Miseq ITS amplicons biofinishes on wood
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PROVIDER: PRJEB13755 | ENA |
REPOSITORIES: ENA
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Project description:The fungal composition of natural formed biofinishes on oil treated wood
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Project description:Wood fungal community composition in stems of living trees
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Project description:The fungal response to compositional differences in softwood as measured by transcriptomics, proteomics and enzyme activities showed a partial tailoring to wood composition.
2019-04-09 | PXD009818 | Pride
Project description:The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study we evaluated how well the white-rot fungus Dichomitus squalens has adapted to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analysed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant polysaccharides not present in its natural habitat.
2017-01-05 | GSE79674 | GEO
Project description:Wood maturation produces two distinct wood tissues: juvenile wood (JW) and mature wood (LW), which are the major cause of wood qaulity variation within a tree. We investigate transcriptome reorganization during wood maturation process in radiata pine using a newly developed 18k cDNA microarrays. Developing xylem tissues from nine sampled trees at 5- and 13-year-old each were randomly divided into three groups with three trees each. Total RNA samples extracted from three trees within a group were pooled at equal amount before using for microarray experiments. Using this pooling strategy three biological replicates were formed for each microarray experiment. Dye swap was applied in each biological replicate. Comparisons between JW and MW in spring (EW) and autumn (LW) were arranged in two separate microarray experiments: juvenile earlywood (JE) vs. mature earlywood (ME), juvenile latewood (JL) vs. mature latewood (ML)
2011-06-01 | E-GEOD-20535 | biostudies-arrayexpress
Project description:AIM: By adopting comparative transcriptomic approach, we investigated the gene expression of wood decomposing Basidiomycota fungus Phlebia radiata. Our aim was to reveal how hypoxia and lignocellulose structure affect primary metabolism and the expression of wood decomposition related genes. RESULTS: Hypoxia was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides by the fungus. Our results manifest how oxygen depletion affects not only over 200 genes of fungal primary metabolism but also plays central role in regulation of secreted CAZyme (carbohydrate-active enzyme) encoding genes. Based on these findings, we present a hypoxia-response mechanism in wood-decaying fungi divergent from the regulation described for Ascomycota fermenting yeasts and animal-pathogenic species of Basidiomycota.
2020-02-01 | GSE141153 | GEO
Project description:Many brown rot fungi are capable of rapidly degrading wood and are copper-tolerant. To better understand the genes that control these processes, we examined gene expression of Fibroporia radiculosa growing on wood treated with a copper-based preservative that combined copper carbonate with dimethyldidecylammonium carbonate. A global profiling strategy called RNA-Seq was used to quantify gene expression of the fungus at days 31 and 154. At day 31, the preservative was still protecting the wood, which showed no strength loss. At day 154, the effects of the preservative were gone, and the wood exhibited 52% strength loss. Statistical analysis identified 917 genes that were differentially expressed (FDR < 1E-4). Transcripts that showed higher expression levels at the early time point were controlling increased oxalate metabolism, laccase for hydroquinone-driven hydroxyl free radical production, pectin degradation, ATP production, xenobiotic detoxification, copper resistance, and stress response. Transcripts that showed higher expression levels at the late time point were involved in degradation of cellulose, hemicellulose, and pectin, hexose transport, oxalate catabolism, catabolism of laccase substrates, extracellular proton reduction, and remodeling of the fungal cell membrane and cell wall to enhance survival at low pH.
2012-11-26 | GSE35333 | GEO
Project description:Fomitiporia mediterranea (Fmed) is one of the main fungal species found in grapevine wood rot, also called “amadou”, one of the most typical symptoms of grapevine trunk disease Esca. This fungus is functionally classified as a white-rot, able to degrade all wood structure polymers, i.e., hemicelluloses, cellulose, and the most recalcitrant component, lignin. Specific enzymes are secreted by the fungus to degrade those components, namely carbohydrate active enzymes for hemicelluloses and cellulose, which can be highly specific for given polysaccharide, and peroxidases, which enable white-rot to degrade lignin, with specificities relating to lignin composition as well. Furthermore, besides polymers, a highly diverse set of metabolites often associated with antifungal activities is found in wood, this set differing among the various wood species. Wood decayers possess the ability to detoxify these specific extractives and this ability could reflect the adaptation of these fungi to their specific environment. The aim of this study is to better understand the molecular mechanisms used by Fmed to degrade wood structure, and in particular its potential adaptation to grapevine wood. To do so, Fmed was cultivated on sawdust from different origins: grapevine, beech, and spruce. Carbon mineralization rate, mass loss, wood structure polymers contents, targeted metabolites and secreted proteins were measured. We used the well-known white-rot model Trametes versicolor for comparison. Whereas no significant degradation was observed with spruce, a higher mass loss was measured on Fmed grapevine culture compared to beech culture. Moreover, on both substrates, a simultaneous degradation pattern and the degradation of wood extractives were demonstrated, and proteomic analyses identified a relative overproduction of oxidoreductases involved in lignin and extractive degradation on grapevine cultures, and only few differences in carbohydrate active enzymes. These results could explain at least partially the adaptation of Fmed to grapevine wood structural composition compared to other wood species and suggest that other biotic and abiotic factors should be considered to fully understand the potential adaptation of Fmed to its ecological niche.
2022-09-27 | PXD036889 | Pride
Project description:Agaricomycetes produce the most efficient enzyme systems to degrade wood and the most complex morphological structures in the fungal kingdom. Despite decades-long interest in their genetic bases, the evolution and functional diversity of both wood-decay and fruiting body formation are incompletely known.Here, we perform comparative genomic and transcriptomic analyses of wood-decay and fruiting body development in Auriculariopsis ampla and Schizophyllum commune (Schizophyllaceae), species with secondarily simplified morphologies and enigmatic wood-decay strategy and weak pathogenicity to woody plants. The plant cell wall degrading enzyme repertoires of Schizophyllaceae are transitional between those of white rot species and less efficient wood-degraders such as brown rot or mycorrhizal fungi. Rich repertoires of suberinase and tannase genes were found in both species, with tannases restricted to Agaricomycetes that preferentially colonize bark-covered wood, suggesting potential complementation of their weaker wood-decaying abilities and adaptations to wood colonization through the bark. Fruiting body transcriptomes of A. ampla and S. commune revealed a high rate of divergence in developmental gene expression, but also several genes with conserved developmental expression, including novel transcription factors and small-secreted proteins, some of the latter might represent fruiting body effectors. Taken together, our analyses highlighted novel aspects of wood-decay and fruiting body development in a widely distributed family of mushroom-forming fungi.
2019-06-18 | GSE132826 | GEO