N-Enrichement experiment
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ABSTRACT:
REPOSITORIES: ENA
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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: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:Tree species preferences of deadwood-inhabiting fungi in temperate forests
| PRJEB21052 | ENA
Project description:Arbuscular mycorrhizal (AM) symbiosis develops through fungal colonization of root epidermal and cortical cells, culminating in the formation of arbuscules, transient, tree-like intracellular hyphal structures for nutrient exchange. To dissect the complexity of AM establishment in rice (Oryza sativa) roots colonized by Rhizophagus irregularis, we conducted spatial transcriptomics of plant and fungal genes at single-cell resolution. This revealed differences in transcriptional activity between fungal structures and reprogramming of plant cell-identity markers upon colonization. Furthermore, cells hosting similarly developed arbuscules showed striking transcriptional heterogeneity, suggesting hidden functional diversity at the individual cell level. For stage-resolved profiling of translation, we used AM-stage specific Translating Ribosome Affinity Purification RNA sequencing (TRAP-seq) with promoters active at discrete stages of symbiosis or arbuscule development. This revealed extensive spatiotemporal changes in the ribosome-bound transcript population, including sets of phosphate, nitrogen, and carbon transporters and regulators with specific enrichment and depletion patterns at different stages of arbuscule development. Rice transcripts encoding cell wall biosynthesis genes and defense markers were present in low abundance at early stages but highly abundant at late stages of the arbuscule lifespan, supporting a host-driven shift toward arbuscule termination. Together, these findings highlight the nuanced dynamic regulation of AM symbiosis at the cellular level, refining our understanding of how nutrient exchange and fungal development are coordinated in space and time.
2026-04-27 | GSE308140 | GEO
Project description:Effect of N deposition in a highly N-limited habitat: deadwood
| PRJEB15650 | ENA
Project description:Amplicon-based fungal metagenomic sequencing for the identification of fungal species in brain tissue from Alzheimer's disease. The study consists in 14 samples, sequenced using Illumina's paired-end technology.
| EGAD00001003196 | EGA
Project description:Pioneering fungal communities in restored deadwood
| PRJEB65744 | ENA