differences in freeze-drying stability. Hydrolases in general showed high stability, whereas laccase and Mn peroxidase of P. ostreatus were the least stable.

SEM-FTIR spectroscopic evaluation of deterioration in an historic coffered ceiling

Microorganisms generally degrade wood when moisture, oxygen and other environmental factors provide favorable growing conditions. Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) were used to study the development and transformation of the products formed during the biomineralization process that follows the deterioration of wood from an historical coffered ceiling (Cloister of St Francesc (XIV century), Palma de Mallorca, Spain). After fungi colonization, cellulose and lignin disappear and inorganic salts are formed. Thus, the secretion of numerous acids (initially oxalic acid) by fungal hyphae also leads to the precipitation of authigenic salts. Damaged cells or tissues enhance the formation and growth of crystals, which is strongly favored by fungi that function as calcification nuclei. Finally, the presence of dihydrated calcium sulfate reveals the contribution of environmental factors to the weathering of wood.

Recent developments on cellulases and carbohydrate-binding modules with cellulose affinity

This review concerns basic research on cellulases and cellulose-specific carbohydrate-binding modules (CBMs). As a background, glycosyl hydrolases are also briefly reviewed. The nomenclature of cellulases and CBMs is discussed. The main cellulase-producing organisms and their cellulases are described. Synergy, enantioseparation, cellulases in plants, cellulosomes, cellulases and CBMs as analytical tools and cellulase-like enzymes are also briefly reviewed.

Cryo-FE-SEM & TEM immuno-techniques reveal new details for understanding white-rot decay of lignocellulose

High-resolution Cryo-Field Emission Scanning Electron Microscopy (HR-Cryo-FE-SEM) and immuno-cytochemistry were used to reveal novel details on the morphological events and spatial distribution of oxidoreductive enzymes during the degradation of birch wood by the white-rot fungi Phlebia radiata and mutant strain P radiata Cel 26. Cryo-observations of fractured fibres showed degradation across the cell wall by P. radiata (wild) to progress by delamination and removal of concentric orientated aggregates from the secondary S2 cell wall. Decay by P radiata Cel 26 progressed by removal of materials (lignin and hemicelluloses) between the aggregates (primarily cellulose) that remained even after advanced decay. With both decay patterns, extracellular slime materials were present uniting lumina hyphae with the attacked fibre wall. The extracellular slime material had two morphological forms: viz a fibrillar (often tripartite) and a 'gel-form', the former found in discrete bands progressing across the lumen onto the fibre wall. Using TEM immunocytochemistry, laccase, manganese peroxidase (MnP) and diarylpropane enzymes were localized in the periplasmic space of luminal hyphae, in association with the cell membrane, periplasmic vesicles and fungal cell wall. Extracellularly, the three enzymes were found associated with the slime and tripartite membranes and with the birch cell walls at all stages of attack through to middle lamella corner decay. Enzyme distribution was correlated with morphological changes in cell wall structure. The association of extracellular slime with these enzymes and sites of decay strongly suggests a major role for this matrix in fibre cell wall decomposition.

Enzymatic and fungal treatments on sugarcane bagasse for the production of mechanical pulps

Crude ligninolytic enzyme extracts from Phanerochaete chrysosporium fungi were applied to sugarcane bagasse, prior to thermomechanical (TMP) and chemithermomechanical pulping (CTMP), and their properties were compared with the normal TMP and CTMP and also with TMP and CTMP pretreated with Ceriporiopsis subvermispora and P. chrysosporium fungi. The sugarcane bagasse was impregnated with the crude enzyme extract containing lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase (Lac). The results show that pretreatment with enzyme crude extract is an advantageous way to produce TMP and CTMP from sugarcane bagasse, as compared with only fungal pretreatment. Enzymatic pretreatments need only hours to enhance pulping and paper properties, compared with the weeks necessary for fungal treatments. Higher pulp yields were obtained compared with the fungal pretreatments. Enzymatic pretreatment reduced the energy consumption in a proportion similar to that of C. subvermispora fungal pretreatment and increased the pulp tensile index compared with the normal TMP and CTMP pulps, although the tensile strength was somewhat lower than that for pulps from C. subvermispora fungal pretreatment before CTMP processing. An advantage of enzymatic pretreatment is that brightness is increased compared with normal TMP and CTMP processes, whereas fungal pretreatments reduce the brightness.

