Ontology highlight
ABSTRACT:
PROVIDER: PRJNA883830 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21713668_1.fastq.gz | Fastqsanger.gz | |||
| SRR21713668_2.fastq.gz | Fastqsanger.gz | |||
| SRR21713669_1.fastq.gz | Fastqsanger.gz | |||
| SRR21713669_2.fastq.gz | Fastqsanger.gz | |||
| SRR21713670_1.fastq.gz | Fastqsanger.gz |
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Project description:As the phyllosphere is a resource-limited niche, microbes have evolved different survival strategies by collaborating or competing with other organisms. This leads to the establishment of network structures which are stabilised by so-called microbial hub organisms. An already identified hub in the Arabidopsis thaliana phyllosphere is the oomycete pathogen Albugo laibachii. From wild Arabidopsis plants with white rust symptoms we isolated the basidiomycete yeast Moesziomyces albugensis, which is closely related to plant pathogenic smut fungi. It suppresses the infection of A. laibachii in lab experiments and inhibits growth of several bacterial phyllosphere members. The transcriptomic response of M. albugensis to presence of A. laibachii and bacterial SynCom members was investigated by using RNA sequencing. Interestingly, several genes encoding secretory proteins, mostly glycoside hydrolases and peptidases, are particularly induced upon interaction with A. laibachii.
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Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.
2013-06-21 | GSE48198 | GEO
Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces. We designed transcriptome arrays and investigated which genes had different transcript levels in the phyllosphere of common bean (Phaseolus vulgaris) as compared to agar surfaces. Since water availability is considered an important factor in phyllosphere survival and activity, we included both high and low relative humidity treatments for the phyllosphere-grown cells. In addition, we determined the expression profile under pollutant exposure by the inclusion of two agar surface treatments, i.e. with and without 4-chlorophenol.
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Project description:Plants are colonized by a variety of microorganisms, the plant microbiota. In the phyllosphere, the above-ground parts of plants, bacteria are the most abundant inhabitants. Most of these microorganisms are not pathogenic and the plant responses to commensals or to pathogen infection in the presence of commensals are not well understood. We report the Arabidopsis leaf transcriptome after 3 to 4 weeks of colonization by Methylobacterium extorquens PA1 and Sphingomonas melonis Fr1, representatives of two abundant genera in the phyllosphere, compared to axenic plants. In addition, we also sequenced the transcriptome of Arabidopsis 2 and 7 days after spray-infection with a low dose of P. syringae DC3000 and in combination with the commensals.
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Project description:Within the human gut reside diverse microbes coexisting with the host in a mutually advantageous relationship. We comprehensively identified the modulatory effects of phylogenetically diverse human gut microbes on the murine intestinal transcriptome. Gene-expression profiles were generated from the whole-tissue intestinal RNA of mice colonized with various single microbial strains. The selection of microbe-specific effects, from the transcriptional response, yielded only a small number of transcripts, indicating that symbiotic microbes have only limited effects on the gut transcriptome overall. Moreover, none of these microbe-specific transcripts was uniformly induced by all microbes. Interestingly, these responsive transcripts were induced by some microbes but repressed by others, suggesting different microbes can have diametrically opposed consequences.
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Project description:Positive and negative ecological interactions shape the dynamics and composition of natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein-based, are not well understood and only a small percentage of such interactions has been studied. We hypothesize that secreted proteins are a powerful and highly specific toolset to shape and defend a favorable plant niche. Here, we have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to inhibit and promote the growth of bacteria through secretion of proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the secreted proteome of Albugo candida combined with machine-learning predictors enabled the selection of candidates for heterologous expression and study of their inhibitory activity in vitro. We found that three of the candidate proteins showed a selective antimicrobial activity on several gram-positive bacterial strains isolated from Arabidopsis thaliana. We could ascribe the antibacterial activity of the candidates to their intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins that have an antimicrobial activity under apoplastic conditions and therefore are potential biocontrol tools for a targeted manipulation of the microbiome.
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