Bacterial sequencing data
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ABSTRACT:
PROVIDER: PRJEB96790 | ENA |
REPOSITORIES: ENA
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Project description:This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.
2024-04-20 | GSE263823 | GEO
Project description:This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.
2024-04-20 | GSE263918 | GEO
Project description:This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.
2024-04-20 | GSE263917 | GEO
Project description:Plant premature senescence is a major reason for agricultural losses caused by abiotic stress. Tools for suppressing stress-induced plant senescence are important but rare. Herein we report that diacetyl, a natural compound emitted by a plant-beneficial bacterium, suppresses ABA-mediated foliar senescence in Arabidopsis thaliana under various abiotic stress conditions. Our results established diacetyl as an effective protector of stress-induced plant senescence and disclosed a molecular mechanism for bacteria-enhanced plant stress-resistance.
2025-03-04 | GSE197968 | GEO
Project description:Although some mechanisms are known how plant growth beneficial bacteria help plants to grow under stressful conditions, we still know little how the metabolism of host plants and bacteria is coordinated during the establishment of functional interaction. In the present work, using single and dual transcriptomics, we studied the reprograming of metabolic and signaling pathways of Enterobacter sp. SA187 with Arabidopsis thaliana during the change from free-living to endophytic host-microbe interaction. We could identify major changes in primary and secondary metabolic pathways in both the host and bacteria upon interaction, with an important role of the sulfur metabolism and retrograde signaling in mediating plant resistance to salt stress. Also, we studied the effect of SA187 endogenous compounds and its role on sulfur metabolism and consequently salt tolerance. These data should help future research in the field of beneficial plant-microbe interactions for developing sophisticated strategies to improve agriculture of crops under adverse environmental conditions. transcriptome of Arabidopsis thaliana organs with beneficial microbe, beneficial microbe endogenous compound, and ethylene precursor
2021-02-25 | GSE145884 | GEO
Project description:Coral bleaching and coral reef degradation become severe as the surface seawater temperature rises. Much research to date has focused on the bacterial community composition properties within the coral holobiont, but less attention has been paid to the interactions of bacteria and corals under thermal stress. We investigated the changes of coral symbiotic bacteria and metabolites under thermal stress, and analyzed the internal relationship between bacteria and metabolites as well as their relationship with coral health. We found obvious signs of coral bleaching after heating treatment, and the interaction within symbiotic bacterial community became closer. The coral symbiotic bacterial community and metabolites changed significantly under thermal stress, and bacteria such as Flavobacterium, Shewanella and Psychrobacter increased significantly. Bacteria associated with stress tolerance, biofilm formation and mobile elements decreased, and bacterial DMSP metabolism increased slightly after heating treatment. Differential metabolites in corals after heating treatment were associated with cell cycle regulation and antioxidant. This study revealed the correlation between differential metabolites and bacterial community composition changes in corals under thermal stress, and providing valuable insight on metabolomics research of corals.
2022-10-27 | MTBLS5272 | MetaboLights
Project description:Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly understood that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during interactions with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. The interaction displays two distinct phases: first, there is a coexisting phase in which the alga grows exponentially and the bacterium grows as well. The interaction shifts to pathogenic when the virulence of Sulfitobacter D7 towards E. huxleyi is invoked upon exposure to high concentrations of algal dimethylsulfoniopropionate (DMSP), which occurs when the algae reach stationary growth or when DMSP is applied exogenously to algae in exponential growth. We aimed to unravel the response of Sulfitobacter D7 to the pathogenicity-inducing compound, DMSP, and to different algae-derived infochemicals that affect the lifestyle of the bacterium. We grew Sulfitobacter D7 in conditioned media (CM) derived from algal cultures at the different growth phases, exponential and stationary (Exp-CM and Stat-CM, respectively), in which DMSP concentration is low and high, respectively. This enabled us to separate between different phases of the interaction with E. huxleyi, i.e., Exp-CM representing the coexisting phase, and Stat-CM representing the pathogenic phase. An additional pathogenicity-inducing treatment was Exp-CM supplemented with 100 µM DMSP (herein Exp-CM+DMSP). This condition mimicked co-cultures to which we added DMSP exogenously and thus induced Sulfitobacter D7 pathogenicity, which lead to death of exponentially growing E. huxleyi. In order to identify bacterial genes that are specifically responsive to DMSP, and are not affected by other algae-derived factors, we grew Sulfitobacter D7 in defined minimal medium (MM), lacking algal metabolites, supplemented with 100 µM DMSP (herein MM+DMSP), and examined the transcriptional response. After 24 h of Sulfitobacter D7 growth in all 5 media, triplicates were taken for transcriptomic analysis. Altogether, this experimental design allowed to expand our understanding on the bacterial response to DMSP, algal infochemicals and which of these are essential for coexistence and pathogenicity.
2023-01-17 | GSE193203 | GEO
Project description:RNA-based regulation is ubiquitous in all microbes yet generating a global map of RNA–RNA interactions has been a formidable challenge. Here, TRIC-seq is introduced as an unbiased approach to map transcriptome-wide RNA–RNA interactions in several bacterial species. Applying TRIC-seq to Escherichia coli captured thousands of unique interactions, unveiling not only the targets of regulatory small RNAs (sRNAs) but also novel non-canonical regulatory interactions involving ribosomal RNAs, transfer RNAs, and messenger RNAs, including a widespread interaction between the 3’ extension of the 16S rRNA and the 5'UTRs of stress-response mRNAs. Unsupervised clustering of the interactome revealed a highly modular architecture, clustered by sRNA interactions. TRIC-seq is presented as a genetics-free approach that can be applied to any bacteria to de novo reveal regulatory RNAs along with their regulons at high specificity and resolution. TRIC-seq revealed a vast, functionally coherent cluster of mRNAs that aggregates and is excluded from ribosomes, providing compelling evidence for bacterial RNA condensates that share key properties with eukaryotic stress granules. TRIC-seq’s robust mapping provides a powerful platform to uncover RNA structures and generating foundational data for the next generation of biological models.
2025-10-01 | GSE305265 | GEO