A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interaction between a single commensal species and a single pathogenic species. The next step is therefore to explore the relationships between host–microbial communities (microbiota) and microbial members with potential pathogenic behavior (pathobiota) in a realistic ecological context. In the present study, we investigated such relationships within root-associated and leaf-associated bacterial communities of 163 ecologically contrasted Arabidopsis thaliana populations sampled across two seasons in southwest of France. In agreement with the theory of the invasion paradox, we observed a significant humped-back relationship between microbiota and pathobiota α-diversity that was robust between both seasons and plant organs. In most populations, we also observed a strong dynamics of microbiota composition between seasons. Accordingly, the potential pathobiota composition was explained by combinations of season-specific microbiota operational taxonomic units. This result suggests that the potential biomarkers controlling pathogen’s invasion are highly dynamic.

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This work was funded by the Région Midi-Pyrénées (CLIMARES project), the LABEX TULIP (ANR-10-LABX-41, ANR-11-IDEX-0002-02), and the Métaprogramme MEM (INRA, Metabar programme). Part of this work was carried out on the Toulouse Plant–Microbe Phenotyping facility (http://tpmp.inra.fr), which is part of the Laboratoire des Interactions Plantes Micro-organismes, LIPM—UMR INRA441/CNRS2594. We are also grateful to the staff of the LIPM greenhouse for their assistance during growth chamber experiments.

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  1. These authors contributed equally: Claudia Bartoli, Léa Frachon.


  1. LIPM, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France

    • Claudia Bartoli
    • , Léa Frachon
    • , Mylène Rigal
    • , Carine Huard-Chauveau
    • , Baptiste Mayjonade
    • , Dominique Roby
    • , Sébastien Carrère
    •  & Fabrice Roux
  2. IRHS, INRA, AGROCAMPUS-Ouest, Université d’ Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France

    • Matthieu Barret
  3. INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France

    • Catherine Zanchetta
    •  & Olivier Bouchez


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Correspondence to Fabrice Roux.

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