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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
Project description:We report the discovery of a beta-glucosidase gene (Pgβglu-1) whose expression underpins natural resistance to a major forest pest, the spruce budworm (SBW) in white spruce (Picea glauca (Voss.) Moench). We performed a microarray experiment to compare resistant (R) and non-resistant (N-R) trees. Pgβglu-1 transcripts levels uniquely were up to 1000 times higher in phenotypically resistant trees and correlated with accumulation of acetophenones compounds that reduce SBW development. These resistance traits were heritable, temporally correlated with the emergence of the most damaging larval stages and were highly variable in the natural population across a large geographic area. The recombinant gene product specifically catalyzed the release of biologically active acetophenones from their glucoside precursors. SBW outbreaks have become more frequent and intense; therefore, the phenotypic diversity resulting from variation in Pgβglu-1 expression may be a key for the adaptability of spruce populations.
2014-05-06 | GSE57301 | GEO
Project description:We report the discovery of a beta-glucosidase gene (PgM-NM-2glu-1) whose expression underpins natural resistance to a major forest pest, the spruce budworm (SBW) in white spruce (Picea glauca (Voss.) Moench). We performed a microarray experiment to compare resistant (R) and non-resistant (N-R) trees. PgM-NM-2glu-1 transcripts levels uniquely were up to 1000 times higher in phenotypically resistant trees and correlated with accumulation of acetophenones compounds that reduce SBW development. These resistance traits were heritable, temporally correlated with the emergence of the most damaging larval stages and were highly variable in the natural population across a large geographic area. The recombinant gene product specifically catalyzed the release of biologically active acetophenones from their glucoside precursors. SBW outbreaks have become more frequent and intense; therefore, the phenotypic diversity resulting from variation in PgM-NM-2glu-1 expression may be a key for the adaptability of spruce populations. Transcriptome profiling was carried out with needles from 7 resistant and 7 non-resistant trees (harvested on June 17th, 2010), and 3 samples per tree (n=42) with a custom microarray developed for spruce species and comprising oligonucleotide probes for 23,853 unique P. glauca gene sequences (Raherison et al., 2012).
2014-05-06 | E-GEOD-57301 | biostudies-arrayexpress