Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1272145 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33838928_1.fastq.gz | Fastqsanger.gz | |||
| SRR33838928_2.fastq.gz | Fastqsanger.gz | |||
| SRR33838929_1.fastq.gz | Fastqsanger.gz | |||
| SRR33838929_2.fastq.gz | Fastqsanger.gz | |||
| SRR33838930_1.fastq.gz | Fastqsanger.gz |
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Project description:Plant growth promotion by biodynamic preparations
| PRJEB65929 | ENA
Project description:Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome-wide analyses of 7,488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site-directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101. Comparative transcriptome analysis of Arabidopsis treated with Pf. SS101, a growth and ISR promoting rhizobacteria and plants treated with cysH mutant of Pf.SS101 that fails to induce the afformentioned phenotypes
2017-08-26 | GSE103117 | GEO
Project description:Background: MicroRNAs play important roles in the adaptive responses of plants to nutrient deficiencies. Here, we sequenced two small RNA libraries from B-deficient and -sufficient (control) Citrus sinensis leaves, respectively, using Illumina sequencing in order to identify the potential miRNAs related to the tolerance of citrus to B-deficiency. Results: Ninety one (83 known and 8 novel) up- and 81 (75 known and 6 novel) downregulated miRNAs were isolated from B-deficient leaves. The great alteration of miRNA expression might contribute to the tolerance of citrus to B-deficiency. The adaptive responses of miRNAs to B-deficiency might related to several aspects: (a) attenuation of plant growth and development by repressing auxin signaling due to decreased TIR1 level and ARF-mediated gene expression by altering the expression of miR393, miR160 and miR3946; (b) maintaining leaf phenotype and enhancing the stress tolerance by up-regulating NACs targeted by miR159, miR782, miR3946 and miR7539; (c) activation of the stress responses and antioxidant system through down-regulating the expression of miR164, miR6260, miR5929, miR6214, miR3946 and miR3446; (d) decreasing the expression of major facilitator superfamily protein genes targeted by miR5037, thus lowering B export from plants. Also, B-deficiency-induced downregulation of miR408 might play a role in plant tolerance to B-deficiency by regulating Cu homeostasis and enhancing superoxide dismutase activity. Conclusions: Our study reveals some novel responses of citrus to B-deficiency, which increase our understanding of the adaptive mechanisms of citrus to B-deficiency at the miRNA (post-transcriptional) level.
2017-02-10 | GSE72108 | GEO
Project description:Plant growth promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short- term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Transcriptional profiles were determined by microarray analysis (Affymetrix ATH1 Genome Array) in Arabidopsis thaliana plants inoculated with the PGPR bacterial model Burkholderia phytofirmans PsJN
2013-05-31 | GSE47092 | GEO
Project description:Some plant growth promoting bacteria (PGPB) do not need to colonize plant roots to trigger the growth promotion mechanisms, as they emit volatile organic compounds (VOCs), which are small gaseous signaling molecules that mediate short- and long-distance interactions between plants and microorganisms. Therefore, VOCs-producing PGPB can be an eco-friendly solution to increase agricultural production. We aimed to understand the mechanisms underlying the VOC-mediated growth promotion effect on Setaria viridis, a model plant of C4 metabolism, by investigating its molecular, cellular, physiological and phenotypical changes triggered by these bioactive compounds. Remarkably, we screened and selected two bacteria, Pseudomonas and Burkholderia, capable of increasing the biomass of S. viridis plants by up to 4-fold in a co-cultivation system, wherein plant and bacteria only share the same atmosphere. A total of 2,871 differentially expressed genes (DEGs) were identified in S. viridis plants when exposed to VOCs from at least one of the three isolates (AI2, CTB and MTS) compared to the mock control. Then, a Gene Ontology analysis was performed. Comparing AI2 and mock treatment, 80 and 26 up- and down-regulated GOs were identified, respectively, while when comparing CTB and mock treatment, 94 up- and 36 down-regulated GOs were identified. Among these differential GOs in at least one of the growth promotion treatments compared to one or both controls we found categories like “aromatic compound biosynthetic process” (GO:0019438), “abscisic acid binding” (GO:0010427), "systemic acquired resistance" (GO:0009627), and “chitin catabolic process” (GO:0006032). Other GOs were only regulated in the treatments containing bacteria, such as “sucrose biosynthetic process” (GO:0005986), “L-phenylalanine metabolic process” (GO:0006558), “cell surface receptor signaling pathway” (GO:0007166), and “regulation of nitrogen compound metabolic process” (GO:0051171). Overall, the enrichment analysis showed a diverse spectrum of categories related to primary and secondary metabolisms, hormone pathways, enzymatic activities, plant defense and resistance, among others. Together with the other omic and target analyses, the study suggests that bacterial VOCs were able to boost photosynthesis, increasing the sugar content, that fuels respiration and cell wall modulation. Besides, VOCs were able to trigger defense response.
