Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1048497 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:LEAF-FUNGAL ENDOPHYTES OF NEOTROPICAL GYMNOSPERMS: A CULTURE-BASED, SANGER SEQUENCING AND WHOLE GENOME APPROACH
| PRJNA1048478 | ENA
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:Two potato cultivars, Russet Burbank and Bionta, were inoculated with three different endophytes containing different AHL types. The impact of the endophytes to the different cultivars was measured by gene expression analysis with a customized microarray B. phytofirmans type strain PsJN was originally isolated as a contaminant from surface-sterilized, Glomus vesculiferum-infected onion roots (Nowak et al., 1998), whereas strain P6 RG6-12 was isolated from the rhizosphere of a grassland in the Netherlands (Salles et al., 2006). This strain was selected based on its similarity to strain PsJN based on 16S rRNA gene homology, and similar phenotypic features. Both strains were generally cultivated on King's medium (King et al., 1954). For the mutant AHL to the strain B. phytofirmans PsJN a quorum quenching approach as described by Wopperer et al., 2006 was employed. Plasmid pMLBAD-aiiA, which contains aiiA, the Bacillus sp. 240B1 lactonase gene, was transferred to B. phytofirmans PsJN by triparental mating as described by de Lorenzo and Timmis (1994). 2 cultivars, 3 endophytes
2010-05-19 | E-GEOD-12862 | biostudies-arrayexpress
Project description:Broad-host root endophytes establish long-term interactions with a large variety of plants, thereby playing a significant role in natural and managed ecosystems and in evolution of land plants. To exploit plants as living substrates and to establish a compatible interaction with morphologically and biochemically extremely different hosts, endophytes must respond and adapt to different plant signals and host metabolic states. Here we identified host-adapted colonization strategies and host-specific effector candidates of the mutualistic root endophyte Piriformospora indica by a global investigation of fungal transcriptional responses to barley and Arabidopsis at different symbiotic stages. Additionally we examined the role played by nitrogen in these two diverse associations. Cytological studies and colonization analyses of a barley mutant and fungal RNAi strains show that distinct physiological and metabolic signals regulate host-specific lifestyle in P. indica. This is the foundation for exploring how distinct fungal and host symbiosis determinants modulate biotrophy in one host and saprotrophy in another host and, ultimately, gives hints into the mechanisms underlying host adaptation in root symbioses.
2013-07-22 | GSE47775 | GEO
Project description:Broad-host root endophytes establish long-term interactions with a large variety of plants, thereby playing a significant role in natural and managed ecosystems and in evolution of land plants. To exploit plants as living substrates and to establish a compatible interaction with morphologically and biochemically extremely different hosts, endophytes must respond and adapt to different plant signals and host metabolic states. Here we identified host-adapted colonization strategies and host-specific effector candidates of the mutualistic root endophyte Piriformospora indica by a global investigation of fungal transcriptional responses to barley and Arabidopsis at different symbiotic stages. Additionally we examined the role played by nitrogen in these two diverse associations. Cytological studies and colonization analyses of a barley mutant and fungal RNAi strains show that distinct physiological and metabolic signals regulate host-specific lifestyle in P. indica. This is the foundation for exploring how distinct fungal and host symbiosis determinants modulate biotrophy in one host and saprotrophy in another host and, ultimately, gives hints into the mechanisms underlying host adaptation in root symbioses. Arabidopsis and barley roots were inoculated with Piriformospora indica and grown for 14 days. Additionally P. indica was grown on 1/10 PNM medium alone. Samples were taken 3 and 14 dpi (Arabidopsis), 14 dpi (barley) and 3dpi (1/10 PNM). Each experiment was performed in three independent biological repetitions. Piriformospora indica gene expression examined only.
2013-07-22 | E-GEOD-47775 | biostudies-arrayexpress
Project description:Secondary growth is a key characteristic evolved from seed plants and generates secondary xylem—the most abundant tissue on Earth. Recent studies have uncovered xylem developmental lineages in eudicots and magnoliids of angiosperms. However, xylem development in gymnosperms, the other representative clade of seed plants, remained elusive. We performed single-cell transcriptomics for xylem cells of conifers (Cunninghamia lanceolata), the major clade in gymnosperms. Using Seurat and scVI-based cross-species integration, we reconstructed the xylem differentiation trajectories and revealed that the radial system is conserved across seed plants, while the axial system in C. lanceolata exhibits a composite lineage architecture resembling both eudicots and magnoliids. To validate these trajectories, we established a multi-modal spatial framework incorporating spatial transcriptomics, spatial proteomics, and spatial metabolomics. These three spatial layers provided orthogonal evidence confirming cell-type identities and trajectory inference. Additionally, we identified a xylem cell population unique to gymnosperms, suggesting a lineage-specific specialization. Together, our findings uncover a more complex ancestral xylem architecture in gymnosperms and propose a progressive simplification of axial developmental programs from gymnosperms to angiosperms, highlighting a trajectory of reductive evolution in seed plant vascular development.
2025-12-07 | GSE253891 | GEO