Defining the core Arabidopsis thaliana root microbiome

By Derek S. Lundberg, Sarah L. Lebeis, Sur Herrera Paredes, Scott M. Yourstone, Jase Gehring, S. Malfatti, J. Tremblay, A. Engelbrektson, Victor Kunin, Tijana Del Rio and 6 more. Nature, 2012

2,516 citations recorded by the source corpus.

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.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/8c18820147588a943b83c6e99c379764e9849831

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In Plant Science

1. G. Berg
2. P. Bakker
3. C. Pieterse
4. A. Sessitsch
5. J. Raaijmakers
6. R. Mendes
7. Petr Baldrian
8. S. Compant

Citations in the corpus

• Thirty-one years of rice-rice-green manure rotations shape the rhizosphere microbial community and enrich beneficial bacteria (2017, background): “Lundberg et al. (2012) and Mendes et al. (2014) already found that the taxonomic and functional diversity of microbial communities in the rhizosphere and bulk soils could be quite different, and both plant and soil properties had very strong impacts on shaping the microbial community in the…”
• The Impact of Genetic Changes during Crop Domestication (2018, background): “, [125,132]) with enormous potential for agriculture and plant biology.”
• The Plant Microbiota: Systems-Level Insights and Perspectives. (2016, background): “thaliana and found that all three compartments host stable and significantly different communities across multiple environments (18, 77).”
• Culture-independent molecular tools for soil and rhizosphere microbiology (2013, methodology): “Recently, this method has been extensively used to characterize composition and diversity of soil microbial communities [20,107,160–163] and has also been applied to understand the effect of heavy metals and disturbances on soil microbial communities [162,164,165].”
• Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species (2015, background): “Previous studies investigating the microbial communities associated with diverse plant hosts have demonstrated that sample type (plant compartment), host species, geographic location, and season are all capable of influencing community composition, although the extent to which each plays a role has ”
• Bacterial diversity amplifies nutrient‐based plant–soil feedbacks (2015, background): “thaliana (Thomas 2001; Bulgarelli et al. 2012; Lundberg et al. 2012).”
• Microbial interactions within the plant holobiont (2018, neutral): “The factors impacting the structure of bacterial communities in plants include soil type [28, 29], plant compartment [30–34], Fig.”
• Drought Stress and Root-Associated Bacterial Communities (2018, background): “It should be noted that the term ‘soil’ in the context of microbiome studies may be used to refer to root zone soil, rhizosphere soil, or bulk soil, where the latter is assumed to be largely free of direct root influence and has higher diversity than rhizosphere soil (Lundberg et al., 2012).”