Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1284395 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacillus amyloliquefaciens FZB42 is a representative organism for Gram positive soil bacteria associated with plant roots and beneficial to plant growth. It is of immense importance to understand mechanisms of this class of bacteria adapting to rhizosphere. In this work employing differential RNA sequencing (RNA-seq) and Northern blot, we systematically identified transcription start sites of mRNAs as well as non-coding regulatory RNAs in FZB42. The genes regulated at different growth phases and located in polycistronic operons were also identified. A set of genes were re-annotated. In addition, a sRNA named Bas01 was identified to be involved in Bacillus sporulation and biofilm formation. The result we obtained provides valuable data for investigation of Bacillus gene expression and molecular details of rhizobacterial interaction with host plants.
2015-10-28 | GSE66681 | GEO
Project description:<p>Background</p><p>Wheat crown rot (WCR) caused by Fusarium spp. lacks durable, sustainable control. Engineering the rhizosphere with defined synthetic microbial communities (SynComs) offers a route to combined disease suppression and growth promotion. We aimed to build a cross-kingdom SynCom and evaluate its impacts on plant performance and the soil–microbiome system.</p><p>Results</p><p>We assembled a two-member SynCom comprising an antagonistic fungus (Trichoderma harzianum) and a growth-promoting bacterium (Bacillus rugosus). In greenhouse trials, SynCom inoculation reduced WCR severity by ~71% and improved vigor, more than doubling shoot and root biomass and increasing grain weight by ~13% versus non-inoculated controls. SynCom-treated plants maintained higher chlorophyll and antioxidant enzyme activities under pathogen challenge, with reduced oxidative stress markers relative to pathogen-only plants. Amplicon sequencing showed increased rhizosphere microbial diversity, enrichment of beneficial taxa (e.g., Mortierella), and suppression of Fusarium. SynCom also enhanced soil enzyme activities and nutrient availability and promoted accumulation of defense-related metabolites in the rhizosphere.</p><p>Conclusions</p><p>A tailored cross-kingdom SynCom establishes a disease-suppressive, growth-promoting soil environment that mitigates wheat crown rot while improving yield components. These findings support microbiome engineering as a practical, sustainable strategy for wheat production and warrant field-scale validation and formulation development.</p>
2025-09-06 | MTBLS12945 | MetaboLights
Project description:The natural biotope of Bacillus subtilis is the upper layer of soil where it grows as a biofilm. To mimic this physiological development and study the impact of nanoparticles during the formation of a biofilm in a contaminated soil, we have studied the proteomic response of the ancestral strain Bacillus subtilis 3610, which is able to form biofilm contrary to the 168 laboratory strain. The bacteria were grown on soft agar plates containing n-ZnO, n-TiO2 or ZnSO4 metal ion.
2018-10-24 | PXD006444 | Pride
Project description:To study long-term elevated CO2 and enriched N deposition interactive effects on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. There exist antagonistic CO2×N interactions on microbial functional genes associated with C, N, P S cycling processes. More strong antagonistic CO2×N interactions are observed on C degradation genes than other genes. Remarkably antagonistic CO2×N interactions on soil microbial communities could enhance soil C accumulation.
2018-05-01 | GSE98512 | GEO
Project description:During growth in their ecological niche fungi encounter many (micro)organisms that compete for nutrients and /or have antagonistic activity. However, little is known about responses of fungi upon exposure to other microbes. In this project we want to gain insight in induced responses of C. cinerea towards bacteria through comparison of the transcriptome of vegetative C. cinerea mycelium either grown alone or exposed to the bacterial species Escherichia coli or Bacillus subtilis
2018-09-30 | E-MTAB-6876 | biostudies-arrayexpress
Project description:Bacillus amyloliquefaciens FZB42 is a representative organism for Gram positive soil bacteria associated with plant roots and beneficial to plant growth. It is of immense importance to understand mechanisms of this class of bacteria adapting to rhizosphere. In this work employing differential RNA sequencing (RNA-seq) and Northern blot, we systematically identified transcription start sites of mRNAs as well as non-coding regulatory RNAs in FZB42. The genes regulated at different growth phases and located in polycistronic operons were also identified. A set of genes were re-annotated. In addition, a sRNA named Bas01 was identified to be involved in Bacillus sporulation and biofilm formation. The result we obtained provides valuable data for investigation of Bacillus gene expression and molecular details of rhizobacterial interaction with host plants. Examination of transcriptome profile of rhizobacterium B. amyloliquefaciens FZB42 grown under six conditions.
2015-10-28 | E-GEOD-66681 | biostudies-arrayexpress
Project description:Plant growth-promoting rhizobacteria (PGPR) are soil beneficial microorganisms that colonize plant roots for nutritional purposes and accordingly benefit plants by increasing plant growth or reducing disease. But it still remains unclear which mechanisms or pathways are involved in the interactions between PGPR and plants. To understand the complex plant-PGPR interactions, the changes in the transcriptome of typical PGPR standard Bacillus subtilis in responding to rice seedlings were analyzed. We compared and anylyzed the transcriptome changes of the bacteria Bacillus subtilis OKB105 in response to rice seedings for 2 h. Total RNA was extracted and Random priming cDNA synthesis, cDNA fragmentation and terminal labeling with biotinylated GeneChip DNA labeling reagent, and hybridization to the Affymetrix GeneChip Bacillus subtilis Genome Array.
2014-10-17 | E-GEOD-62421 | biostudies-arrayexpress
Project description:<p>Wheat is a major staple crop grown across the globe. Fusarium crown rot (FCR) of wheat, caused by Fusarium pseudograminearum, is a destructive soil-borne disease that lacks effective sustainable control measures. Here, we assembled a cross-kingdom synthetic microbial community (SMC) comprising Trichoderma harzianum T19, Bacillus subtilis BS-Z15, and four other Bacillus strains, and evaluated its biocontrol efficacy against FCR under non-sterile soil conditions. The SMC treatment significantly suppressed FCR, reducing the disease severity index by approximately 70%. Wheat growth and yield were simultaneously enhanced: SMC inoculation nearly doubled plant biomass (with fresh and dry weights ~100% higher) and increased thousand-kernel weight by ~14% compared to the controls. In the rhizosphere, SMC improved soil health by elevating soil organic matter and nitrogen levels by over 50%, while mitigating pathogen-induced nutrient imbalances (excess available P and K) and boosting nutrient-cycling enzyme activities. Amplicon sequencing revealed that SMC suppressed pathogenic Fusarium in the rhizosphere and enriched beneficial microbes, including antagonistic fungi (Trichoderma, Chaetomium) and plant growth-promoting bacteria (Pseudomonas, Paenibacillus). Co-occurrence network analysis showed that SMC treatment restructured the rhizosphere microbial network with higher connectivity, stability, and a prevalence of positive cooperative interactions under F. pseudograminearum stress. Defense-related metabolites, such as epi-jasmonic acid, allantoin, Nβ-acetyltryptamine, and dihydrodaidzein, accumulated to higher levels with SMC, consistent with KEGG enrichment in pathways related to amino acid biosynthesis, carbon metabolism, signal transduction, and plant defense. These findings demonstrate that the cross-kingdom SMC modulates soil nutrients, microbial community structure, and rhizosphere metabolites to synergistically promote wheat growth and enhance resistance to FCR.</p>
2025-09-06 | MTBLS12946 | MetaboLights