Mechanisms of wood degradation by brown-rot fungi: chelator-mediated cellulose degradation and binding of iron by cellulose

Exploring the Biological Pathways of Siderophores and Their Multidisciplinary Applications: A Comprehensive Review

Siderophores are a class of small molecules renowned for their high iron binding capacity, essential for all life forms requiring iron. This article provides a detailed review of the diverse classifications, and biosynthetic pathways of siderophores, with a particular emphasis on siderophores synthesized via nonribosomal peptide synthetase (NRPS) and non-NRPS pathways. We further explore the secretion mechanisms of siderophores in microbes and plants, and their role in regulating bioavailable iron levels. Beyond biological functions, the applications of siderophores in medicine, agriculture, and environmental sciences are extensively discussed. These applications include biological pest control, disease treatment, ecological pollution remediation, and heavy metal ion removal. Through a comprehensive analysis of the chemical properties and biological activities of siderophores, this paper demonstrates their wide prospects in scientific research and practical applications, while also highlighting current research gaps and potential future directions.

Influence of the chemical content of sawdust on the levels of important macronutrients and ash composition in Pearl oyster mushroom (Pleurotus ostreatus)

Influence of chemical composition of sawdust on the nutritional profile of oyster mushrooms (Pleurotus ostreatus) has yet to receive significant research attention. This information will help mushroom growers to select specific sawdust for the production of mushroom with desired dietary preferences. This study assessed the influence of the chemical composition of sawdust on the macronutrients and ash content of the pearl oyster mushrooms. The American Standard for Testing Materials and other widely accepted protocols were used to determine the C-N ratio, pH, lignin, hemicellulose and cellulose contents of mixed sawdust from tropical wood species. The study evaluated the fat, crude fibre, crude protein, carbohydrate, and ash content of the oyster mushroom cultivated on the sawdust. Cellulose constituted the largest component of the sawdust (47.82%), followed by lignin (33.29%). The yield of the mushroom (on 0.05 kg of sawdust) ranged from 490.1 to 540.9 g (biological efficiency: 44-50%); the average carbohydrates constituent in the mushroom was 56.28%. pH of the sawdust influenced the crude protein, carbohydrate, fat and ash content of oyster mushrooms (p<0.05) most significantly. The hemicelluloses also had a significant effect (p<0.05) on the mushroom's minerals, fat and crude fiber content. The study revealed that the mushroom producers would likely obtain high protein content using sawdust with low pH (slightly acidic to slightly basic) in the oyster mushroom. Mushrooms grown on substrates, rich in hemicelluloses, had low fat and high crude fiber content.

First Description of Non-Enzymatic Radical-Generating Mechanisms Adopted by Fomitiporia mediterranea: An Unexplored Pathway of the White Rot Agent of the Esca Complex of Diseases

Fomitiporia mediterranea (Fmed) is the primary Basidiomycota species causing white rot in European vineyards affected by the Esca complex of diseases (ECD). In the last few years, an increasing number of studies have highlighted the importance of reconsidering the role of Fmed in ECD etiology, justifying an increase in research interest related to Fmed's biomolecular pathogenetic mechanisms. In the context of the current re-evaluation of the binary distinction (brown vs. white rot) between biomolecular decay pathways induced by Basidiomycota species, our research aims to investigate the potential for non-enzymatic mechanisms adopted by Fmed, which is typically described as a white rot fungus. Our results demonstrate how, in liquid culture reproducing nutrient restriction conditions often found in wood, Fmed can produce low molecular weight compounds, the hallmark of the non-enzymatic "chelator-mediated Fenton" (CMF) reaction, originally described for brown rot fungi. CMF reactions can redox cycle with ferric iron, generating hydrogen peroxide and ferrous iron, necessary reactants leading to hydroxyl radical (^•OH) production. These observations led to the conclusion that a non-enzymatic radical-generating CMF-like mechanism may be utilized by Fmed, potentially together with an enzymatic pool, to contribute to degrading wood constituents; moreover, indicating significant variability between strains.

Oxygen Radical-Generating Metabolites Secreted by Eutypa and Esca Fungal Consortia: Understanding the Mechanisms Behind Grapevine Wood Deterioration and Pathogenesis

Eutypa dieback and Esca complex are fungal diseases of grape that cause large economic losses in vineyards. These diseases require, or are enhanced by, fungal consortia growth which leads to the deterioration of the wood tissue in the grapevine trunk; however, pathogenesis and the underlying mechanisms involved in the woody tissue degradation are not understood. We examined the role that the consortia fungal metabolome have in generating oxygen radicals that could potentially play a role in trunk decay and pathogenesis. Unique metabolites were isolated from the consortia fungi with some metabolites preferentially reducing iron whereas others were involved in redox cycling to generate hydrogen peroxide. Metabolite suites with different functions were produced when fungi were grown separately vs. when grown in consortia. Chelator-mediated Fenton (CMF) chemistry promoted by metabolites from these fungi allowed for the generation of highly reactive hydroxyl radicals. We hypothesize that this mechanism may be involved in pathogenicity in grapevine tissue as a causal mechanism associated with trunk wood deterioration/necrosis in these two diseases of grape.

