Ontology highlight
ABSTRACT:
PROVIDER: PRJNA643664 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12133100_1.fastq.gz | Fastqsanger.gz | |||
| SRR12133100_2.fastq.gz | Fastqsanger.gz | |||
| SRR12133101_1.fastq.gz | Fastqsanger.gz | |||
| SRR12133101_2.fastq.gz | Fastqsanger.gz | |||
| SRR12133102_1.fastq.gz | Fastqsanger.gz |
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Project description:In this study, examinations were performed on how the ECM fungus Paxillus involutus degrade complex, plant and litter material by using elemental analyses, FTIR spectroscopy, pyrolysis-GC/MS, and synchronous fluorescence spectroscopy together with microarray analyses screening 12,214 gene models, derived from 454 sequenced cDNA libraries. Rineau, F., Roth, D., Shah, F., Smits, M., Johansson, T., Canbäck, B., Bjarke Olsen, P., Persson, P., Nedergaard Grell, M., Lange, L., & Tunlid, A. (201X) Expression levels tune enzymatic exploitation of plant litter material by ectomycorrhizal fungi (manuscript in preparation). A 18-subarray study (data from 18 subarrays collected from two 12-plex microarrays (IDs 468335 and 468400) using total RNA recovered from three separate wild-type glass-bead cultures after amendments of various soil-derived substrates.
2012-02-01 | E-GEOD-34402 | biostudies-arrayexpress
Project description:In this study, examinations were performed on how the ECM fungus Paxillus involutus degrade complex, plant and litter material by using elemental analyses, FTIR spectroscopy, pyrolysis-GC/MS, and synchronous fluorescence spectroscopy together with microarray analyses screening 12,214 gene models, derived from 454 sequenced cDNA libraries. Rineau, F., Roth, D., Shah, F., Smits, M., Johansson, T., Canbäck, B., Bjarke Olsen, P., Persson, P., Nedergaard Grell, M., Lange, L., & Tunlid, A. (201X) Expression levels tune enzymatic exploitation of plant litter material by ectomycorrhizal fungi (manuscript in preparation).
2012-02-01 | GSE34402 | GEO
Project description:Endophytic fungi are root-inhabiting fungi that can promote plant growth in a variety of ways. They can directly stimulate plant growth by producing phytohormones, such as auxin and gibberellins. They can also indirectly promote plant growth by helping plants to acquire nutrients, such as nitrogen and phosphorus, and by protecting plants from pests and pathogens.In this study, we used a proteomic approach to identify the proteins that are expressed in rice plants after they are treated with endophytic fungi. We found that the treatment with endophytic fungi resulted in the expression of a number of proteins involved in plant growth, nutrient acquisition, and defense. These results suggest that endophytic fungi can promote plant growth and improve plant resilience to stress.
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Project description:Vulvovaginal candidiasis (VVC) affects nearly ¾ of women during their lifetime and its symptoms seriously reduce quality of life. Although Candida albicans is a common commensal, it is unknown if VVC results from a commensal to pathogenic state switch, if only some strains can cause VVC, and/or if there is displacement of commensal strains with more pathogenic strains. We studied a set of VVC and Colonizing C. albicans strains to identify consistent in vitro phenotypes associated with one group or the other. We find that the strains do not differ in overall genetic profile or behavior in culture media (i.e. MLST profile, rate of growth, filamentation), but they show strikingly different behavior during their interactions with vaginal epithelial cells. Epithelial infections with VVC-derived strains yielded stronger fungal proliferation and shedding of fungi and epithelial cells. RNA-seq analysis of representative epithelial cell infections with selected pathogenic or commensal isolates identified several differentially activated epithelial signaling pathways, including the integrin, ferroptosis and type I interferon pathways; the latter has been implicated in damage protection. The type I interferon pathway is activated more by the Colonizing strains, while type I interferon inhibition selectively increases fungal shedding of only the colonizing fungi. These data suggest that VVC strains may intrinsically have more pathogenic potential via differential elicitation of epithelial responses, including type I interferon pathway. Therefore, it may be possible to evaluate pathogenic potential in vitro to refine VVC diagnosis.
2023-02-07 | GSE207081 | 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.
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Project description:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural material on earth. It consists of complex carbohydrates and aromatic polymers found in plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability.Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases, and pectinases involved in lignocellulosic biomass degradation. We sequenced the transcriptomes of Aspergillus fumigatus Z5 induced by sucrose, xylan, cellulose and rice straw, respectively. There were 444, 1711 and 1386 significantly differently (q-value ≤ 0.0001 and |log2 of the ratio of the RPM values| ≥ 2) expressed genes in xylan, cellulose and rice straw,respectively, relative to sucrose control.
2015-11-22 | GSE55086 | 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
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Project description:Abstract: A large part of the nitrogen in forest soils is found in recalcitrant organic matter-protein complexes. Ectomycorrhizal fungi are thought to have a key role in the decomposition and mobilization of nitrogen from such complexes. The knowledge on the functional mechanisms of these processes, and how they are regulated by carbon from the host plant and the availability of more easily available forms of nitrogen sources are limited. We used spectroscopic analyses and transcriptome profiling to examine how the presence/absence of glucose and ammonium regulates the decomposition and mobilization of nitrogen from litter material by the ectomycorrhizal fungus Paxillus involutus. Amendments of glucose triggered the assimilation of nitrogen and the decomposition of the litter material. Concomitantly, the expression of genes encoding enzymes involved in oxidative (i.e. Fenton chemistry) degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism were upregulated in concert. Addition of ammonium had minute effects on both the expression of transcripts and decomposition of litter material, and only when glucose was present. Based on the spectroscopic analyses, three major types of chemical modifications of the litter material were observed. Each of them was correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggests that the expression of the decomposition and nitrogen assimilation machinery of ectomycorrhizal fungi can be firmly regulated by the host carbon supply, i.e. priming, and that the availability of inorganic nitrogen as such has limited effects on the saprotrophic activities. Rineau F, Shah F., Smits M.M., Persson P., Johansson T., Carleer R., Troein C., Tunlid A. (2013) Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus (submitted) A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 467991) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of various soil-derived substrates. Transcriptome profiling to examine how the presence/absence of glucose and ammonium regulates the decomposition and mobilization of nitrogen from litter material by the ectomycorrhizal fungus Paxillus involutus.
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