2025-11-01 | GSE279578 | GEO
Project description:Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa, is an important citrus disease that produces chlorotic injuries on leaves and reduced fruit size. This bacterium colonizes plant xylem, thereby interrupting sap flow. Other disease symptoms depend on environmental factors, since asymptomatic and symptomatic CVC plants may be genetically similar. The endophytic microbiome comprises many microbial species that may interact with pathogens, reducing disease symptoms and improving plant growth. However, the genetic and physiological mechanisms that underlie this interaction are largely unknown. In this study, the citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 was isolated from healthy plants. This bacterium was able to colonize citrus xylem and could be transferred from plant to plant by Bucephalogonia xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta, as a result of co-transmission by the same insect vector. To better understand how X. fastidiosa genetic responds to the presence of M. mesophilicum in the same environment, we used microarrays to evaluate the transcriptional profile of X. fastidiosa, after in vitro co-cultivation with M. mesophilicum SR1.6/6. The results showed that during co-cultivation with M. mesophilicum, X. fastidiosa downregulated genes related to growth, while genes related to energy production (cellular respiration) and transport were upregulated. Moreover, X. fastidiosa modulates genes associated with molecular recognition, nutrient competition and the stress response, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium
2014-04-18 | GSE56901 | GEO
Project description:Plants rely on complex signaling networks to regulate growth and to interact with their environment, including beneficial microbes such as plant growth–promoting rhizobacteria (PGPR). Among these microbes, Caulobacter RHG1 has been shown to enhance plant growth and is recognized by Arabidopsis roots via specific receptor-like kinases (RLKs), but the molecular mechanisms underlying the plant growth-promotion effect remain largely unknown. To investigate these mechanisms, we used an integrative approach combining proteomics and phosphoproteomics to explore how RHG1 stimulates growth in Arabidopsis thaliana. Our findings suggest that RHG1 is perceived at the root-level and this, via phosphorylation-based signaling pathways, triggers early protein-based effects that are characterized by timely modulation of defense and developmental processes, which eventually lead to plant growth promotion. Understanding the mechanisms behind such beneficial plant-microbe interactions can pave the way for more effective commercialization of PGPR-based agricultural products, and our approach offers valuable insights for future research in this field.
2026-04-17 | PXD068190 | Pride
Project description:Huanglongbing (HLB) is considered the most destructive disease in Citrus production and threatens the future of the industry. Microbial derived defence elicitors have gained recognition for their role in plant defence priming. A transcriptomic assessment using GeneChip microarray of the hour 6 samples revealed differential expression of 565 genes when MFA was applied to healthy trees and 909 genes when applied infected citrus trees when compared to their respective controls. There were 403 uniquely differentially expressed genes in response to MFA following an intersectional analysis of both healthy and infected citrus trees. The transcriptomic analysis revealed that several genes associated with plant development, growth and defence were upregulated in response to MFA, including, multiple PR genes, lignin formation genes, ROS related genes, hormone synthases and hormone regulators.
2021-11-15 | E-MTAB-10919 | biostudies-arrayexpress