<i>In situ</i> relationships between microbiota and potential pathobiota in <i>Arabidopsis thaliana</i>

Bartoli, Claudia; Frachon, Léa; Barret, Matthieu; Rigal, Mylène; Huard-Chauveau, Carine; Mayjonade, Baptiste; Zanchetta, Catherine; Bouchez, Olivier; Roby, Dominique; Carrère, Sébastien; Roux, Fabrice

doi:10.1101/261602

Cited by 18 publications

(3 citation statements)

References 69 publications

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“…We selected seventeen sites with variable soil characteristics across a climatic gradient from Sweden to Spain. At each site, A. thaliana and sympatric grasses occur naturally 54, 55, 3, 1, 15 ( Supplementary Table 1, Fig. 1a ).…”

Section: Methodsmentioning

confidence: 99%

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

Thiergart

Durán

Ellis

et al. 2019

Preprint

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20Factors that drive continental-scale variation in root microbiota and plant adaptation are poorly 21 understood. We monitored root-associated microbial communities in Arabidopsis thaliana and co-22 occurring grasses at 17 European sites across three years. Analysis of 5,625 microbial community 23 profiles demonstrated strong geographic structuring of the soil biome, but not of the root microbiota. 24Remarkable similarity in bacterial community composition in roots of A. thaliana and grasses was 25 explained by the presence of a few diverse and geographically widespread taxa that disproportionately 26 colonize roots across sites. In a reciprocal transplant between two A. thaliana populations in Sweden 27and Italy, we uncoupled soil from location effects and tested their respective contributions to root 28 2 microbiota variation and plant adaptation. The composition of the root microbiota was affected by 29 location and soil origin, and to a lesser degree by host genotype. The filamentous eukaryotes were 30 particularly strongly affected by location. Strong local adaptation between the two A. thaliana 31 populations was observed, with difference in soil properties and microbes of little importance for the 32 observed magnitude of adaptive differentiation. Our results suggest that, across large spatial scales, 33 climate is more important than are soil conditions for plant adaptation and variation in root-associated 34 filamentous eukaryotic communities. 35 36 differentiation among plant populations is still limited beyond classical examples of adaptation to 57 extreme soil conditions 25 . 58 59Here, we tested whether roots of A. thaliana and co-occurring grasses growing in various soils and 60 climatic environments establish stable associations with bacterial and filamentous eukaryotic 61 communities across a latitudinal gradient in Europe. In a reciprocal transplant between two A. thaliana 62 populations in Sweden and Italy, we uncoupled soil from location effects and experimentally tested the 63 hypothesis that soil properties and climate drive root microbiota assembly and adaptive differentiation 64 between the two A. thaliana populations. 65 66We found that a widespread set of bacteria, but not filamentous eukaryotes, establish stable associations 67 with roots of A. thaliana and grasses across 17 sites in Europe, despite strong geographical structuring 68 and variation in the surrounding soil communities. The reciprocal transplant of soil and plant genotypes 69 between two native A. thaliana populations in northern and southern Europe showed that the 70 composition of root microbiota was more affected by soil properties and location than by host genotype. 71The effect of soil was stronger than that of location for root-associated bacteria, whereas the effect of 72 location was stronger for root-associated fungi and oomycetes. Transplant location, rather than origin 73 of soil, also largely accounted for strong selection against the nonlocal A. thaliana genotype at each site. 74Our results suggest that climat...

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Section: Methodsmentioning

confidence: 99%

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

Thiergart

Durán

Ellis

et al. 2019

Preprint

Self Cite

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“…In contrast, the interaction and rivalry of the pathobiota and other members of the plant microbiome influence the development of pathogens. In contrast, plants interact in their natural habitat with various potentially harmful microbes [28]. We still don't know how the pathobiota and plant microflora will interact in response to ongoing abiotic stressors.…”

Section: Pathogen-plant Interactionmentioning

confidence: 99%

Impact of Climate Change on Soil Activity (Nitrifying, Denitrifying) and Other Interactions

Hivare

Kalbande

Jadhav

et al. 2023

Climate Change Management

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Though the soil is our motherland, it directly influences quantitative and qualitative crop traits, which determine food security and human health. Unfortunately, it is a complicated environment for microbes, and the anatomy and physiology of microorganisms in soil are immensely complicated. These ambiguities make it difficult to forecast the consequences of climate change on the behavior of soil microorganisms. Drought stress is currently the most severe Impact of climate change and significant, concerning, and dangerous abiotic stresses that cause changes in the soil environment that influence soil organisms such as microbes and plants. It alters the functionality and activity of soil microorganisms in charge of essential ecosystem services and processes. Due to the decrease in microbial activity and production of enzymes (such as oxidoreductases, hydrolases, dehydrogenases, catalase, urease, phosphatases, and glucosidase) and disruption of microbial structure caused by these stress conditions, soil fertility declines, plant productivity falls, and economic loss occurs. To identify more effective strategies for reducing the effects of drought and managing agricultural activities under challenging conditions profitably, a thorough understanding of many factors is needed to address potential approaches like genome editing and molecular analysis (metagenomics, transcriptomics, and metabolomics).

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“…The effect of the microbiota is not limited to human health: works in plant biology show that the root microbiota can improve resistance to stress (Trivedi et al, 2017). Molecules produced by the microbiota can also have a profound impact on stress tolerance (Bernardo et al, 2017), plant health (Mendes et al, 2011) and pathogen control (Bartoli et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Incorporating phylogenetic information in microbiome abundance studies has no effect on detection power and FDR control

Bichat

Ambroise

Plassais

et al. 2020

Preprint

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We consider the problem of incorporating evolutionary information (e.g. taxonomic or phylogenic trees) in the context of metagenomics differential analysis. Recent results published in the literature propose different ways to leverage the tree structure to increase the detection rate of differentially abundant taxa. Here, we propose instead to use a different hierachical structure, in the form of a correlation-based tree, as it may capture the structure of the data better than the phylogeny. We first show that the correlation tree and the phylogeny are significantly different before turning to the impact of tree choice on detection rates. Using synthetic data, we show that the tree does have an impact: smoothing p-values according to the phylogeny leads to equal or inferior rates as smoothing according to the correlation tree. However, both trees are outperformed by the classical, non hierachical, Benjamini-Hochberg (BH) procedure in terms of detection rates. Other procedures may use the hierachical structure with profit but do not control the False Discovery Rate (FDR) a priori and remain inferior to a classical Benjamini-Hochberg procedure with the same nominal FDR. On real datasets, no hierarchical procedure had significantly higher detection rate that BH. Although intuition advocates the use of a hierachical structure, be it the phylogeny or the correlation tree, to increase the detection rate in microbiome studies, current hierachical procedures are still inferior to non hierachical ones and effective procedures remain to be invented.

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In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana

Cited by 18 publications

References 69 publications

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations

Impact of Climate Change on Soil Activity (Nitrifying, Denitrifying) and Other Interactions

Incorporating phylogenetic information in microbiome abundance studies has no effect on detection power and FDR control

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