Role of perhydroxyl radical in the chelator-mediated Fenton reaction

The chelator-mediated Fenton (CMF) chemistry is one of the main biological non-enzymatic systems for oxygen-centered radical generation. Perhydroxyl radical (HO2•) is a secondary radical specie in CMF systems, however, despite...

Phylogenetic and Functional Diversity of Saprolegniales and Fungi Isolated from Temperate Lakes in Northeast Germany

The contribution of fungi to the degradation of plant litter and transformation of dissolved organic matter (humic substances, in particular) in freshwater ecosystems has received increasing attention recently. However, the role of Saprolegniales as one of the most common eukaryotic organisms is rarely studied. In this study, we isolated and phylogenetically placed 51 fungal and 62 Saprolegniales strains from 12 German lakes. We studied the cellulo-, lignino-, and chitinolytic activity of the strains using plate assays. Furthermore, we determined the capacity of 10 selected strains to utilize 95 different labile compounds, using Biolog FF MicroPlates™. Finally, the ability of three selected strains to utilize maltose and degrade/produce humic substances was measured. Cladosporium and Penicillium were amongst the most prevalent fungal strains, while Saprolegnia, Achlya, and Leptolegnia were the most frequent Saprolegniales strains. Although the isolated strains assigned to genera were phylogenetically similar, their enzymatic activity and physiological profiling were quite diverse. Our results indicate that Saprolegniales, in contrast to fungi, lack ligninolytic activity and are not involved in the production/transformation of humic substances. We hypothesize that Saprolegniales and fungi might have complementary roles in interacting with dissolved organic matter, which has ecological implications for carbon cycling in freshwater ecosystems.

The Effects of Iron Rust on the Ageing of Woods and Their Derived Pulp Paper

The accelerated ageing of wood in terms of heating or iron rusting has a potential effect on the physio-mechanical, chemical and biological properties of wood. The effects of accelerated ageing on the mechanical, physical and fungal activity properties of some wood materials (Schinus terebinthifolius, Erythrina humeana, Tectona grandis, Pinus rigida and Juglans nigra) were studied after several cycles of heating and iron rusting. The fungal activity was assayed against the growth of Aspergillus terreus, Aspergillus niger, Fusarium culmorum and Stemphylium solani. In addition, the mechanical and optical properties of paper sheets produced from those wood pulps by means of Kraft cooking were evaluated. The mechanical and chemical properties of the studied wood species were affected significantly (p < 0.05) by the accelerated ageing, compared to control woods. With Fourier transform infrared (FTIR) spectroscopy, we detected an increase in the intensity of the spectra of the functional groups of cellulose in the heated samples, which indicates an increase in cellulose content and decrease in lignin content, compared to other chemical compounds. For pulp properties, woods treated by heating showed a decrease in the pulp yield. The highest significant values of tensile strength were observed in pulp paper produced from untreated, heated and iron-rusted P. rigida wood and they were 69.66, 65.66 and 68.33 N·m/g, respectively; we calculated the tear resistance from pulp paper of untreated P. rigida (8.68 mN·m²/g) and T. grandis (7.83 mN·m²/g) and rusted P. rigida (7.56 mN·m²/g) wood; we obtained the values of the burst strength of the pulp paper of untreated woods of P. rigida (8.19 kPa·m²/g) and T. grandis (7.49 kPa·m²/g), as well as the fold number of the pulp paper of untreated, heated and rusted woods from P. rigida, with values of 195.66, 186.33 and 185.66, respectively. After 14 days from the incubation, no fungal inhibition zones were observed. Accelerated ageing (heated or iron-rusted) produced significant effects on the mechanical and chemical properties of the studied wood species and affected the properties of the produced pulp paper.

Determination of landfill gas generation potential from lignocellulose biomass contents of municipal solid waste

The presence of heat, methane (CH₄) and oxygen in landfill sub-surface causes initiation of spontaneous waste ignition posing severe environmental impacts. A municipal solid waste (MSW) reactor (trough) was designed to monitor landfill gases (LFGs) i.e., CH₄ and CO₂ and its potential from different waste categories (synthetic waste, fresh waste, 3-month, 6-month, 3-year and 5-year-old waste) collected from open MSW dumpsite. The quantity of cellulose (C), hemicellulose (H) and lignin (L) contents (C + H: L) present in organic waste fraction of each waste category was determined. Results showed that fresh waste which has higher ratio of C + H: L is responsible for maximum CH₄ and CO₂ generation i.e., 31,660 and 46,078 ml/g of volatile solid, respectively. The ratio of C + H: L observed in fresh waste, 3-month, 6-month, 3-year and 5-year-old waste was 2.62, 1.70, 1.32, 1.21 and 1, respectively. The study also showed that LFG generation is directly proportional to lignocellulose biomass contents present in MSW. Artificial neural network (ANN) modelling was used for the cross validation of CH₄ yield (valuable product) which showed ±4% error between experimental and predicted data.

Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola"

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed gene expression levels of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression was observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species—aspen, pine, and spruce—under various culture conditions. We found that F. pinicola is able to modify gene expression (transcription levels) across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.

Regioselective degradation of [beta] 1,3 glucan by ferrous ion and hydrogen peroxide (Fenton oxidation)

Many species use Fe⁺² and H₂O₂ to oxidize a wide variety of compounds to simpler molecules. Both pathogen killing by leukocytes (neutrophils and lymphocytes) and degradation of cellulose by brown rot fungi rely on excretion of Fe⁺² ions and H₂O₂, the Fenton reagent. To elucidate the mechanism of Fenton oxidation of carbohydrates, β1,3 glucan (laminaran), a major fungal wall polysaccharide, was oxidized using a molar ratio of monomer/Fe⁺²/H₂O₂ of 10:1:1 (primarily). We labeled the reaction products and profiled them as fluorescent-labeled molecules in polyacrylamide gels and as hydrophobic-tagged molecules using reverse phase liquid chromatography/mass spectrometry (HPLC/MS). Sub-stoichiometric concentrations of Fe⁺² and H₂O₂ fragmented laminaran into smaller molecules containing carbonyl and carboxylic acid groups visible on fluorescent-labeled carbohydrate polyacrylamide gel electrophoresis. HPLC/MS analysis of glucan fragments showed masses consistent with six classes of molecules: aldoses, dialdoses, uronic acids, hexosuloses, aldonic acids, and hexulosonic acids. The results were consistent with published mechanisms where hydrogen radical (H•) abstraction from a C-H or O-H bond begins a cascade of reactions leading to 1) C-C bond cleavage to produce aldose/dialdose pairs; 2) oxo-group (O = ) addition to produce uronic and aldonic acids; 3) hydroxyl group (HO-) addition to produce gluconolactone and hexosuloses; and 4) hexulosonic acids. Most products resulted from regioselective H• abstractions characteristic of oxidations by ferryl-oxo ion [(FeO)⁺²] or perferryl-oxo ion [(FeO)⁺³] in close contact with specific positions in the glycan. Therefore, oxidations initiated by regioselectively-bound Fe ions were the predominant initiators of polysaccharide degradations.

Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1

Lignin is the second most abundant carbon polymer on earth and despite having more fuel value than cellulose, it currently is considered a waste byproduct in many industrial lignocellulose applications. Valorization of lignin relies on effective and green methods of de-lignification, with a growing interest in the use of microbes. Here we investigate the physiology and molecular response of the novel facultative anaerobic bacterium, Tolumonas lignolytica BRL6-1, to lignin under anoxic conditions. Physiological and biochemical changes were compared between cells grown anaerobically in either lignin-amended or unamended conditions. In the presence of lignin, BRL6-1 accumulates higher biomass and has a shorter lag phase compared to unamended conditions, and 14% of the proteins determined to be significantly higher in abundance by log2 fold-change of 2 or greater were related to Fe(II) transport in late logarithmic phase. Ferrozine assays of the supernatant confirmed that Fe(III) was bound to lignin and reduced to Fe(II) only in the presence of BRL6-1, suggesting redox activity by the cells. LC-MS/MS analysis of the secretome showed an extra band at 20 kDa in lignin-amended conditions. Protein sequencing of this band identified a protein of unknown function with homology to enzymes in the radical SAM superfamily. Expression of this protein in lignin-amended conditions suggests its role in radical formation. From our findings, we suggest that BRL6-1 is using a protein in the radical SAM superfamily to interact with the Fe(III) bound to lignin and reducing it to Fe(II) for cellular use, increasing BRL6-1 yield under lignin-amended conditions. This interaction potentially generates organic free radicals and causes a radical cascade which could modify and depolymerize lignin. Further research should clarify the extent to which this mechanism is similar to previously described aerobic chelator-mediated Fenton chemistry or radical producing lignolytic enzymes, such as lignin peroxidases, but under anoxic conditions.

Carbohydrate-binding module O-mannosylation alters binding selectivity to cellulose and lignin

Improved understanding of the effect of protein glycosylation is expected to provide the foundation for the design of protein glycoengineering strategies. In this study, we examine the impact of O-glycosylation on the binding selectivity of a model Family 1 carbohydrate-binding module (CBM), which has been shown to be one of the primary sub-domains responsible for non-productive lignin binding in multi-modular cellulases. Specifically, we examine the relationship between glycan structure and the binding specificity of the CBM to cellulose and lignin substrates. We find that the glycosylation pattern of the CBM exhibits a strong influence on the binding affinity and the selectivity between both cellulose and lignin. In addition, the large set of binding data collected allows us to examine the relationship between binding affinity and the correlation in motion between pairs of glycosylation sites. Our results suggest that glycoforms displaying highly correlated motion in their glycosylation sites tend to bind cellulose with high affinity and lignin with low affinity. Taken together, this work helps lay the groundwork for future exploitation of glycoengineering as a tool to improve the performance of industrial enzymes.

