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Cited by 2,879Plant-Microbe Interactions and ImmunityMicrobial Community Ecology and PhysiologyLegume Nitrogen Fixing Symbiosis

Defining the core Arabidopsis thaliana root microbiome

Open access
Lundberg, Derek S., Lebeis, Sarah L., Paredes, Sur Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna +8 more·2012·Nature
DOI 10.1038/nature11237PMC PMC4074413
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Abstract

Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant-microbe interactions derived from complex soil communities.

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  • Soil, roots, and the phyllosphere harbour complex microbiomes of thousands of bacterial and fungal species that may suppress diseases, act as pathogens, or affect plant health and growth.

    “Soil, roots, and the phyllosphere harbour complex microbiomes consisting of thousands of bacterial and fungal species that may suppress diseases, act as pathogens, or affect plant health and growth by various other mechanisms [5–8].”

    From Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi (2017) · cites this paper as [7]

    The paper’s opening discussion (page unavailable in our copy) describes complex soil and root microbiota that can benefit or undermine plant health, including by promoting growth, suppressing pathogens, or acting as pathogens. It studies bacteria in soil and roots, but does not substantiate the claim that all three habitats, including the phyllosphere, harbour thousands of bacterial and fungal species; the phyllosphere appears only in a reference title. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • The contributions and functions of the large majority of species in plant, rhizosphere, or soil microbiomes are still mostly unknown.

    “Microbiomes of plants, rhizosphere, or soil have been elucidated by large-scale, DNA sequencing-based metagenomics approaches [7, 15, 16], but the contributions and functions of the large majority of the species are still mostly unknown.”

    From Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi (2017) · cites this paper as [7]

    In the section labeled Abstract (page not given), the paper describes its sequencing results as a step toward defining the Arabidopsis root microbiome’s functional capacity and says that detailed characterization of its isolates remains to be done. That supports a knowledge gap for this root microbiome, but not the broader claim that the contributions and functions of a large majority of species across plant, rhizosphere, and soil microbiomes are unknown. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Cites

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Research works printed but not linked: 23

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Authors
Lundberg, D. S., Lebeis, S. L., Paredes, S. H., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Rio, T. G. D., Edgar, R. C., Eickhorst, T., Ley, R. E., Hugenholtz, P., Tringe, S. G., & Dangl, J. L.
Affiliations
  • University of North Carolina at Chapel Hill (US)
  • Joint Genome Institute (US)
  • University of Bremen (DE)
  • Cornell University (US)
  • The University of Queensland (AU)
Corresponding author
Dangl, Jeffery L.
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2012-08
Volume
488
Issue
7409
Pages
86-90
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature11237
PMC
PMC4074413
OpenAlex
W1973831267
Cited by
2,879
References
2
Citations by year
2026: 153 · 2025: 206 · 2024: 251 · 2023: 235 · 2022: 293 · 2021: 308 · 2020: 299 · 2019: 257 · 2018: 194 · 2017: 202 · 2016: 145 · 2015: 126 · 2014: 103 · 2013: 85 · 2012: 13
FWCI
119.55
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • National Institute of General Medical Sciences (K12GM000678)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Legume Nitrogen Fixing Symbiosis
Keywords
Arabidopsis thaliana, root microbiome, rhizosphere, root endophytes, soil bacteria, soil type, host genotype, actinobacteria, Proteobacteria, Bacteroidetes, Chloroflexi, 16S rRNA gene sequencing, plant-microbe interactions, plant growth promotion, plant disease resistance
MeSH terms
Genotype, RNA, Ribosomal, 16S, Soil Microbiology, Symbiosis, Arabidopsis, In Situ Hybridization, Fluorescence, Sequence Analysis, DNA, Plant Roots, Proteobacteria, Ribotyping, Actinobacteria, Metagenome, Rhizosphere, Endophytes

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