Terrestrial metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:High-throughput sequencing of Arabidopsis thaliana endogenous small RNAs by 454 pyrosequencing. Keywords: high-throughput sequencing
2006-11-02 | GSE5228 | 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.
2013-07-22 | GSE47775 | 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:Characterization of gene expression levels with RNA-seq was performed on self-renewing (SR) and senescent (SEN) human adult adipose derived mesenchymal stem cells (hADSCs) using the Roche 454 pyrosequencing platform.
2017-08-15 | GSE77284 | GEO
Project description:The small RNAs of Selaginella moellendorffii were sampled by direct pyrosequencing (454 Life Sciences). These data represent microRNAs, siRNAs, and other expressed small RNAs of ~18-~28 nts. in length. Keywords: Small RNA sequencing - high throughput
2007-06-30 | GSE7320 | GEO
Project description:Fungal communities in tropical forest soils Metagenome
| PRJNA270839 | ENA
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:<p>The composition and changes of the fungal population and of the metabolites present in grapes and in ferments of Vitis vinifera L. cv. Corvina, one of the major components of the Amarone musts, were dissected aiming at the identification of constant characteristics possibly influenced by the productive process. The fungal populations and metabolomic profiles were analyzed in three different vintages. 454-pyrosequencing on the ribosomal ITS1 region has been used to identify the fungal population present in Corvina grapes and fresh must. Samples were also subjected to metabolomics analysis measuring both free volatile compounds and glycosylated aroma precursors through an untargeted approach with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. Albeit strongly dependent on the climate, both the mycobiota and metabolome of Corvina grapes and fresh musts show some characteristics recursive in different vintages. Such persistent characteristics are likely determined by the method adopted to produce Amarone or other dry wines made from partially dried grapes. In particular, the harsh conditions imposed by the prolonged withering appear to contribute to the shaping of the fungal populations. The fungal genera and metabolites present in different vintages in V. vinifera L. cv. Corvina grapes and fresh musts represent core components of the peculiar technique of production of Amarone. Their identification allows the in-depth understanding and improved control of the process of production of this economically and culturally relevant wine.</p><p><br></p><p><strong>Linked cross omic data sets:</strong></p><p>Meta-taxonomics data associated with this study are available in the European Nucleotide Archive (ENA): accession number <a href='https://www.ebi.ac.uk/ena/browser/view/PRJEB15229' rel='noopener noreferrer' target='_blank'>PRJEB15229</a>.</p>
2017-11-14 | MTBLS392 | MetaboLights