ArticleNature communications2023
Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 52 citations in OpenAlex.
- From dividing to dormant: embracing the full activity spectrum for environmental microorganisms.Microbiology and molecular biology reviews : MMBR · 2026Review
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- Towards an Omics-Guided Framework for Microbial Biological Control of Fungal and Oomycete Diseases inInternational journal of molecular sciences · 2026Review
- Genomic Insights Into Biocontrol and Plant Growth-Promoting Mechanisms of Paenibacillus maysiensis LHJ6 Against Root Rot in Panax notoginseng.Plant, cell & environment · 2026Article
- The microbial unknome, a repertoire for microbial chatting?Heredity · 2026Review
- From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.Plants (Basel, Switzerland) · 2026Review
- Article
- Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.Microbiology spectrum · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Soil Nutrient Availability By Beneficial Bacteria of Forest Trees: From Mechanisms To Applications.Microbial ecology · 2026Review
- CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.Nature communications · 2026Article
- Enrichment is not necessarily recruitment in root microbiome assembly.The ISME journal · 2026Review
- Evolutionary mechanisms underlying bacterial adaptation to the plant environment.FEMS microbiology reviews · 2026Review
- Mechanisms for the formation and maintenance of microhabitat self-organization in the root system of orchid.Frontiers in genetics · 2026Review
- Soil microbial processes shaping seed performance: linking soil microbiomes to sustainable agriculture.Frontiers in microbiology · 2026Review
- The combined application of chemical and microbial fertilizers enhanced microbial diversity and improved soil fertility in the peanut rhizosphere within a sugarcane-peanut intercropping system.Frontiers in microbiology · 2026Article
- Bacterial fitness for plant colonization is influenced by plant growth substrate.The New phytologist · 2025Article
- High-quality genome assemblies of 152 root commensal bacteria from the model legume Lotus japonicus.Scientific data · 2025Article
- The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization.mSystems · 2025Article
- Meta-Transcriptomes From Microcosms From a Cr Impacted Soil Provides Insights Into the Metabolic Response of the Microbial Populations to Acetate Stimulation.Environmental microbiology reports · 2025Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
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.
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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.