Iron-regulated proteins in Phanerochaete chrysosporium and Lentinula edodes: differential analysis by sodium dodecyl sulfate polyacrylamide gel electrophoresis and two-dimensional polyacrylamide gel electrophoresis profiles

Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis (2-DE) were used to identify iron-responsive proteins in the white-rot species (Phanerochaete chrysosporium and Lentinula edodes), by comparing the differential patterns of cellular and membrane proteins obtained from iron-sufficient and iron-deficient mycelia. Six cellular proteins induced by iron restriction have been observed in SDS-PAGE for P. chrysosporium and twelve for L. edodes. In 2-DE, the numbers of iron-restricted induced proteins were 12 and 9, respectively, in a resolution range of 15-60 kDa and pI 4.5-8.1. SDS-PAGE for the plasma membrane protein did not show differences, whereas the outer-membrane protein profile showed 6 and 5 proteins induced by iron depletion in P. chrysosporium and L. edodes, respectively. The results presented here are important data to unravel mechanisms of biosynthesis and/or transport of the iron-complexing agents in ligninolytic fungi and to further correlate them to the ligninolytic processes.

Purification and characterization of pyranose oxidase from the white rot fungus Trametes multicolor

We purified an intracellular pyranose oxidase from mycelial extracts of the white rot fungus Trametes multicolor by using ammonium sulfate fractionation, hydrophobic interaction, ion-exchange chromatography, and gel filtration. The native enzyme has a molecular mass of 270 kDa as determined by equilibrium ultracentrifugation and is composed of four identical 68-kDa subunits as determined by matrix-assisted laser desorption ionization mass spectrometry. Each subunit contains one covalently bound flavin adenine dinucleotide as its prosthetic group. The enzyme oxidizes several aldopyranoses specifically at position C-2, and its preferred electron donor substrates are D-glucose, D-xylose, and L-sorbose. During this oxidation reaction electrons are transferred to oxygen, yielding hydrogen peroxide. In addition, the enzyme catalyzes the two-electron reduction of 1,4-benzoquinone, several substituted benzoquinones, and 2,6-dichloroindophenol, as well as the one-electron reduction of the ABTS [2,2'-azinobis(3-ethylbenzthiazolinesulfonic acid)] cation radical. As judged by the catalytic efficiencies (k(cat)/K(m)), some of these quinone electron acceptors are much better substrates for pyranose oxidase than oxygen. The optimum pH of the pyranose oxidase-catalyzed reaction depends strongly on the electron acceptor employed and varies from 4 to 8. It has been proposed that the main metabolic function of pyranose oxidase is as a constituent of the ligninolytic system of white rot fungi that provides peroxidases with H(2)O(2). An additional function could be reduction of quinones, key intermediates that are formed during mineralization of lignin.

A critical review of cellobiose dehydrogenases

Cellobiose dehydrogenase (CDH) is an extracellular enzyme produced by various wood-degrading fungi. It oxidizes soluble cellodextrins, mannodextrins and lactose efficiently to their corresponding lactones by a ping-pong mechanism using a wide spectrum of electron acceptors including quinones, phenoxyradicals, Fe(3+), Cu(2+) and triiodide ion. Monosaccharides, maltose and molecular oxygen are poor substrates. CDH that adsorbs strongly and specifically to cellulose carries two prosthetic groups; namely, an FAD and a heme in two different domains that can be separated after limited proteolysis. The FAD-containing fragment carries all known catalytic and cellulose binding properties. One-electron acceptors, like ferricyanide, cytochrome c and phenoxy radicals, are, however, reduced more slowly by the FAD-fragment than by the intact enzyme, suggesting that the function of the heme group is to facilitate one-electron transfer. Non-heme forms of CDH have been found in the culture filtrate of some fungi (probably due to the action of fungal proteases) and were for a long time believed to represent a separate enzyme (cellobiose:quinone oxidoreductase, CBQ). The amino acid sequence of CDH has been determined and no significant homology with other proteins was detected for the heme domain. The FAD-domain sequence belongs to the GMC oxidoreductase family that includes, among others, Aspergillus niger glucose oxidase. The homology is most distinct in regions that correspond to the FAD-binding domain in glucose oxidase. A cellulose-binding domain of the fungal type is present in CDH from Myceliophtore thermophila (Sporotrichum thermophile), but in others an internal sequence rich in aromatic amino acid residues has been suggested to be responsible for the cellulose binding. The biological function of CDH is not fully understood, but recent results support a hydroxyl radical-generating mechanism whereby the radical can degrade and modify cellulose, hemicellulose and lignin. CDH has found technical use in highly selective amperometric biosensors and several other applications have been suggested.

