Plant microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA735611 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15057207_1.fastq.gz | Fastqsanger.gz | |||
| SRR15057207_2.fastq.gz | Fastqsanger.gz | |||
| SRR15057208_1.fastq.gz | Fastqsanger.gz | |||
| SRR15057208_2.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: we here adress the gene regulation of G.rosea in response to plant signals in the switch from asymbiotic to presymbiotic growth. Methods: -Strigolactone response: Spores of G.rosea were treated with GR24 (a synthetic strigolactone analog) and collected at 2 days after treatment. Control conditions: spores treated with solvent (M medium acetone 0.1%. Assay and control were performed in triplicates. -Root exsudate response: a cellophane membrane allowing molecule exchanges was deposited on in vitro Daucus carotta roots. Spores were spotted on this membrane and collected 10 days later. Control conditions: spores were spotted on cellophane membrane directly deposited on solid M medium. Assay and control were performed in triplicates. -Fungal gene expression were analyzed on mRNA were sequenced by Illumina HiSeq. sequencing Reads were firstly used in the de novo assembly of Gigaspora rosea Non Redundent Virtual Transcript and then mapped on the assembled transcriptome using CLC genomics workbench. Results: while GR24 triggered the regulation of only few genes which includes 32 genes upregulated (fold chang >2; FDR<0,05, experiment difference>10) and 61 downregulated (fold change < -2; FDR<0,05,experiment difference>10) genes, root exudates regulated several times more genes. A total of 390 genes were up-regulated by root exudates and 442 genes were down-regulated. Moreover, a majority of the genes (23 of 32 upregulated and 25 of 61 downregulated genes) regulated by GR24 were also regulated by root exudates. This is in consistant with the fact that strigolactones secreted from plant root are already characterized as a group of plant signals during AM symbiosis. The result that a large part of genes were differentialy expressed in reponse to root exudates but not GR24 suggested the presence of other plant signals than strigolactones. Conclusions: as a key player during the switch from asymbiotic to presymbiotic growth of G.rosea, plant root secreted signals - including but not limited to striglactones - significantly modified the expression of many G.rosea genes. The genes differentially expressed are mainly involved in oxidation-redution and metabolic processes that might contribute to prepare G.rosea for the following steps of symbiotic association with the host plant.
2016-03-07 | GSE67906 | GEO
Project description:Purpose: The recent publication of the fungal mutualist R. irregularis genome facilitated transcriptomic studies. We here adress the gene regulation of R. irregularis in response to plant signals in the switch from asymbiotic to presymbiotic growth Methods: Spores of R. irregularis were treated with GR24 (strigolactone synthetic analog) and collected at 1 hour, 2 days, 7 days and 14 days after induction. To stimulate the fungus with root exudates, a cellophane membrane allowing molecule exchanges was deposited on in vitro Daucus carotta roots. Spores were spotted on this membrane and collected 14 days after. To monitor fungal gene regulation, control conditions were also prepared and mRNA were sequenced by HiSeq Illumina. Read were mapped on the genome assembly with CLCworkbench Results: At 1 hour, GR24 triggered the overexpression (fold change >2; FDR<0,05) of 123 genes and the repression (fold change < -2; FDR<0,05) of 17 genes. At 2 days, 33 genes were induced, 13 repressed ; at 7 days 106 genes were induced and 13 repressed and at 14 days 19 genes were induced and 10 repressed. Few genes overlap between the different time point. Root exudates induced 251 genes and repressed 63 genes. Few genes were regulated by both GR24 and root exudates. Conclusions: GR24 kinetic showed that fungal gene regulation is sequential, quick and involves hundreds of genes. Among those genes, a chitin synthase, involved either in fungal growth either in symbiotic signal production was strongly induced at 1hour, 7 days and 14 days. As few genes are regulated in response to root exudates and GR24, we propose that other plant signals play a role in ealy steps and trigger fungal gene regulation. Several genes coding for putative secreted peptides were induced in response to these plant signals. These genes might be effectors involved in early plant defense manipulation, then facilitating root entry. Thus, they are good candidates to investigate early steps of plant penetration.