Improved understanding of the effect of protein glycosylation is expected to provide the foundation for the design of protein glycoengineering strategies.

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.

Application of Hydrochar Altered Soil Microbial Community Composition and the Molecular Structure of Native Soil Organic Carbon in a Paddy Soil

The benefits and disadvantages of hydrochar incorporation into soil have been heavily researched. However, the effect of hydrochar application on the soil microbial communities and the molecular structure of native soil organic carbon (SOC) has not been thoroughly elucidated. This study conducted an incubation experiment at 25 °C for 135 days using a soil column with 0.5 and 1.5% hydrochar-amended paddy soil to explore the interconnections between changes in soil properties and microbial communities and shifts in native SOC structure using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) and NMR after hydrochar application. Hydrochar addition decreased the labile SOC fraction by 15.6-33.6% and increased the stable SOC fraction by 10.3-27.0%. These effects were significantly stronger for 1.5% hydrochar-treated soil. Additionally, hydrochar addition induced the native SOC with 1.0-3.0% more carbon and 6.0-13.0% higher molecular weight. The SOC in hydrochar-amended soil contained more aromatic compounds but fewer carbohydrates and lower polarity. This was resulted by a statistically significant reduction in Sphingobacterium, which was active in polycyclic aromatic hydrocarbon degradation, and an increase in Flavobacterium, Anaerolinea, Penicillium, and Acremonium, which were the efficient decomposers of labile SOC. These findings will help elucidate the potential influence of hydrochar on the carbon biogeochemical cycle in the soil.

Chelator-mediated biomimetic degradation of cellulose and chitin

Non-enzymatic degradation of wood via a chelator-mediated Fenton (CMF) system is the primary method for initial attack in brown rot fungal decomposition of wood, the most common type of fungal degradation of terrestrial carbon biomass on the planet. In this study, the degradation of thin films of cellulose and chitin by a CMF system was investigated and compared to enzymatic hydrolysis. The kinetics of the rapid cellulose and chitin deconstruction and the morphologies of the degraded cellulose and chitin surfaces were studied by quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM), respectively. The QCM-D results quantitatively indicated that ~90 wt% of the regenerated cellulose or chitin was capable of being deconstructed by CMF action alone. While enzymatic degradation was consistent with stripping of layers from the surface of the cellulose or chitin films, the CMF process exhibited a pronounced two stage process with a rapid initial depolymerization throughout the films. The initial degradation rates for both model surfaces by the CMF system were faster than enzyme action. This research suggests that the CMF process should be applicable for the deconstruction of a wide variety of polysaccharides over Fenton chemistry alone.

Biochemical characterization of Serpula lacrymans iron-reductase enzymes in lignocellulose breakdown

Putative iron-reductase (IR) genes from Serpula lacrymans with similarity to the conserved iron-binding domains of cellobiose dehydrogenase (CDH) enzymes have been identified. These genes were cloned and expressed to functionally characterize their activity and role in the decomposition of lignocellulose. The results show that IR1 and IR2 recombinant enzymes have the ability to depolymerize both lignin and cellulose, are capable of the reduction of ferric iron to the ferrous form, and are capable of the degradation of nitrated lignin. Expression of these genes during wheat straw solid-state fermentation was shown to correlate with the release of compounds associated with lignin decomposition. The results suggest that both IR enzymes mediate a non-enzymatic depolymerisation of lignocellulose and highlight the potential of chelator-mediated Fenton systems in the industrial pre-treatment of biomass.

pH-Dependent Relationship between Catalytic Activity and Hydrogen Peroxide Production Shown via Characterization of a Lytic Polysaccharide Monooxygenase from Gloeophyllum trabeum

