Wood decay metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA575777 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10235500.fastq.gz | Fastqsanger.gz | |||
| SRR10235600.fastq.gz | Fastqsanger.gz | |||
| SRR10235501.fastq.gz | Fastqsanger.gz | |||
| SRR10235601.fastq.gz | Fastqsanger.gz | |||
| SRR10235502.fastq.gz | Fastqsanger.gz |
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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:Vuilleminia comedens is a basidiomycete pioneer species in attached angiosperm branches, especially beech (Fagus sylvaticus), initiating decomposition of lignocellulose. Pioneer species exert priority effects on subsequent colonisers influencing community structure. Wood decay is an essential part of the carbon cycle, underpinning forest ecosystem processes, but despite its clear importance, remarkably little is known about the pioneer species which begin the process of lignocellulose decomposition. This work studied the transcriptome and proteome of V. comedens growing in inoculated beech wood blocks in the laboratory. Our analysis focused on nutrient acquisition by decomposition of lignocellulose, and the specialised metabolic processes utilised by the fungus to mitigate against the effects of both plant defence compounds and the toxic derivatives produced as a result of lignin breakdown. Our results show that V. comedens expresses transcripts encoding a large range of enzymes associated with lignocellulose decomposition and metabolism of carbohydrate-based compounds, suggesting a broad-based approach to nutrient acquisition. Furthermore, the transcriptome included an array of genes for specialised metabolism and xenobiotic mitigation, some of which were highly expressed, suggesting that the chemical environment that V. comedens inhabits during wood decay is a significant challenge to successful growth. The proteomic data support the importance of lignin decomposition and xenobiotic mitigation to V. comedens.
2020-06-16 | GSE100126 | GEO
Project description:Wood-decomposition in terrestrial ecosystems is a very important process with huge ecologic consequences. This decomposition process is a combination of biological respiration, leaching and fragmentation, mainly triggered by organismic activities. In order to gain a deeper insight into these microbial communities and their role in deadwood decay, we used metaproteomics. Metaproteomics is an important tool and offers the ability to characterize the protein complement of environmental microbiota at a given point in time. In this dataset, we provide data of an exemplary beech wood log and applied different extraction methods to provide the proteome profile of beech dead wood and their corresponding fungal-bacterial community.
2020-05-27 | PXD016801 | Pride
Project description:Decomposition of lignin-rich wood by fungi drives nutrient recycling in woodland ecosystems. Fluctuating abiotic conditions are known to promote the functioning of ecological communities and ecosystems. In the context of wood decay, fluctuating temperature increases decomposition rates. Metabolomics, in tandem with other ‘omics tools, can highlight the metabolic processes affected by experimental treatments, even in the absence of genome sequences and annotations. Globally, natural wood decay communities are dominated by the phylum Basidiomycota. We examined the metabolic responses of Mucidula mucida, a dominant constituent of pioneer communities in beech branches in British woodlands, and Exidia glandulosa, a stress-selected constituent of the same communities, in response to constant and diurnally cycling temperature. We applied untargeted metabolomics and proteomics to beech wood blocks, colonised by M. mucida or E. glandulosa and exposed to either diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design. Metabolites and proteins linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under-enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely E. glandulosa showed little differential response to the experimental treatments. By demonstrating temperature dependant metabolic signatures related to nutrient acquisition in a generalist wood decay fungus, we provide new insights into how abiotic conditions can affect community-mediated decomposition and carbon turnover in forests. We show that mechanisms underpinning important biogeochemical processes can be highlighted using untargeted metabolomics and proteomics in the absence of well-annotated genomes.
2021-06-03 | PXD026003 | Pride
Project description:1. Decomposition of lignin-rich wood by fungi drives nutrient recycling in woodland ecosystems. Fluctuating abiotic conditions are known to promote the functioning of ecological communities and ecosystems. In the context of wood decay, fluctuating temperature increases decomposition rates. Metabolomics, in tandem with other ‘omics tools, can highlight the metabolic processes affected by experimental treatments, even in the absence of genome sequences and annotations. Globally, natural wood decay communities are dominated by the phylum Basidiomycota. We examined the metabolic responses of Mucidula mucida, a dominant constituent of pioneer communities in beech branches in British woodlands, and Exidia glandulosa, a stress-selected constituent of the same communities, in response to constant and diurnally cycling temperature. 2. We applied untargeted metabolomics and proteomics to beech wood blocks, colonised by M. mucida or E. glandulosa and exposed to either diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design. 3. Metabolites and proteins linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under-enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely E. glandulosa showed little differential response to the experimental treatments. 4. Synthesis. By demonstrating temperature dependant metabolic signatures related to nutrient acquisition in a generalist wood decay fungus, we provide new insights into how abiotic conditions can affect community-mediated decomposition and carbon turnover in forests. We show that mechanisms underpinning important biogeochemical processes can be highlighted using untargeted metabolomics and proteomics in the absence of well-annotated genomes.
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Project description:AIM: By adopting comparative transcriptomic approach, we investigated the gene expression of wood decomposing Basidiomycota fungus Phlebia radiata. Our aim was to reveal how hypoxia and lignocellulose structure affect primary metabolism and the expression of wood decomposition related genes. RESULTS: Hypoxia was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides by the fungus. Our results manifest how oxygen depletion affects not only over 200 genes of fungal primary metabolism but also plays central role in regulation of secreted CAZyme (carbohydrate-active enzyme) encoding genes. Based on these findings, we present a hypoxia-response mechanism in wood-decaying fungi divergent from the regulation described for Ascomycota fermenting yeasts and animal-pathogenic species of Basidiomycota.
2020-02-01 | GSE141153 | GEO
Project description:Metatranscriptome of decayed wood fungal communities from Pinus contorta in Bitterroot National Forest, Montana, United States - GP2-1
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Project description:Metatranscriptome of decayed wood fungal communities from Pinus contorta in Bitterroot National Forest, Montana, United States - GP2-2E
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Project description:Metatranscriptome of decayed wood fungal communities from Pinus contorta in Bitterroot National Forest, Montana, United States - GP1-1
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Project description:Metatranscriptome of decayed wood fungal communities from Pinus contorta in Bitterroot National Forest, Montana, United States - GP1-2E
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