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REPOSITORIES: ENA
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Project description:Fungal diversity and niche differentiation in decaying logs and stumps
| PRJEB18707 | ENA
Project description:Deadwood plays a crucial role in forest ecosystems, but we have limited information about the specific fungal taxa and extracellular lignocellulolytic enzymes that are actively involved in the decomposition process in situ. To investigate this, we studied the fungal metaproteome of twelve deadwood tree species in a replicated, eight-year experiment. Key fungi observed included genera of white-rot fungi (Basidiomycota, e.g. Armillaria, Hypholoma, Mycena, Ischnoderma, Resinicium), brown-rot fungi (Basidiomycota, e.g. Fomitopsis, Antrodia), diverse Ascomycota including xylariacous soft-rot fungi (e.g. Xylaria, Annulohypoxylon, Nemania) and various wood-associated endophytes and saprotrophs (Ascocoryne, Trichoderma, Talaromyces). These fungi used a whole range of extracellular lignocellulolytic enzymes, such as peroxidases, peroxide-producing enzymes, laccases, cellulases, glucosidases, hemicellulases (xylanases) and lytic polysaccharide monooxygenases (LPMOs). Both the fungi and enzymes were tree-specific, with specialists and generalists being distinguished by network analysis. The extracellular enzymatic system was highly redundant, with many enzyme classes of different origins present simultaneously in all decaying logs. Strong correlations were found between peroxide-producing enzymes (oxidases) and peroxidases as well as LPMOs, and between ligninolytic, cellulolytic and hemicellulolytic enzymes. The overall protein abundance of lignocellulolytic enzymes was reduced by up to -30% in gymnosperm logs compared to angiosperm logs, and gymnosperms lacked ascomycetous enzymes, which may have contributed to the lower decomposition of gymnosperm wood. In summary, we have obtained a comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in several temperate forest tree species, which can help to improve our understanding of the complex ecological processes in forest ecosystems.
2024-04-22 | PXD041962 | Pride
Project description:Soil-wood interactions: influence of decaying logs on composition of soil fungal communities
| PRJEB20576 | ENA
Project description:Using 21K spruce microarray (that contains 21.8 thousand unique transcripts) we performed analysis of the transcriptome response of interior spruce (Picea glauca x engelmannii) inoculated with the spruce beetle (Dendroctonus rufipennis) vectored blue stain fungal pathogen Leptographium abietinum or treated with wounding. This microarray analysis revealed large transcriptome reorganization with close to 2000 transcripts (10% of the studied transcriptome) differentially expressed within two weeks of treatment, with the wounding response affecting close to 5% of the interior spruce transcriptome.
2012-12-01 | GSE23678 | GEO
Project description:Using 21K spruce microarray (that contains 21.8 thousand unique transcripts) we performed analysis of the transcriptome response of interior spruce (Picea glauca x engelmannii) inoculated with the spruce beetle (Dendroctonus rufipennis) vectored blue stain fungal pathogen Leptographium abietinum or treated with wounding. This microarray analysis revealed large transcriptome reorganization with close to 2000 transcripts (10% of the studied transcriptome) differentially expressed within two weeks of treatment, with the wounding response affecting close to 5% of the interior spruce transcriptome. RNA was isolated from the bark of interior spruce inoculated with Leptographium abietinum, treated with wounding, or untreated control for three time points (6h, 2days and 2 weeks). Three independent biological replicates were included for each treatment and each time point. Three hybridizations were performed for each comparison of different treatments (fungal, wounding, control) within each time point (6 hours, 2 days, 2 weeks) and one hybridization was performed for the comparison of the same treatments between time points (total 36 hybridizations/slides).
2012-12-01 | E-GEOD-23678 | biostudies-arrayexpress
Project description:Fungal communities in decayed logs of Pinus densiflora
| PRJDB3141 | ENA
Project description:Fungal community in Pinus densiflora logs for seedling regeneration
| PRJDB13698 | ENA