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that perform oxidative cleavage of recalcitrant polysaccharides. We have purified and characterized a recombinant family AA9 LPMO, LPMO9B, from Gloeophyllum trabeum (GtLPMO9B) which is active on both cellulose and xyloglucan. Activity of the enzyme was tested in the presence of three different reductants: ascorbic acid, gallic acid, and 2,3-dihydroxybenzoic acid (2,3-DHBA). Under standard aerobic conditions typically used in LPMO experiments, the first two reductants could drive LPMO catalysis whereas 2,3-DHBA could not. In agreement with the recent discovery that H₂O₂ can drive LPMO catalysis, we show that gradual addition of H₂O₂ allowed LPMO activity at very low, substoichiometric (relative to products formed) reductant concentrations. Most importantly, we found that while 2,3-DHBA is not capable of driving the LPMO reaction under standard aerobic conditions, it can do so in the presence of externally added H₂O₂ At alkaline pH, 2,3-DHBA is able to drive the LPMO reaction without externally added H₂O₂, and this ability overlaps entirely the endogenous generation of H₂O₂ by GtLPMO9B-catalyzed oxidation of 2,3-DHBA. These findings support the notion that H₂O₂ is a cosubstrate of LPMOs and provide insight into how LPMO reactions depend on, and may be controlled by, the choice of pH and reductant.IMPORTANCE Lytic polysaccharide monooxygenases promote enzymatic depolymerization of lignocellulosic materials by microorganisms due to their ability to oxidatively cleave recalcitrant polysaccharides. The properties of these copper-dependent enzymes are currently of high scientific and industrial interest. We describe a previously uncharacterized fungal LPMO and show how reductants, which are needed to prime the LPMO by reducing Cu(II) to Cu(I) and to supply electrons during catalysis, affect enzyme efficiency and stability. The results support claims that H₂O₂ is a natural cosubstrate for LPMOs by demonstrating that when certain reductants are used, catalysis can be driven only by H₂O₂ and not by O₂ Furthermore, we show how auto-inactivation resulting from endogenous generation of H₂O₂ in the LPMO-reductant system may be prevented. Finally, we identified a reductant that leads to enzyme activation without any endogenous H₂O₂ generation, allowing for improved control of LPMO reactivity and providing a valuable tool for future LPMO research.

Multiple iron reduction by methoxylated phenolic lignin structures and the generation of reactive oxygen species by lignocellulose surfaces

Chelator-mediated Fenton chemistry is capable of reducing non-stochiometric amounts of iron via hydroquinone oxidation. These types of reactions have previously been demonstrated to be promoted by some lignocellulose degrading fungi in generating hydroxyl radicals to permit lignified plant cell wall deconstruction. Here we demonstrate that lignocellulose surfaces, when exposed by chemical treatment or fragmentation, can promote a similar multi-oxidative mechanism in the presence of iron. Iron reduction by lignin surfaces permits the generation of hydroxyl radicals in the cell wall to help explain fungal non-enzymatic cell wall deconstruction, and it also provides an explanation for certain phenomenon such as the anthropogenic generation of formaldehyde by wood. The mechanism also provides a basis for the generation of electrons by lignin that are required by certain fungal redox enzymes active in plant cell wall degrading systems. Overall, the data demonstrate that iron found naturally in lignocellulose materials will promote the oxidation of phenolic lignin compounds in the naturally low pH environments occurring within lignified plant cell walls, and that this activity is promoted by cell wall fragmentation.

Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass

Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.

Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed the gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression and RNA editing were observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression and RNA editing encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. There was no overlap between differentially expressed and differentially edited genes, suggesting that these may provide F. pinicola with independent mechanisms for responding to different conditions. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. In contrast, the suites of genes subject to RNA editing were much less affected by culture conditions. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi.IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that enable fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species, aspen, pine, and spruce, under various culture conditions. We examined both gene expression (transcription levels) and RNA editing (posttranscriptional modification of RNA, which can potentially yield different proteins from the same gene). We found that F. pinicola is able to modify both gene expression and RNA editing profiles across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.

Magnetic mapping of distribution of wood ash used for fertilization of forest soil

The effect of wood-ash fertilization on forest soils has been assessed mainly through geochemical methods (e.g., content of soil organic matter or nutrients). However, a simple and fast method of determining the distribution of the ash and the extent of affected soil is missing. In this study we present the use of magnetic susceptibility, which is controlled by Fe-oxides, in comparing the fertilized soil in the forest plantation of pine and oak with intact forest soil. Spatial and vertical distribution of magnetic susceptibility was measured in an oak and pine plantation next to stems of young plants, where wood ash was applied as fertilizer. Pattern of the susceptibility distribution was compared with that in non-fertilized part of the plantation as well as with a spot of intact natural forest soil nearby. Our results show that the wood-ash samples contain significant amount of ferrimagnetic magnetite with susceptibility higher than that of typical forest soil. Clear differences were observed between magnetic susceptibility of furrows and ridges. Moreover, the dispersed ash remains practically on the surface, does not penetrate to deeper layers. Finally, our data suggest significant differences in surface values between the pine and oak plants. Based on this study we may conclude that magnetic susceptibility may represent a simple and approximate method of assessing the extent of soil affected by wood-ash.