Use of confocal microscopy in examining fungi and bacteria in wood

When used in conjunction with digital image processing techniques, confocal laser scanning microscopy (CLSM) enables non-invasive optical sectioning, allowing micromorphologies of wood decay to be examined at any depth within a relatively thick (0.05-0.1 mm) wood specimen without incision. In this study, the use of specially tailored multi-fluorescent staining techniques with CLSM produced new information concerning spatial relationships between fungi and bacteria and the wood substrate, particularly in regard to their 3D characteristics. Glutaraldehyde fixation and a chitin fluorescent probe were used to locate fungal hyphae in wood. Bacteria colonising wood were examined using a fluorescent phospholipid probe. By counterstaining wood with this probe and a fluorescent dye specific for Gram-positive bacteria, it was possible to clearly distinguish Gram types through simultaneous, multichannel fluorescent CLSM imaging. The combination of glutaraldehyde fixation and phospholipid probing proved to be reliable for detecting wood-degrading bacteria in wood cell walls.

Fungal production of citric and oxalic acid: importance in metal speciation, physiology and biogeochemical processes

The production of organic acids by fungi has profound implications for metal speciation, physiology and biogeochemical cycles. Biosynthesis of oxalic acid from glucose occurs by hydrolysis of oxaloacetate to oxalate and acetate catalysed by cytosolic oxaloacetase, whereas on citric acid, oxalate production occurs by means of glyoxylate oxidation. Citric acid is an intermediate in the tricarboxylic acid cycle, with metals greatly influencing biosynthesis: growth limiting concentrations of Mn, Fe and Zn are important for high yields. The metal-complexing properties of these organic acids assist both essential metal and anionic (e.g. phosphate) nutrition of fungi, other microbes and plants, and determine metal speciation and mobility in the environment, including transfer between terrestrial and aquatic habitats, biocorrosion and weathering. Metal solubilization processes are also of potential for metal recovery and reclamation from contaminated solid wastes, soils and low-grade ores. Such 'heterotrophic leaching' can occur by several mechanisms but organic acids occupy a central position in the overall process, supplying both protons and a metal-complexing organic acid anion. Most simple metal oxalates [except those of alkali metals, Fe(III) and Al] are sparingly soluble and precipitate as crystalline or amorphous solids. Calcium oxalate is the most important manifestation of this in the environment and, in a variety of crystalline structures, is ubiquitously associated with free-living, plant symbiotic and pathogenic fungi. The main forms are the monohydrate (whewellite) and the dihydrate (weddelite) and their formation is of significance in biomineralization, since they affect nutritional heterogeneity in soil, especially Ca, P, K and Al cycling. The formation of insoluble toxic metal oxalates, e.g. of Cu, may confer tolerance and ensure survival in contaminated environments. In semi-arid environments, calcium oxalate formation is important in the formation and alteration of terrestrial subsurface limestones. Oxalate also plays an important role in lignocellulose degradation and plant pathogenesis, affecting activities of key enzymes and metal oxido-reduction reactions, therefore underpinning one of the most fundamental roles of fungi in carbon cycling in the natural environment. This review discusses the physiology and chemistry of citric and oxalic acid production in fungi, the intimate association of these acids and processes with metal speciation, physiology and mobility, and their importance and involvement in key fungal-mediated processes, including lignocellulose degradation, plant pathogenesis and metal biogeochemistry.