2018-02-01 | GSE67913 | GEO
Project description:Assessment of Microbes for Improving Wild Rice Restoration
| PRJNA719786 | ENA
Project description:Purpose: The recent publication of the fungal mutualist R. irregularis genome facilitated transcriptomic studies. We here adress the gene regulation of R. irregularis in response to root exudates from rice wild-type and osnope1 (no perception candidate - mutant unable to host arbuscular mycorrhizal fungi) Methods: Spores of R. irregularis were treated with root exudates and collected at 1 hour, 24 hours and 7 days after addition. To monitor fungal gene regulation, control conditions were also prepared at T0, 1h, 24h and 7d. mRNA were sequenced by HiSeq Illumina. Reads were mapped on the Rhizophagus irregularis genome assembly (Gloin1 - Tisserant et al., PNAS, 2013) using CLCworkbench suite. Results: -At 1h, a set of 92 fungal genes were found up-regulated in response to wt root exudates (92), not to osnope1 root exudates, many of them being involved in cell signaling. -At 24h and 7d, numerous genes putatively involved in primary metabolism were up-regulated in response to wt root exudates, not in response to osnope1 root exudates -Several vital genes involved in cell development are repressed in response to osnope1 RE compared to wt RE. Conclusions: these results argue for a high metabolic activity induced by wt root exudates, not by osnope1 root exudates.
2017-02-04 | GSE65595 | GEO
Project description:Seeds are crucial for plant reproduction, dispersal, and agriculture. Seed quality and vigour greatly impact crop production, referring to their ability to germinate rapidly and uniformly under varying environmental conditions, producing healthy seedlings that can withstand biotic and abiotic stress accentuated by global climate change. During germination, seeds release exudates, complex mixtures of organic and inorganic molecules, into the micro-environment surrounding them, known as the spermosphere. These exudates play a pivotal role in seedling development and overall plant fitness by influencing microbial selection, growth, and interactions in the spermosphere, ultimately shaping the plant's microbiome. Our research demonstrated that germinating seeds release diverse metabolites, peptides, proteins, and small RNAs in the exudates, some with functional properties like antimicrobial or antioxidant activities. To understand the composition and functional properties of germinating seed exudates, we conducted our study using eight common bean seed genotypes produced under two contrasted locations in France. We investigated the diversity of peptides in the spermosphere.
2024-04-19 | PXD051625 |
Project description:Two diazotrophic bacteria, BPMP-PU-28 and BPMP-EL-40, isolated from the rhizosphere of a wild wheat ancestor (T. t. dicoccoides) grown in soil from its refuge area in the Fertile Crescent or from south of France, respectively, were shown to behave as efficient Plant Growth Promoting Rhizobacteria (PGPR) upon interaction with an elite wheat cultivar (Anvergur), providing about 50% of the seed nitrogen content in plants grown under low assimilable nitrogen availability. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar and to analyze the exo-metabolomes and exo-proteomes of the two strains. Altered root development was observed, with distinctive responses according to the strain, BPMP-PU-28 also inducing a strong increase in root hair length and density. Exo-metabolome analysis revealed a complex set of secondary metabolites including fatty acids potentially involved in volatile organic compounds (VOCs) metabolism, cyclopeptides that could act as phytohomone mimetics, quorum sensing molecules having inter-kingdom signaling properties and nutrient ion chelators. The exo-proteome comprised a set of strain specific enzymatic activities (e.g., proteases) and structural proteins belonging to outer-membrane vesicles likely to sequester metabolites, peptides and enzymes in their lumen. Thus, the wheat ability to establish efficient beneficial interactions with PGPR has not been profoundly reprogrammed during domestication and breeding, and PGPR constitutively exude rich and complex metabolomes and proteomes, in absence of partner roots, which could allow numerous mechanisms to simultaneously contribute to plant growth promotion and thereby broaden the range of responsive plant species.