Molecular Networks of Postia placenta Involved in Degradation of Lignocellulosic Biomass Revealed from Metadata Analysis of Open Access Gene Expression Data

To understand the common gene expression patterns employed by P. placenta during lignocellulose degradation, we have retrieved genome wide transcriptome datasets from NCBI GEO database and analyzed using customized analysis pipeline. We have retrieved the top differentially expressed genes and compared the common significant genes among two different growth conditions. Genes encoding for cellulolytic (GH1, GH3, GH5, GH12, GH16, GH45) and hemicellulolytic (GH10, GH27, GH31, GH35, GH47, GH51, GH55, GH78, GH95) glycoside hydrolase classes were commonly up regulated among all the datasets. Fenton's reaction enzymes (iron homeostasis, reduction, hydrogen peroxide generation) were significantly expressed among all the datasets under lignocellulolytic conditions. Due to the evolutionary loss of genes coding for various lignocellulolytic enzymes (including several cellulases), P. placenta employs hemicellulolytic glycoside hydrolases and Fenton's reactions for the rapid depolymerization of plant cell wall components. Different classes of enzymes involved in aromatic compound degradation, stress responsive and detoxification mechanisms (cytochrome P450 monoxygenases) were found highly expressed in complex plant biomass substrates. We have reported the genome wide expression patterns of genes coding for information, storage and processing (KOG), tentative and predicted molecular networks involved in cellulose, hemicellulose degradation and list of significant protein-ID's commonly expressed among different lignocellulolytic growth conditions.

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.

Modification of the nanostructure of lignocellulose cell walls via a non-enzymatic lignocellulose deconstruction system in brown rot wood-decay fungi

Wood decayed by brown rot fungi and wood treated with the chelator-mediated Fenton (CMF) reaction, either alone or together with a cellulose enzyme cocktail, was analyzed by small angle neutron scattering (SANS), sum frequency generation (SFG) spectroscopy, Fourier transform infrared (FTIR) analysis, X-ray diffraction (XRD), atomic force microscopy (AFM), and transmission electron microscopy (TEM). Results showed that the CMF mechanism mimicked brown rot fungal attack for both holocellulose and lignin components of the wood. Crystalline cellulose and lignin were both depolymerized by the CMF reaction. Porosity of the softwood cell wall did not increase during CMF treatment, enzymes secreted by the fungi did not penetrate the decayed wood. The enzymes in the cellulose cocktail also did not appear to alter the effects of the CMF-treated wood relative to enhancing cell wall deconstruction. This suggests a rethinking of current brown rot decay models and supports a model where monomeric sugars and oligosaccharides diffuse from the softwood cell walls during non-enzymatic action. In this regard, the CMF mechanism should not be thought of as a "pretreatment" used to permit enzymatic penetration into softwood cell walls, but instead it enhances polysaccharide components diffusing to fungal enzymes located in wood cell lumen environments during decay. SANS and other data are consistent with a model for repolymerization and aggregation of at least some portion of the lignin within the cell wall, and this is supported by AFM and TEM data. The data suggest that new approaches for conversion of wood substrates to platform chemicals in biorefineries could be achieved using the CMF mechanism with >75% solubilization of lignocellulose, but that a more selective suite of enzymes and other downstream treatments may be required to work when using CMF deconstruction technology. Strategies to enhance polysaccharide release from lignocellulose substrates for enhanced enzymatic action and fermentation of the released fraction would also aid in the efficient recovery of the more uniform modified lignin fraction that the CMF reaction generates to enhance biorefinery profitability.

Transcriptome and Secretome Analyses of the Wood Decay Fungus Wolfiporia cocos Support Alternative Mechanisms of Lignocellulose Conversion

Certain wood decay basidiomycetes, collectively referred to as brown rot fungi, rapidly depolymerize cellulose while leaving behind the bulk of cell wall lignin as a modified residue. The mechanism(s) employed is unclear, but considerable evidence implicates the involvement of diffusible oxidants generated via Fenton-like chemistry. Toward a better understanding of this process, we have examined the transcriptome and secretome of Wolfiporia cocos when cultivated on media containing glucose, purified crystalline cellulose, aspen (Populus grandidentata), or lodgepole pine (Pinus contorta) as the sole carbon source. Compared to the results obtained with glucose, 30, 183, and 207 genes exhibited 4-fold increases in transcript levels in cellulose, aspen, and lodgepole pine, respectively. Mass spectrometry identified peptides corresponding to 64 glycoside hydrolase (GH) proteins, and of these, 17 corresponded to transcripts upregulated on one or both woody substrates. Most of these genes were broadly categorized as hemicellulases or chitinases. Consistent with an important role for hydroxyl radical in cellulose depolymerization, high transcript levels and upregulation were observed for genes involved in iron homeostasis, iron reduction, and extracellular peroxide generation. These patterns of regulation differ markedly from those of the closely related brown rot fungus Postia placenta and expand the number of enzymes potentially involved in the oxidative depolymerization of cellulose.

IMPORTANCE

The decomposition of wood is an essential component of nutrient cycling in forest ecosystems. Few microbes have the capacity to efficiently degrade woody substrates, and the mechanism(s) is poorly understood. Toward a better understanding of these processes, we show that when grown on wood as a sole carbon source the brown rot fungus W. cocos expresses a unique repertoire of genes involved in oxidative and hydrolytic conversions of cell walls.

