Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1134146 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29763234_1.fastq.gz | Fastqsanger.gz | |||
| SRR29763234_2.fastq.gz | Fastqsanger.gz | |||
| SRR29763235_1.fastq.gz | Fastqsanger.gz | |||
| SRR29763235_2.fastq.gz | Fastqsanger.gz | |||
| SRR29763236_1.fastq.gz | Fastqsanger.gz |
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Project description:Root microbiota is important for plant growth and fitness. Little is known about whether and how the assembly of root microbiota may be controlled by epigenetic regulation, which is crucial for gene transcription and genome stability. Here we show that dysfunction of the histone demethylase IBM1 (INCREASE IN BONSAI METHYLATION 1) in Arabidopsis thaliana substantially reshaped the root microbiota, with the majority of the significant amplicon sequence variants (ASVs) being decreased. Transcriptome analyses of plants grown in soil and in sterile growth-medium jointly disclosed salicylic acid (SA)-mediated autoimmunity and production of the defense metabolite camalexin in the ibm1 mutants. Analyses of genome-wide histone modifications and DNA methylation highlighted epigenetic modifications permissive for transcription at several important defense regulators. Consistently, ibm1 mutants showed increased resistance to the pathogen Pseudomonas syringae DC3000 with stronger immune responses. In addition, ibm1 showed substantially impaired plant growth-promotion in response to beneficial bacteria; the impairment was partially mimicked by exogenous application of SA to wild type plants, and by a null mutation of AGP19 that is important for cell expansion and that is repressed with DNA hyper methylation in ibm1. IBM1-dependent epigenetic regulation imposes strong and broad impacts on plant-microbe interactions and thereby shapes the assembly of root microbiota.
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Project description:Legumes establish nitrogen-fixing symbiosis with beneficial rhizobia. On the other hand, they might be attacked concomitantly by pathogens raising the question of potential trade-off between mutualism and immunity. Here, using a tripartite system involving the model legume Lotus japonicus, its rhizobial symbiont Mesorhizobium loti and the soil-borne pathogen Ralstonia solanacearum we investigated such trade-offs. We found that interaction with M. loti increases plant resistance against the pathogen without impairing mutualism. Genetic and proteomics characterisation indicate that Lotus resistance is mediated by Effector Triggered Immunity and is associated with distinct proteome modifications in roots and nodules. The inoculation of rhizobia, even if they are not mutualist, increases plant resistance. Our results question the concept of interference between efficient defense reactions and mutualistic interactions and is of great interest for agricultural purposes as it not only restricts pathogen colonisation but would also preserve nitrogen fixation and yield.
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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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