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We are interested in the interactions between bacteria and their hosts. The microbiota play a critical role for the health and growth of plants, but how beneficial microbes are recognized remains poorly understood. This is especially true in the phyllosphere, the compartment composed of the aboveground organs of the plant which includes stem, leaves, flowers and fruits. Recent evidence suggests that several plant species have evolved or co-opted an ancient pathway enabling symbiont capture and consistent vertical transmission. Gaining insight into the mechanisms used to recognize beneficial symbionts at the leaf surface is essential in order to leverage the richness and diversity of the plant microbiome in agriculture.

More specifically, our research focuses on obligate or vertically-transmitted mutualistic symbioses. These are notoriously difficult to study by traditional methods because molecular processes between the host and symbionts have often been intertwined by millions of years of co-evolution. They are however the most promising in terms of application and understanding of co-evolution between host and bacteria. Obligate symbioses can be viewed as some of the most successful biological partnerships and a tremendous source of biological innovation.

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Evolution of leaf symbioses



















Various plant species of the Rubiaceae and Primulaceae form permanent associations with bacteria, often visible in the form of galls on the leaves (Figure, reproduced from Pinto-Carbó et al., 2018, doi: 10.1016 / j.pbi .2018.01.001).

Uncommonly in plants, symbiotic bacteria seem to be transmitted vertically via seeds, and to be necessary for the normal development of their host. We have demonstrated that symbiotic bacteria produce copious amounts of secondary metabolites with insecticidal or allelopathic properties, possibly playing a role in the protection of the host plant. The group continues to study these binary associations, which provide a valuable model to study the evolution of beneficial associations between endophytic bacteria and their hosts.

Publications on the topic:

  • Pinto-Carbó, M., Gademann, K., Eberl, L., and Carlier, A. 2018. “Leaf Nodule Symbiosis: Function and Transmission of Obligate Bacterial Endophytes.” Ed. Sebastian Schormack and Caroline Gutjahr. Current Opinion in Plant Biology 44: 23–31.

  • Pinto-Carbó, M., Sieber, S., Dessein, S., Wicker, T., Verstraete, B., Gademann, K., Eberl, L., and Carlier, A *. Evidence of horizontal gene transfer between obligate leaf nodule symbionts. 2016. ISME J. 10 (9): 2092– 2105.

  • Crüsemann, M .; Reher, R .; Schamari, I .; Brachmann, A .; Ohbayashi, T .; Kuschak, M .; Malfacini, D .; Seidinger, A .; Pinto-Carbó, M .; Reuter, T .; Kehraus, S .; Hallab, A .; Mergaert, P .; Kikuchi, Y .; Schäberle, T, Fleischmann, B., Kostenis, E., Wenzel, D., Müller, C., Piel, J, Carlier, A., Eberl, L., König, G. Heterologous expression, biosynthetic studies and ecological function of the selective Gq-signaling inhibitor FR900359. 2018. Angewandte Chemie Intl. Ed. (3): 836–840.

  • Carlier, A., Fehr, L., Pinto-Carbó, M., Schäberle, T., Reher, R., Dessein, S., König, G., and Eberl, L. 2016. “The Genome Analysis of Candidatus Burkholderia Crenata Reveals That Secondary Metabolism May Be a Key Function of the Ardisia Crenata Leaf Nodule Symbiosis. ” Environmental Microbiology 18 (8): 2507–2522.

The model symbiosis Dioscorea sansibarensis / Orrella dioscoreae

Unlike the leaf symbiosis of Primulaceae and Rubiaceae which are difficult to manipulate in the laboratory, the symbiosis between the species of wild yam Dioscorea sansibarensis and the bacterium Orrella dioscoreae offers an ideal experimental system to understand the recruitment of symbiotic functions in the phyllosphere. The team establishes innovative methods for the manipulation of the symbiotic cycle in order to better understand the bases of the specificity between plants and extracellular bacteria in the phyllosphere.


Recent publications on the topic:

  • Bram Danneels, Juan Viruel, Krista Mcgrath, Steven B. Janssens, Nathan Wales, Paul Wilkin, Aurelien Carlier *. Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing. Current Biology. (2021).

  • De Meyer, F., Danneels, B., Acar, T. et al. Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. ISME J 13, 1831–1844 (2019).

Job opportunities

*** Postdoc opportunity beginning 2023 ***

We seek a candidate for a 3-year ANR-funded project aiming at understanding the function and ecological role of plant leaf symbioses. The project is at the interface between the fields of microbiology/plant biology and natural product chemistry and focuses on understanding the mechanisms driving the ecological success of plant-bacteria symbioses, especially leaf symbioses. The ideal candidate should have demonstrated experience in multi-omics (genomics, transcriptomics or metabolomics), a good understanding of host-bacteria associations, and a strong interest for chemical ecology. 

To apply, please send your cv and cover letter (including names and contact of 2 references) to aurelien.carlier (at)



Our main collaborations are with the groups of Petya Krasteva (with Thibault Sana, IECB CNRS, France), Leo Eberl, University of Zurich (CH); Paul Wilkin, Kew Botanical Garden (UK); Steven Janssens (Meise Botanical Garden, BE); Max Crüsemann and Gabriele König (Bonn University, DE). We also maintain close collaborations with the Laboratory of Microbiology of the University of Ghent (BE, chair Prof. Peter Vandamme).

Ongoing funding


Our research is possible thanks to the support of:

  • ANR project "RESIDE" 2023-2026

  • INRAE ​​SPE Camessym project (2019-2022)

  • ANR PHYLLOSYM project (2019-2022)

  • LabEx TULIP "Junior" Chair (2019-2024)


Former members


  • Tessa Acar (PhD student 2017-2021)

  • Bram Danneels (PhD student and postdoc, 2017-2022)

  • Thibault Sana (postdoc 2020-2021)

  • Marine Beaumel (intern, summers 2021 and 2022)

  • Sarah Ranty-Roby (2019-2021)

  • Dr. Olivier Coen (postdoc 2020-2021)

  • Adrien Javois (Master student 2021)

  • Tim Stralla (Master 1 student 2020)

At LM-UGent:

  • Dr. Shanshan Qi (PhD student 2017-2021)

  • Mathijs Deprez (Master student 2020)

  • Youness Assoued (Master student 2018)

  • Diete Van Steenbergen (Master student 2017)

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Thèmes de recherche



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