Enhancing anaerobic digestion of cotton stalk by pretreatment with a microbial consortium (MC1)

Microbial pretreatment is beneficial in some anaerobic digestion systems, but the consortia used to date have not been able to effectively increase methane production from cotton stalk. In this study, a thermophilic microbial consortium (MC1) was used for pretreatment in order to enhance biogas and methane production yields. The results indicated that the concentrations of soluble chemical oxygen demand and volatile organic products increased significantly in the early stages of pretreatment. Ethanol, acetic acid, propionic acid, and butyric acid were the predominant volatile organic products in the MC1 hydrolysate. Biogas and methane production yields from cotton stalk were significantly increased following MC1 pretreatment. In addition, the methane production rate from the treated cotton stalk was greater than that from the untreated sample.

Discovery of 12-mer peptides that bind to wood lignin

Lignin, an abundant terrestrial polymer, is the only large-volume renewable feedstock composed of an aromatic skeleton. Lignin has been used mostly as an energy source during paper production; however, recent interest in replacing fossil fuels with renewable resources has highlighted its potential value in providing aromatic chemicals. Highly selective degradation of lignin is pivotal for industrial production of paper, biofuels, chemicals, and materials. However, few studies have examined natural and synthetic molecular components recognizing the heterogeneous aromatic polymer. Here, we report the first identification of lignin-binding peptides possessing characteristic sequences using a phage display technique. The consensus sequence HFPSP was found in several lignin-binding peptides, and the outer amino acid sequence affected the binding affinity of the peptides. Substitution of phenylalanine7 with Ile in the lignin-binding peptide C416 (HFPSPIFQRHSH) decreased the affinity of the peptide for softwood lignin without changing its affinity for hardwood lignin, indicating that C416 recognised structural differences between the lignins. Circular dichroism spectroscopy demonstrated that this peptide adopted a highly flexible random coil structure, allowing key residues to be appropriately arranged in relation to the binding site in lignin. These results provide a useful platform for designing synthetic and biological catalysts selectively bind to lignin.

Comparison and evaluation of concurrent saccharification and anaerobic digestion of Napier grass after pretreatment by three microbial consortia

Napier grass is potentially a viable feedstock for biofuel production. The present study investigated biological pretreatment of Napier grass by three microbial consortia followed by saccharification and anaerobic digestion. The pretreatment efficiencies of three microbial consortia were compared in terms of degradation ability, saccharide and biogas yield. The lignocellulose loss rates of Napier grass varied largely. The biomass pretreated by the consortium WSD-5 gave 43.4% and 66.2% total sugar yield under low and moderate loadings of commercial enzyme mixtures, while the highest yield was 83.2% pretreated by the consortium MC1 under a high enzyme loading. The maximum methane yield of pretreated samples by the consortia MC1, WSD-5 and XDC-2 were 259, 279, 247ml/g VS, respectively, which were 1.39, 1.49 and 1.32times greater than the values of the untreated controls. This study showed that pretreatments by MC1, WSD-5 and XDC-2 were capable of significantly enhancing both the saccharide and methane yields from Napier grass.

Plant-polysaccharide-degrading enzymes from Basidiomycetes

SUMMARY

Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.

Improvement of halophilic cellulase production from locally isolated fungal strain

Halophilic cellulases from the newly isolated fungus, Aspergillus terreus UniMAP AA-6 were found to be useful for in situ saccharification of ionic liquids treated lignocelluloses. Efforts have been taken to improve the enzyme production through statistical optimization approach namely Plackett–Burman design and the Face Centered Central Composite Design (FCCCD). Plackett–Burman experimental design was used to screen the medium components and process conditions. It was found that carboxymethylcellulose (CMC), FeSO₄·7H₂O, NaCl, MgSO₄·7H₂O, peptone, agitation speed and inoculum size significantly influence the production of halophilic cellulase. On the other hand, KH₂PO₄, KOH, yeast extract and temperature had a negative effect on enzyme production. Further optimization through FCCCD revealed that the optimization approach improved halophilic cellulase production from 0.029 U/ml to 0.0625 U/ml, which was approximately 2.2-times greater than before optimization.

Siderophores in environmental research: roles and applications

Siderophores are organic compounds with low molecular masses that are produced by microorganisms and plants growing under low iron conditions. The primary function of these compounds is to chelate the ferric iron [Fe(III)] from different terrestrial and aquatic habitats and thereby make it available for microbial and plant cells. Siderophores have received much attention in recent years because of their potential roles and applications in various areas of environmental research. Their significance in these applications is because siderophores have the ability to bind a variety of metals in addition to iron, and they have a wide range of chemical structures and specific properties. For instance, siderophores function as biocontrols, biosensors, and bioremediation and chelation agents, in addition to their important role in weathering soil minerals and enhancing plant growth. The aim of this literature review is to outline and discuss the important roles and functions of siderophores in different environmental habitats and emphasize the significant roles that these small organic molecules could play in applied environmental processes.

