Wood-Cadillac biofilter fungi
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB97411 | ENA |
REPOSITORIES: ENA
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Project description:Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β‐glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single‐species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) employed secondary metabolite (SM) synthesis in response to a competitor, as shown by the upregulation of several SM-synthesizing genes in the interaction. R. placenta (Antrodia clade) instead upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that an oxidative burst may be a response to competitors in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving abundant unknowns on the battlefield. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.
2020-05-22 | GSE151023 | 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:Wood-degrading fungi play a critical role in global carbon cycling, and their varied mechanisms for deconstruction offer pathways for industrial bioconversion. In this study, we used comparative genomics to isolate upregulation patterns among fungi with brown rot (carbohydrate-selective) or white rot (lignin-degrading) nutritional modes. Specifically, we used whole-transcriptome profiling to compare early, middle, and late decay stages on wood wafers, matching differentially-expressed gene (DEG) patterns with fungal growth and enzyme activities. This approach highlighted 34 genes uniquely upregulated in early brown rot stages, with notable candidates involved in generating reactive oxygen species (ROS) as a pretreatment mechanism during brown rot. This approach further isolated 18 genes in late brown rot stages that may be adapted to handle oxidatively-reacted lignocellulose components. By summing gene expression levels in functional classes, we also identified a broad and reliable distinction in glycoside hydrolase (GH) versus lignocellulose oxidative (LOX) transcript counts that may reflect the energy investment burden of lignin-degrading machinery among white rot fungi.
2018-01-05 | GSE108189 | GEO
Project description:Identification of wood-decomposing fungi and their secreted enzymes at different wood proximal depths.
2025-09-15 | PXD048319 | 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:Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers. This SuperSeries is composed of the SubSeries listed below.
2021-08-11 | GSE156901 | GEO
Project description:Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers.
2021-08-11 | GSE156166 | GEO
Project description:Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers.
2021-08-11 | GSE156899 | GEO
Project description:Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers.
2021-08-11 | GSE156164 | GEO