Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1321382 | ENA |
REPOSITORIES: ENA
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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:Host shifts enhance diversification of the ectomycorrhizal fungal genus Strobilomyces
| PRJDB4146 | ENA
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:Mycorrhiza helper bacteria (MHB) promote the formation of ectomycorrhizae between tree roots and ectomycorrhizal fungi. Despite the high relevance of MHB for forestry and for sustainable tree production in tree nurseries, little is known about the properties of the bacteria that contribute to their helper abilities. The MHB strain Pseudomonas fluorescens BBc6R8 is used as a model to study the mechanisms of the helper effect. We took advantage of new technologies to obtain, for the first time, the whole genome sequence of an MHB. Analyses reveal an important plasticity of the genome with numerous functions acquired by horizontal gene tranfer. Genome mining was combined with transcriptomic and mutagenesis approaches to reveal molecular determinants of the helper effect. The data suggest that the production of helper molecules is likely to be constitutive in vitro. The helper effect appears to be pleiotropic and to rely, for a substantial part, on trophic interactions. Despite its helper abilities, the bacterium is also able in specific conditions to outcompete ectomycorrhizal fungi and inhibit their growth. We conclude that the helper bacterium possess a broad range of properties whose expression depending on the biotic and abiotic conditions can result in either a beneficial, neutral or antagonistic interaction between the plant, the ectomycorrhizal fungus and the bacterium.
2014-06-12 | GSE38243 | GEO
Project description:Mycorrhiza helper bacteria (MHB) promote the formation of ectomycorrhizae between tree roots and ectomycorrhizal fungi. Despite the high relevance of MHB for forestry and for sustainable tree production in tree nurseries, little is known about the properties of the bacteria that contribute to their helper abilities. The MHB strain Pseudomonas fluorescens BBc6R8 is used as a model to study the mechanisms of the helper effect. We took advantage of new technologies to obtain, for the first time, the whole genome sequence of an MHB. Analyses reveal an important plasticity of the genome with numerous functions acquired by horizontal gene tranfer. Genome mining was combined with transcriptomic and mutagenesis approaches to reveal molecular determinants of the helper effect. The data suggest that the production of helper molecules is likely to be constitutive in vitro. The helper effect appears to be pleiotropic and to rely, for a substantial part, on trophic interactions. Despite its helper abilities, the bacterium is also able in specific conditions to outcompete ectomycorrhizal fungi and inhibit their growth. We conclude that the helper bacterium possess a broad range of properties whose expression depending on the biotic and abiotic conditions can result in either a beneficial, neutral or antagonistic interaction between the plant, the ectomycorrhizal fungus and the bacterium. The study was performed along a kinetic with three sampling times: before contact between the bacterial colonies and the fungus (14 days after inoculation), at the time of contact (16 days after inoculation) and after an extended period of contact (21 days). For each time, three independent replicates were performed. A control treatment without the fungus was performed in triplicate and sampled at 14 days.
2014-06-12 | E-GEOD-38243 | biostudies-arrayexpress
Project description:Ectomycorrhizal (ECM) fungi are crucial for tree nitrogen (N) nutrition, however, mechanisms governing N transfer from fungal tissues to the host plant are not well understood. ECM fungal isolates, even from the same species, vary considerably in their ability to support tree N nutrition resulting in a range of often unpredictable symbiotic outcomes. In this study, we used isotopic labelling to quantify the transfer of N to the plant host by isolates from the ECM genus Pisolithus known to have significant variability in colonisation and transfer of nutrients to a host. We considered the metabolic fate of N acquired by the fungi and found that the percentage of plant N acquired through symbiosis significantly correlated to the concentration of free amino acids present in the ECM extra-radical mycelium. Transcriptomic analyses complemented these findings with isolates having high amino acid content and N transfer showing increased expression of genes in amino acid transport and catabolic pathways. These results suggest that fungal N metabolism drives transfer to the host plant in this interaction and that relative N transfer may be possible to predict through basic biochemical analyses.
2023-10-27 | GSE235669 | 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
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.
2015-09-24 | GSE64897 | GEO
Project description:Mycorrhizal helper bacterium that enhances ectomycorrhizal establishment
| PRJNA20583 | ENA