2023-03-08 | PXD034914 | Pride
Project description:Rice is a staple food crop worldwide, and its production is severely threatened by phloem-feeding insect herbivores, particularly the brown planthopper (BPH, Nilaparvata lugens), and destructive pathogens. Despite the identification of many BPH resistance genes, the molecular basis of rice resistance to BPH remains largely unclear. Here, we report that the plant elicitor peptide (Pep) signalling confers rice resistance to BPH. Both rice PEP RECEPTORs (PEPRs) and PRECURSORs of PEP (PROPEPs), particularly OsPROPEP3, were transcriptionally induced in leaf sheaths upon BPH infestation. Knockout of OsPEPRs impaired rice resistance to BPH, whereas exogenous application of OsPep3 improved the resistance. Hormone measurement and co-profiling of transcriptomics and metabolomics in OsPep3-treated rice leaf sheaths suggested potential contributions of jasmonic acid biosynthesis, lipid metabolism and phenylpropanoid metabolism to OsPep3-induced rice immunity. Moreover, OsPep3 elicitation also strengthened rice resistance to the fungal pathogen Magnaporthe oryzae and bacterial pathogen Xanthamonas oryzae pv. oryzae and provoked immune responses in wheat. Collectively, this work demonstrates a previously unappreciated importance of the Pep signalling in plants for combating piercing-sucking insect herbivores and promises exogenous application of OsPep3 as an eco-friendly immune stimulator in agriculture for crop protection against a broad spectrum of insect pests and pathogens.
2022-02-23 | MTBLS3518 | MetaboLights
Project description:Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. Here we demonstrate that the SPX-MFS proteins, designated as Phosphate Transporter 5 family (PHT5), also named Vacuolar Phosphate Transporter (VPT), function as vacuolar Pi transporters. Based on 31P-magnetic resonance spectroscopy analysis, Arabidopsis pht5;1 loss-of-function mutants accumulate less Pi and exhibit a lower vacuolar-to-cytoplasmic Pi ratio than controls. Conversely, overexpression of PHT5 leads to massive Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. Furthermore, we show that heterologous expression of OsSPX-MFS1, the rice PHT5 homolog, mediates Pi influx to yeast vacuoles. Our findings uncover a group of Pi transporters in vacuolar membranes that regulate the cytoplasmic Pi homeostasis required for the fitness of plant growth. 10-day seedlings grown on Pi-sufficient medium or followed by 1-day or 3-day Pi starvation, shoot RNA and root RNA were extracted separately
2016-03-28 | E-GEOD-74856 | biostudies-arrayexpress
Project description:Endophytic colonization is a very complex process which is not yet completely understood. Molecules exuded by the plants may act as signals which influence the ability of the microbe to colonize the host or survive in the rhizosphere. Here we investigated whether root exudates of the host might play a role in initiating the endophyte-rice interaction. The whole genome microarray approach was used to investigate the response of the diazotrophic model endophyte, Azoarcus sp. strain BH72, to exudates of O. sativa cv. Nipponbare in order to identify differentially regulated genes. Azoarcus sp. strain BH72 was grown in the presence or absence of root exudates of Oryza sativa cv. Nipponbare for two different time points, and differences in the gene expression profile were monitored. RNA from cells grown on synthetic medium for 1 and 4 hours respectively in presence (experiment) and absence (control) of exudates was used for two color whole genome microarray approach.
2012-11-30 | E-GEOD-35187 | biostudies-arrayexpress
Project description:Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. Here we demonstrate that the SPX-MFS proteins, designated as Phosphate Transporter 5 family (PHT5), also named Vacuolar Phosphate Transporter (VPT), function as vacuolar Pi transporters. Based on 31P-magnetic resonance spectroscopy analysis, Arabidopsis pht5;1 loss-of-function mutants accumulate less Pi and exhibit a lower vacuolar-to-cytoplasmic Pi ratio than controls. Conversely, overexpression of PHT5 leads to massive Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. Furthermore, we show that heterologous expression of OsSPX-MFS1, the rice PHT5 homolog, mediates Pi influx to yeast vacuoles. Our findings uncover a group of Pi transporters in vacuolar membranes that regulate the cytoplasmic Pi homeostasis required for the fitness of plant growth.
2016-03-28 | GSE74856 | GEO