Enhancing the anaerobic digestion of lignocellulose of municipal solid waste using a microbial pretreatment method

The use of biological pretreatment in anaerobic digestion systems has some potential; however, to date, these methods have not been able to effectively increase methane production of lignocellulose of municipal solid waste (LMSW). In this study a thermophilic microbial consortium (MC1) was used as a pretreatment method in order to enhance biogas and methane production yields. The results indicated that sCOD concentration increased significantly in the early stages of pretreatment. Ethanol, acetic acid, propionic acid, and butyric acid were the predominant volatile organic products in the MC1 hydrolysate. Biogas and methane production yields of LMSW significantly increased following MC1 pretreatment. In addition, the methane production rate of the treated LMSW was greater than that observed from the untreated sample.

Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose

BACKGROUND

Renewable lignocellulosic biomass is an advantageous resource for the production of second generation biofuels and other biorefinery products. In Middle Europe, wheat straw is one of the most abundant low-cost sources of lignocellulosic biomass. For its efficient use, an efficient mix of cellulases and hemicellulases is required. In this paper, we investigated how cellulase production by T. reesei on wheat straw compares to that on lactose, the only soluble and also cheap inducing carbon source for enzyme production.

RESULTS

We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30% of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair, iron homeostatis and autophagy. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60% of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional.

CONCLUSIONS

Our data reveal several major differences in the transcriptome between wheat straw and lactose which may be related to the higher enzyme formation on the former and their further investigation could lead to the development of methods for increasing enzyme production on lactose.

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.

Microbial communities in large-scale wood piles and their effects on wood quality and the environment

The demand of renewable energy sources, i.e. biomass, is steadily increasing worldwide to reduce the need of fossil energy sources. Biomass such as energy crops, woody species, forestry and agricultural residues are the most common renewable energy sources. Due to uneven demand for wood fuel, the material is mostly stored outdoors in chip piles or as logs until utilisation. Storage of biomass is accompanied by chemical, physical and biological processes which can significantly reduce the fuel quality. However, heating plants require high-quality biomass to ensure efficient operation, thereby minimising maintenance costs. Therefore, optimised storage conditions and duration times for chipped wood and tree logs have to be found. This paper aims at reviewing available knowledge on the pathways of microbial effects on stored woody biomass and on investigations of the fungal and bacterial community structure and identity. Moreover, potential functions of microorganisms present in wood chip piles and logs are discussed in terms of (1) reduction of fuel quality, (2) catalysing self-ignition processes, and (3) constituting health risk and unfriendly work environment.

Diversity of a mesophilic lignocellulolytic microbial consortium which is useful for enhancement of biogas production

A mesophilic lignocellulolytic microbial consortium BYND-5, established by successive subcultivation, was applied to enhance the biogas production. The degradation efficiency of BYND-5 for rice straw was more than 49.0 ± 1.8% after 7 days of cultivation at 30°C. Various organic compounds, including acetic acid, propionic acid, butyric acid and glycerin were detected during biodegradation. The diversity analysis of BYND-5 was conducted by ARDRA (Amplified ribosomal DNA restriction analysis) of the 16S rDNA clone library. Results indicated that bacterial groups represented in the clone library were the Firmicutes (5.96%), the Bacteroidetes (40.0%), Deferribacteres (8.94%), Proteobacteria (16.17%), Lentisphaerae (2.13%), Fibrobacteraceae (1.7%), and uncultured bacterium (25.1%). Additionally, the enhancement of biogas yield and methane content was directly related to the pretreatment with BYND-5. The microbial community identified herein is potential candidate consortium for the degradation of waste lignocellulose and enhancement of biogas production under the mesophilic temperature conditions.

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.

Soil fungal cellobiohydrolase I gene (cbhI) composition and expression in a loblolly pine plantation under conditions of elevated atmospheric CO2 and nitrogen fertilization

The simultaneous increase of atmospheric CO(2) and nitrogen (N) deposition to terrestrial ecosystems is predicted to alter plant productivity and, consequently, to change the amount and quality of above- and belowground carbon entering forest soils. It is not known how such changes will impact the composition and function of soil fungal communities that play a key role in degrading complex carbon. We sequenced the fungal cellobiohydrolase I gene (cbhI) from soil DNA and cDNA to compare the richness and composition of resident and expressed cbhI genes at a U.S. Department of Energy free air-carbon dioxide enrichment (FACE) site (NC), which had been exposed to elevated atmospheric CO(2) and/or N fertilization treatment for several years. Our results provide evidence that the richness and composition of the cellulolytic fungi surveyed in this study were distinct in the DNA- and cDNA-based gene surveys and were dominated by Basidiomycota that have low or no representation in public databases. The surveys did not detect differences in richness or phylum-level composition of cbhI-containing, cellulolytic fungi that correlated with elevated CO(2) or N fertilization at the time of sampling.