Ontology highlight
ABSTRACT:
PROVIDER: PRJNA589694 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A biological control agent for the plant disease crown gall.
| PRJNA13402 | ENA
Project description:Possitive effects of plant growth promoting bacteria (PGPB) inoculation on plant growth and development are dependent on interaction between bacterial strains and plant roots, which are usually the bacterial niche. Furthermore, phytohormones are key regulators of plant physiology. Ethylene is essential in plant growth and development and in response to drought. Plant sensibility to ethylene is involved in plant response to PGPB strain inoculation and plant growth promotion. We used microarrays to detail the global programme of gene expression underlying plant interaction with two different PGPB strains (isolated from arid soils in southern Spain) regarding to plant sentitivity to ethylene by tomato ethylene receptor 3 (SlETR3).
2018-01-29 | GSE106317 | GEO
Project description:The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescens Pf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA aptamers with specificity for pyoverdine over other siderophores. Two DNA aptamers were isolated, and their features compared. The aptamers were applied to a nanoporous aluminum oxide biosensor and demonstrated to successfully detect PYO-Pf5. This sensor provides a future opportunity to track the locations around plant roots of P. protegens and to monitor PYO-Pf5 production and movement through the soil.
2024-07-18 | GSE225440 | GEO
Project description:Lactobacillus casei is remarkably adaptive to diverse habitats. To understand the evolution and adaptation of Lb. casei strains isolated from different environments, the gene content of 22 Lb. casei strains isolated from various habitats (cheeses, n=8; plant materials, n=8; and human sources, n=6) were examined by comparative genome hybridization with an Lb. casei ATCC 334-based microarray.
2009-03-17 | GSE15030 | GEO
Project description:Organoid cultures were exposed to two different E.Coli strains and a dye control with three biological duplicates. Their original culture was harvested as a control. In total 10 organoid cultures were whole-genome sequenced using the Novaseq6000 platforms. The data is deposited as .bam format.
| EGAD00001005416 | EGA
Project description:Microbial communities colonize plant tissues and contribute to host function. How these communities form and how individual members contribute to shaping the microbial community are not well understood. Synthetic microbial communities, where defined individual isolates are combined, can serve as valuable model systems for uncovering the organizational principles of communities. Using genome-defined organisms, systematic analysis by computationally-based network reconstruction can lead to mechanistic insights and the metabolic interactions between species. In this study, 10 bacterial strains isolated from the Populus deltoides rhizosphere were combined and passaged in two different media environments to form a stable microbial community. The membership and relative abundances of the strains stabilized after around 5 growth cycles and resulted in just a few dominant strains. To unravel the underlying metabolic interactions, the KBase platform was used for constructing community-level models and for elucidating the metabolic processes involved in shaping the microbial communities. These analyses were complemented by growth curves of the individual isolates, pairwise interaction screens, and metaproteomics of the community. Flux balance analysis was used to model the metabolic potential in the microbial community and identify potential metabolic exchanges among the component species. Revealing the mechanisms of interaction among plant-associated microorganisms will provide insights into strategies for engineering microbial communities that can potentially increase plant growth and disease resistance. Further, deciphering the membership and metabolic potentials of a bacterial community will enable the design of synthetic co-cultures with desired biological functions.
2020-12-03 | MSV000086551 | MassIVE
Project description:During the last decades, the use of plant growth promoting bacteria (PGPB) has been found to increase crop yield and quality and to confer abiotic and biotic stress tolerance. However, until now the PGPB mechanism to enhance plant performances is not clearly defined. Recently, our findings demonstrated that inoculations with both Kocuria rhizophila and Streptomyces violaceoruber, as well as their combination, determined an increase of tomato (Solanum lycopersicum) growth and development. In this study, through an advanced differential proteomic approach on tomato leaves, plant molecular mechanisms affected by both K. rhizophila and S. violaceoruber have been elucidated. To this aim, tomato plants were treated with K. rhizophila and/or Streptomyces violaceoruber cultures and grown on coconut fiber in greenhouse. In particular, PGPB treatments were conducted twice, on seed and after two weeks from the seedling by fertirrigation. Thus, the analyses have been performed at 14 days after sowing (DAS) (T1) and 42 DAS (T2). The results confirmed the growth stimulation ability of K. rhizophila/Streptomyces violaceoruber, showing shoot fresh and dry weight significantly improved at each time sampling. For the early phase (DAS-T1) comparative proteomics analysis of tomato plant leaves, 2 biological replicates were set up for the plants used as control (i.e. not subjected to treatment - samples I1 and I2-control I), 2 biological replicates for plants subjected to treatment with K. rhizophila (samples L1 and L2-treatment L), 2 biological replicates for plants subjected to treatment with S. violaceoruber (samples M1 and M2-treatment M), and 2 biological replicates for plants subjected to treatment with a mix of the two bacterial strains (samples N1 and N2-treatment N), for a total of 8 samples of leaf protein extracts. For the late phase (DAS-T2) comparative proteomics analysis of tomato plant leaves, 2 biological replicates were set up for the plants used as control (i.e. not treated - samples A1 and A2 - control A), 2 biological replicates for plants subjected to treatment with K. rhizophila (samples B1 and B2-treatment B), 2 biological replicates for plants subjected to treatment with S. violaceoruber (samples C1 and C2-treatment C), and 2 biological replicates for plants subjected to treatment with a mix of the two bacterial strains (samples D1 and D2-treatment D), for a total of 8 samples of leaf protein extracts. Proteomic analysis was able to identify 239 and 203 significantly differentially represented proteins (DRPs) at T1 and T2, respectively, comparing PGPB-treated vs. untreated control plants. KEGG Orthology (KO) identified DRP belonging to photosynthesis, biosynthesis of secondary metabolites, and carbon metabolism.
2024-05-02 | PXD038137 | Pride