Isolation and partial characterization of an extracellular low-molecular mass component with high phenoloxidase activity from Thermoascus aurantiacus

An extracellular low-molecular mass component (LMMC) with catalytic properties was isolated from liquid cultures containing wheat bran of ascomycete thermophilic Thermoascus aurantiacus. The partially purified LMMC showed very high activity with typical phenoloxidase substrates in the absence of hydrogen peroxide at acidic pH (2.8). However, in this pH range, the phenoloxidase (PO) activity was quickly lost. The LMMC showed a high optimum temperature (80 degrees C) and an elevated thermostability. The molecular mass of the component estimated by gel filtration chromatography was 530 Da. IR and 1H- and 13C-NMR spectra indicated the presence of hydroxamic acid moiety. Qualitative determination of metal ions by several techniques revealed the presence of mainly iron associated with this structure. Iron may be the responsible for the ability for catalyze oxidation reactions, such as o-dianisidine oxidation, by the LMMC. These results suggested the existence of a hydroxamate-type metal-binding component, most likely hydroxamate siderophore. In addition, the chrome azurol S (CAS) universal assay for noncomplexed siderophores detection revealed the production of these compounds by T.aurantiacus in solid and liquid media.

Endoglucanase 28 (Cel12A), a new Phanerochaete chrysosporium cellulase

A 28-kDa endoglucanase was isolated from the culture filtrate of Phanerochaete chrysosporium strain K3 and named EG 28. It degrades carboxymethylated cellulose and amorphous cellulose, and to a lesser degree xylan and mannan but not microcrystalline cellulose (Avicel). EG 28 is unusual among cellulases from aerobic fungi, in that it appears to lack a cellulose-binding domain and does not bind to crystalline cellulose. The enzyme is efficient at releasing short fibres from filter paper and mechanical pulp, and acts synergistically with cellobiohydrolases. Its mode of degrading filter paper appears to be different to that of endoglucanase I from Trichoderma reesei. Furthermore, EG 28 releases colour from stained cellulose beads faster than any other enzyme tested. Peptide mapping suggests that it is not a fragment of another known endoglucanases from P. chrysosporium and peptide sequences indicate that it belongs to family 12 of the glycosyl hydrolases. EG 28 is glycosylated. The biological function of the enzyme is discussed, and it is hypothesized that it is homologous to EG III in Trichoderma reesei and the role of the enzyme is to make the cellulose in wood more accessible to other cellulases.

Production of a novel pyranose 2-oxidase by basidiomycete Trametes multicolor

During a screening for the enzyme pyranose 2-oxidase (P2O) which has a great potential as a biocatalyst for carbohydrate transformations, Trametes multicolor was identified as a promising, not-yet-described producer of this particular enzyme activity. Furthermore, it was found in this screening that the enzyme frequently occurs in basidiomycetes. Intracellular P2O was produced in a growth-associated manner by T. multicolor during growth on various substrates, including mono-, oligo-, and polysaccharides. Highest levels of this enzyme activity were formed when lactose or whey were used as substrates. Peptones from casein and other casein hydrolysates were found to be the most favorable nitrogen sources for the formation of P2O. By applying an appropriate feeding strategy for the substrate lactose, which ensured an elevated concentration of the carbon source during the entire cultivation, levels of P2O activity obtained in laboratory fermentations, as well as the productivity of these bioprocess experiments, could be enhanced more than 2.5-fold.

Electron microscopical observations and chemical analyses supporting Mn uptake in white rot degradedAlstoniaand pine wood stakes exposed in acid coniferous soil

Brownish-black spots and flecks several millimetres wide were frequently recognized on the surface and within nonpreservative-treated hardwood (Alstonia scholaris (R.Br.)) and softwood (Pinus sylvestris L.) test stakes placed in an acid forest soil. Energy-dispersive X-ray microanalysis in conjunction with transmission electron microscopy (TEM) and gross chemical analysis of wood using inductively coupled plasma spectrometry showed the flecks to be composed primarily of Mn, which was selectively removed from the surrounding soil. A similar uptake of Mn into wood stakes placed in presterilized acid soil was not noted, indicating the process resulted from biotic activity. Detailed TEM observations showed intrusion of Mn into the wood cell lumina and into areas of erosion, cavity formation, and decayed middle lamella in Alstonia and pine wood cells attacked by an unknown white rot decay fungus. Distinct zones of apparent delignification were also noted progressing across secondary cell walls and middle lamella regions of attacked cells, although it was unclear if the effect was caused by nonenzymatic attack by Mn, enzymatic attack by the fungus, or a combination of both. Mn is thought to play a major regulating role in both lignin depolymerization and mineralization in the presence of organic acids during white rot decay. Present observations also suggest that uptake of Mn into wood stakes during microbial degradation results from biotic activity and soil type and pH are of major significance.Key words: Mn, test stakes, electron microscopy, white rot decay, inductively coupled plasma spectrometry.