ArticleThe ISME journal2022
Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome.
Article in The ISME journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- The metabolic and anatomical complexity of root microhabitats modulate their interaction with the microbiota.Nature communications · 2026Article
- Root and microbiome synergy in plant heat stress resilience: epigenetic regulation as a frontier for future research.Journal of experimental botany · 2026Review
- Epigenetic Regulation of Root-Associated Microbiota: Mechanisms and Horticultural Applications.Plants (Basel, Switzerland) · 2026Review
- The plant microbiota: From theoretical advances to applications.Fundamental research · 2026Review
- Epigenetic landscape underlying plant-microbiome chemical communication.The ISME journal · 2025Review
- Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae.Nature communications · 2024Article
- Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions.Microorganisms · 2024Review
- MAPK Cascades in Plant Microbiota Structure and Functioning.Journal of microbiology (Seoul, Korea) · 2024Review
- Editorial: Epigenetic regulation behind plant-microbe interactions.Frontiers in plant science · 2024Article
- Review
- Epigenetic regulation of plant immunity: from chromatin codes to plant disease resistance.aBIOTECH · 2023Review
- Plant latent defense response against compatibility.The ISME journal · 2023Review
- The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions.Environmental microbiome · 2023Review
- Microbial fortification of pharmacological metabolites in medicinal plants.Computational and structural biotechnology journal · 2023Review
- History of a model plant growth-promoting rhizobacterium,Frontiers in plant science · 2023Review
Corrections and comments
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Authors and funding
20 authors at 5 institutions in 4 countries.
Funding
Abstract
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 hypermethylation 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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.