High throughput sequencing of soil fungi ITS after litter degradation
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PROVIDER: PRJNA1108896 | ENA |
REPOSITORIES: ENA
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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: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:High-throughput sequencing of soil bacteria and fungi Genome sequencing
| PRJNA1327099 | ENA
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)
2013-04-30 | GSE45303 | GEO
Project description:High-throughput Bifidobacterium isolation
| PRJEB98585 | ENA
Project description:high-throughput sequencing Raw sequence reads
| PRJNA1364771 | ENA
Project description:high-throughput sequencing Raw sequence reads
| PRJNA1308046 | ENA
Project description:high-throughput sequencing Raw sequence reads
| PRJNA1244309 | ENA
Project description:high-throughput sequencing Raw sequence reads
| PRJNA1244750 | ENA
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.
2013-04-30 | E-GEOD-45303 | biostudies-arrayexpress