Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12021300_1.fastq.gz | Fastqsanger.gz | |||
| SRR12021300_2.fastq.gz | Fastqsanger.gz | |||
| SRR12021301.fastq.gz | Fastqsanger.gz | |||
| SRR12021301_1.fastq.gz | Fastqsanger.gz | |||
| SRR12021301_2.fastq.gz | Fastqsanger.gz |
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Project description:ARDS-mediated lung transcriptome alterations were identified in forest musk deer. Moreover, multiple transcripts/genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.
2022-10-19 | GSE191259 | GEO
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:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus. A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 527890) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) grown on Minimum Melin Norkrans medium (MMN) amended with ammonium (C/N ratio 3) and harvested at different times of carbon starvation.)
2014-04-01 | E-GEOD-54940 | biostudies-arrayexpress
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus.
2014-04-01 | GSE54940 | GEO
Project description:Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply. Comparative transcriptomics of ectomycorrhizal (ECM) versus brown-rot (BR) fungi while degrading soil-organic matter
2015-09-24 | E-GEOD-64897 | biostudies-arrayexpress