Microbial Imprinting for Crop Resilience (MiCRop)

Hereto, we will study the evolution of plant-microbiome interactions and identify opportunities for future plant breeding at an unprecedented scale. Our focus is on understanding stress-adaptive microbiomes and their active recruitment by plants across the plant kingdom through a phylogenetic approach. With precision-based methods, we will analyse the root microbiome dynamics of 100 wild and cultivated plant species – related to the five most important food crop families (Brassicaceae, Solanaceae, Fabaceae, Graminaea and Cucurbitaceae) – grown under four major types of environmental stress (nutrient deficiency, drought, pathogen infection, herbivory). This highly ambitious effort will provide unrivalled insight into the evolution and potential of wild plant and crop species across the plant kingdom to select, assemble, and benefit from their microbiomes.

Plant roots house one of the most diverse, yet vastly neglected, microbial communities on earth. The aim of the Gravitation program, Microbial Imprinting for Crop Resilience (MiCRop), is to harness the genomic potential of root microbes as a new platform for improved stress resilience of future crops and sustainable food production.

We will zoom in on the discovery of novel microbiome functions that are recruited by plants to alleviate environmental stress, and get insight into wild microbiome functions in the centres of origin that were ‘lost in translation’ during centuries of crop domestication. Moreover, we will identify novel plant traits that maximise the beneficial functions of the root microbiome and overcome environmental constraints or provide protection against pests and diseases. We will capitalise on our discoveries through our collaboration with the international CGIAR (CG) institutes and partners from the green life sciences industry. Together, we will translate our scientific milestones into deliverables for the design of future microbiome-assisted agroecosystems that are more resilient to environmental stress with less input of agrochemicals.

The research in MiCRop is summarized in the diagram, see www.microp.org for more details.
At UvA we will contribute to WPs 1 and 2 with an emphasis on the Cucurbits, Solanaceae and data integration and to WP 3 with an emphasis on signaling towards mutualistic microbes, trade-offs and the underlying genetics and molecular mechanisms.

Scientists involved in this project

Harro Bouwmeester
Age Smilde
Lemeng Dong
Anouk Zancarini

Company name

Sebastien Jaupitre
Malin Klein
Rob Schuurink
Martijn Rep
Leendert Hamoen
Joris Mooij

In cooperation with

MiCRop is a large collaborative program with PIs Harro Bouwmeester (UvA, coordinator), Marcel Dicke (WUR), Toby Kiers (VU), Corné Pieterse (UU), Jos Raaijmakers (NIOO) and Christa Testerink (WUR). The program is supported by a data analysis team consisting of Bas Dutilh (UU), Fred van Eeuwijk (WUR), Marnix Medema (WUR) and Age Smilde (UvA).


  1. Plant host and drought shape the root associated fungal microbiome in rice

    Andreo-Jimenez, B., A. Heutinck, P. Vandenkoornhuyse, A. Le Van, M. Duhamel, N. Kadam, K. Jagadish, C. Ruyter-Spira, H.J. Bouwmeester, 2019. Peer Journal e7463

  2. A CLE-SUNN module regulates strigolactone content and fungal colonization in arbuscular mycorrhiza

    Müller, L.M. , K. Flokova, E. Schnabel, X. Sun, Z. Fei, J. Frugoli, H.J. Bouwmeester and M.J. Harrison, 2019.  Nature Plants 5(9): 933-939

  3. Science and application of strigolactones

    Aliche, E.B., Screpanti, C., De Mesmaeker, A., Munnik, T., Bouwmeester, H.J., 2020. New Phytologist, in press.

  4. The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice

    Choi, J., Lee, T., Cho, J., Servante, E.K., Pucker, B., Summers, W., Bowden, S., Rahimi, M., An, K., An, G., Bouwmeester, H.J., Wallington, E.J., Oldroyd, G., Paszkowski, U., 2020. Nature Communications 11, art. no. 2114.

  5. An improved strategy to analyse strigolactones in complex sample matrices using UHPLC–MS/MS

    Floková K, Shimels M, Andreo Jimenez B, Bardaro N, Strnad M, Novák O, Bouwmeester HJ, 2020. Plant Methods 16 (1):125  

  6. Strigolactones, a new plant hormone with promising features

    Bouwmeester, H., R. Fonne-Pfister, C. Screpanti. A. De Mesmaeker, 2019.  Angewandte Chemie International Edition doi.org:10.1002/anie.201901626.

  7. Role and exploitation of underground chemical signaling in plants

    Guerrieri, A., L. Dong and H.J. Bouwmeester, 2019. . Pest Management Science ps.5507.