Transcriptome profiling of banana in response to growth-promoting rhizobacteria
Ontology highlight
ABSTRACT:
ORGANISM(S): Musa acuminata
PROVIDER: GSE80495 | GEO | 2016/04/21
SECONDARY ACCESSION(S): PRJNA319058
REPOSITORIES: GEO
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Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates.
2014-11-01 | GSE54987 | GEO
Project description:Musa acuminata and rhizobacteria Pseudomonas fluorescens and Bacillus amyloliquefaciens
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Project description:Root exudates play an important role in plant-microbe interaction. The transcriptional profilings of plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 in response to maize root exudates under static condition, were investigated by an Illumina RNA-seq for understanding the regulatory roles of the root exudates. 4 treatments, including 2 blank control (24 h and 48 h-post inoculation, named as 5 and 15, respectively), and 2 treatments with maize root exudates (24 h and 48 h-post inoculation, named as 7 and 17, respectively)
2014-11-01 | E-GEOD-54987 | biostudies-arrayexpress
Project description:Bacillus amyloliquefaciens FZB42 is a well-studied Gram-positive plant growth-promoting rhizobacteria. In this work we aim to study the effect of the effect of sigD deletion on the transcriptome of FZB42. The transcritomes were compared by two-color microarray of the sigD- mutant and the wildtype of B. amyloliquefaciens FZB42 grown in 1C medium supplemented with soil extract (SE). This submission includes data from two independent experiments with three biological replicates. Here a biological replicate means the bacterial culture from one flask used for RNA preparation. The samples were collected by two performers. The experiments were varied in sample performer, the date of the experiment.
2017-06-20 | E-MTAB-4876 | biostudies-arrayexpress
Project description:RNA-seq of banana plants in response to Bacillus amyloliquefaciens and Pseudomonas fluorescens
2018-08-10 | E-GEOD-80495 | ExpressionAtlas
Project description:Bacillus amyloliquefaciens FZB42 is a well-studied Gram-positive plant growth-promoting rhizobacteria. In this work we aim to study the effect of the effect of sigD deletion on the transcriptome of FZB42. The transcritomes were compared by two-color microarray of the sigD- mutant and the wildtype of B. amyloliquefaciens FZB42 grown in 1C medium supplemented with soil extract (SE) and in 1C medium supplemented with both SE and maize root exudates (RE). This submission includes data from three independent experiments with three biological replicates. Here a biological replicate means the bacterial culture from one flask used for RNA preparation. The samples were collected by two performers. The experiments were varied in sample performer, the date of the experiment.
2017-07-05 | E-MTAB-4636 | biostudies-arrayexpress
Project description:Plants develop mutualistic association with beneficial rhizobacteria. To understand this important phenomenon, early mechanisms for establishing the mutualism are critical. Here we report that active DNA demethylation in plants controls root secretion of myo-inositol, which triggers and further facilitates colonization of the beneficial rhizobacteria Bacillus megaterium strain YC4, thereby allowing for plant growth-promotion. YC4 promotes plant growth but the beneficial effects were lost in the Arabidopsis mutant rdd that is defective in active DNA demethylation. Roots of rdd failed to associate with YC4, meanwhile the level of myo-inositol in root exudates was drastically reduced in rdd. Supplementation of myo-inositol to rdd restored YC4 colonization and plant growth-promotion, while plants with defective myo-inositol monophosphatase also failed in establishing mutualism with YC4. myo-Inositol not only induced chemotaxis of YC4 but also increased YC4 biofilm production, consistent with the transcriptional regulation of YC4 by myo-inositol. In addition, myo-inositol preferentially attracts Bacillus megaterium among the examined bacteria species. Regardless of YC4 inoculation, myo-inositol biosynthesis and catabolism genes are down- and up-regulated, respectively, in rdd compared to wild type plants. The differential expression of myo-inositol homeostasis genes is correlated with local DNA hypermethylation, whereas genetic disruption of the RNA-directed DNA methylation pathway abolished these epigenetic marks and reset the corresponding gene expression patterns, resulting in restored YC4 colonization and plant growth-promotion. Importantly, that active DNA demethylation controls myo-inositol-mediated mutualism between YC4 and plants was also demonstrated in Solanum lycopersicum. Our results uncover an important function of myo-inositol in plant-microbe interactions and its dependence on plant epigenetic regulation.
