Undefined
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB61839 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11344953.fastq.gz | Fastqsanger.gz | |||
| ERR11413821.fastq.gz | Fastqsanger.gz | |||
| ERR11413870.fastq.gz | Fastqsanger.gz | |||
| ERR11413871.fastq.gz | Fastqsanger.gz | |||
| ERR11413872.fastq.gz | Fastqsanger.gz |
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Project description:Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota
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Project description:The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in-planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains’ abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.
2023-11-03 | GSE231841 | GEO
Project description:Suppression of chronic Arabidopsis immune responses is a widespread but typically strain-specific trait across the major bacterial lineages of the plant microbiota. Here, through phylogenetic analysis of 1,765 Xanthomonadales genomes, we show that immunomodulation is a highly conserved, ancestral trait across this core order of the plant microbiota, and preceded specialization of these bacteria as host-adapted pathogens. Rhodanobacter R179, from the deepest branch of the Xanthomonadales, activates immune responses which are dependent on EFR and SOBIR1 cell-surface receptor complexes, yet root transcriptomics suggest the commensal evades host recognition upon prolonged association. This commensal camouflage is likely due to the combined activities of the conserved ABC transporter permease (dssA) and the TonB-dependent transporter (dssB) and the selective elimination of immunogenic elicitors produced by R179, other microbiota members, and the plant host. The ability of R179 to mask itself and other commensals from host recognition is consistent with a convergence of distinct root transcriptomes triggered by immunosuppressive or non-suppressive synthetic communities upon R179 co-inoculation. Although root load of R179 on wild-type and efr fls2 sobir1 mutant plants was indistinguishable in mono-associations, immunomodulation through dssAB provided R179 with a competitive advantage in a community context in the absence of other immunosuppressive bacteria. Furthermore, root colonization of diverse commensal Xanthomonadales strains varied 1,000-fold without detrimental impacts on the host. We propose that conservation of immunomodulation by Xanthomonadales is related to their adaptation to terrestrial habitats and might have contributed to variation in strain-specific root association, which together accounts for their prominent role in plant microbiota establishment.
2024-12-12 | PXD045054 | Pride
Project description:Asymptomatic plants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbiota members can activate host innate immunity, which limits pathogen proliferation and curtails plant growth, a phenomenon known as the growth-defense trade-off. We report that in mono-associations, 41% (62/151) of taxonomically diverse root commensals suppress Arabidopsis root growth inhibition (RGI) triggered by immune-stimulating microbe-/damage-associated molecular patterns. 16S rRNA gene amplicon sequencing data reveal that immune activation alters the profile of synthetic communities (SynComs) comprised of RGI non-suppressive strains, while the presence of RGI-suppressive strains attenuates this effect. Chronic root transcriptional outputs in response to colonization with RGI-suppressive or non-suppressive SynComs share a core of genes with a stereotyped expression pattern. However, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Such SynCom-specific modulation of defense is physiologically relevant as mutation of one commensal-downregulated transcription factor, MYB15, or pre-colonization with an RGI-suppressive SynCom render plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that commensals with contrasting MTI modulating capacities interact with the plant host and together buffer the system against pathogen challenge, defense-associated plant growth inhibition and community shift via a crosstalk with the immune system, leading to commensal-host homeostasis.
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Project description:Asymptomatic plants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth-defense trade-off. We report that in mono-associations, 41% (62/151) of taxonomically diverse root bacteria commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacteria 16S rRNA genes reveal that immune activation alters the profile of synthetic communities (SynComs) comprised of RGI-non-suppressive strains, while the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes with functions related to root development and nutrient transport. Further, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Mutation of one commensal-downregulated transcription factor, MYB15, or pre-colonization with RGI-suppressive SynComs render plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defense-associated growth inhibition, ultimately leading to commensal-host homeostasis.
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Project description:Shotgun Metatranscriptomics Reveals Functional Profiles of Rumen Microbial Ecosystem in Dairy Cows
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Project description:Novel strategies to improve niche colonization and microbial interactions of organohalide-respiring bacteria for remediation of chloroethenes-contaminated sites
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Project description:Co-functioning of bacterial exometabolites drives root microbiota establishment
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Project description:Regulated host cell death is part of a plant defense strategy against pathogens but it is also involved in accommodating certain beneficial root microbes. We have identified extracellular metabolites and intracellular metabolic signals that contribute to beneficial root fungal endophyte colonization, and uncovered a conserved cell death mechanism likely co-opted for establishing plant-endophyte symbiosis.
2024-11-17 | GSE209761 | GEO