ArticleISME communications2023
Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots.
Article in ISME communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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Who cites it
18 citing papers in PubMed, 40 citations in OpenAlex.
- Soil microbial growth rate, trophic strategy, and the oligotroph-copiotroph continuum.Applied and environmental microbiology · 2026Article
- Rhizosphere and Soil Depth Differentially Shape Microbial Community Composition and Assembly inMicroorganisms · 2026Article
- Microbial assembly among plant parts of a tropical tree in different habitats and seasons.Microbiology spectrum · 2026Article
- CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.Nature communications · 2026Article
- Manipulating root-associated microbiomes to boost drought resistance in dryland winter wheat with Streptomyces pactum Act12.BMC microbiology · 2026Article
- Evaluating microbial community profiles of Chile peppers grown on the International Space Station provides implications for fruiting crops.Scientific reports · 2026Article
- Microbial community characterization in semi-hydroponic systems of Starbor kale (Current research in microbial sciences · 2026Article
- Green manuring combined with nitrogen reduction sustained rice productivity and expanded soil organic nitrogen pool via promoting coordinated rhizosphere metabolite-microbiome interactions.Frontiers in plant science · 2026Article
- Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy.Scientific reports · 2025Article
- The contrasting roles of fungal and bacterial diversity and composition in shaping the multifunctionality of rhizosphere and bulk soils across large-scale bamboo forests.BMC microbiology · 2025Article
- A stable 15-member bacterial SynCom promotesFrontiers in microbiology · 2025Article
- Prophage induction drives soybean rhizobacterial community differentiation and nutrient cycling benefiting root development.ISME communications · 2025Article
- Differentiation of soil metabolic function and microbial communities between plantations and natural reforestation.Frontiers in microbiology · 2025Article
- Microbial community dynamics in the soil-root continuum are linked with plant species turnover during secondary succession.ISME communications · 2025Article
- Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications.3 Biotech · 2024Review
- Reproducible growth ofScience advances · 2024Article
- Insights into the gut microbiota characteristics between the organic and traditional feeding chickens based on amplicon and metagenomic sequencing.Frontiers in microbiology · 2024Article
- Developing stable, simplified, functional consortia fromFrontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
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What OpenQuestion holds
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.