2022-12-19 | GSE143427 | GEO
Project description:Plants develop mutualistic association with beneficial rhizobacteria. To understand this important phenomenon, early mechanisms for establishing the mutualism are critical. Here we report that active DNA demethylation in plants controls root secretion of myo-inositol, which triggers and further facilitates colonization of the beneficial rhizobacteria Bacillus megaterium strain YC4, thereby allowing for plant growth-promotion. YC4 promotes plant growth but the beneficial effects were lost in the Arabidopsis mutant rdd that is defective in active DNA demethylation. Roots of rdd failed to associate with YC4, meanwhile the level of myo-inositol in root exudates was drastically reduced in rdd. Supplementation of myo-inositol to rdd restored YC4 colonization and plant growth-promotion, while plants with defective myo-inositol monophosphatase also failed in establishing mutualism with YC4. myo-Inositol not only induced chemotaxis of YC4 but also increased YC4 biofilm production, consistent with the transcriptional regulation of YC4 by myo-inositol. In addition, myo-inositol preferentially attracts Bacillus megaterium among the examined bacteria species. Regardless of YC4 inoculation, myo-inositol biosynthesis and catabolism genes are down- and up-regulated, respectively, in rdd compared to wild type plants. The differential expression of myo-inositol homeostasis genes is correlated with local DNA hypermethylation, whereas genetic disruption of the RNA-directed DNA methylation pathway abolished these epigenetic marks and reset the corresponding gene expression patterns, resulting in restored YC4 colonization and plant growth-promotion. Importantly, that active DNA demethylation controls myo-inositol-mediated mutualism between YC4 and plants was also demonstrated in Solanum lycopersicum. Our results uncover an important function of myo-inositol in plant-microbe interactions and its dependence on plant epigenetic regulation.
2022-12-19 | GSE143434 | GEO
Project description:Plants develop mutualistic association with beneficial rhizobacteria. To understand this important phenomenon, early mechanisms for establishing the mutualism are critical. Here we report that active DNA demethylation in plants controls root secretion of myo-inositol, which triggers and further facilitates colonization of the beneficial rhizobacteria Bacillus megaterium strain YC4, thereby allowing for plant growth-promotion. YC4 promotes plant growth but the beneficial effects were lost in the Arabidopsis mutant rdd that is defective in active DNA demethylation. Roots of rdd failed to associate with YC4, meanwhile the level of myo-inositol in root exudates was drastically reduced in rdd. Supplementation of myo-inositol to rdd restored YC4 colonization and plant growth-promotion, while plants with defective myo-inositol monophosphatase also failed in establishing mutualism with YC4. myo-Inositol not only induced chemotaxis of YC4 but also increased YC4 biofilm production, consistent with the transcriptional regulation of YC4 by myo-inositol. In addition, myo-inositol preferentially attracts Bacillus megaterium among the examined bacteria species. Regardless of YC4 inoculation, myo-inositol biosynthesis and catabolism genes are down- and up-regulated, respectively, in rdd compared to wild type plants. The differential expression of myo-inositol homeostasis genes is correlated with local DNA hypermethylation, whereas genetic disruption of the RNA-directed DNA methylation pathway abolished these epigenetic marks and reset the corresponding gene expression patterns, resulting in restored YC4 colonization and plant growth-promotion. Importantly, that active DNA demethylation controls myo-inositol-mediated mutualism between YC4 and plants was also demonstrated in Solanum lycopersicum. Our results uncover an important function of myo-inositol in plant-microbe interactions and its dependence on plant epigenetic regulation.
2022-12-19 | GSE143433 | GEO
Project description:Unlike pathogens that trigger plant defense responses, beneficial microbes are compatible with plants. One possible reason for the compatibility is that the microbial factors from beneficial microbes are inert in that they do not trigger plant defense responses. Little is known about the mechanisms underlying this seemingly inert relation. Here we report that Arabidopsis lacking the gene Growth-Promotion 1 (GP1) becomes defensive to microbial volatiles from Bacillus amyloliqueficiens strain GB03, a beneficial rhizobacterium. The gp1 mutant was isolated in a forward genetic screen for mutants that show defectiveness in GB03-triggered plant inducible vigor. GP1 encodes a stearoyl-ACP desaturase that catalyzes the desaturation of stearic acid (18:0) to oleic acid (18:1). Consistently, plant inducible vigor was also impaired by chemical enhancement of 18:1 catabolism, while genetic disruption of 18:1 catabolism largely restored the inducible vigor in gp1. When exposed to GB03-emitted microbial volatiles (GMVs), wild type plants showed transcriptional up-regulation of growth-promoting processes and down-regulation of defense responses; in contrast, the gp1 transcriptome displayed elevated defense responses when treated with GMVs. Meanwhile disruption of salicylic acid-mediated defense partially restored plant inducible vigor in gp1. Microbiota profiling revealed that GP1 dysfunction alters the assemblage of plant-associated rhizobacteria communities, including a reduction in the Bacillaceae family that is known to contain many beneficial rhizobacteria species. Consistently, gp1 mutants showed severely impaired root colonization of GB03. Our findings suggest that GP1 prevents the plant defense system from being mistakenly activated by non-pathogenic microbial factors, thereby allowing mutualistic association between the plant and beneficial microbes.
2022-10-04 | GSE139154 | GEO