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Dr A.A.C. (Anouk) Zancarini

Assistant Professor (tenure track)
Faculty of Science
Swammerdam Institute for Life Sciences

Visiting address
  • Science Park 904
  • Room number:C2.219
Postal address
  • Postbus 1210
    1000 BE Amsterdam
  • Research


    The soil is a reservoir of microorganisms, which play key roles in ecosystems and can improve plant growth and health. Moreover, plants exert selective forces on the soil microbial communities through root exudation, which both provides organic carbon that can be used for microbial growth and plays an important role as signaling molecules in root-microbe interaction. We know that the composition of root exudates varies with the environmental conditions, the plant developmental stage, plant species and cultivars, and as a result so does the plant microbiome. However, the mechanisms involved in the microbiome selection by the plant are still poorly understood.


    Research objectives

    The aim of my research is to better understand how plants can select a beneficial microbiome for a better plant growth, nutition and health under abiotic/biotic stress and find new lever to improve plant stress tolerance by identifying candidate genes, metabolites and microorganisms.

    To do so, I am using phenotypic and multi omics data (such as genomics, transcriptomics, metabolomics and metagenomics) and working on their integration using advance data analysis and computational tools.


    I am part of both Plant Hormone Biology group and Biosystems Data Analysis group and I am involved in the Systems Biology Priority Area.

  • Teaching

    I am involved in the following courses:

    • Bachelor's programme Biology - Keystone Project III: Big data course
    • Bachelor's programme Biology - Ecogenomics course
    • Master's programme Green Life Sciences - Tools in molecular data analysis course
    • Master's programme Bioinformatics and Systems Biology

    I am coordinating the Master course Tools in molecular data analysis

  • Open Master student projects

    Students interested in plant-microbe interactions, omics data analysis and integration are welcome to contact me.

    • Project for students in Biology: Root-knot nematodes are major pest species in agriculture and cause enormous yield losses. Research is starting to focus on finding a sustainable resistance to root-knot nematodes, by investigating the interaction between plant roots, micro-organisms and nematodes in the rhizosphere. We already assessed tolerance to Meloidogyne incognita of ten tomato genotypes using a resistance score scale and we measured plant root exudates. In this project, you will have first to develop a more accurate method to assess root-knot nematode tolerance of the different tomato genotypes. Then, you will have to assess the microbiome using a metabarcoding approach. Finally, using biostatistical approaches and machine learning, you will have to test the relationship among the plant tolerance phenotype, the root exudates and the microbiome and find candidate molecules that are linked to the presence of beneficial microbes in the plant tolerance to root-knot nematodes.
    • Project for students in Bioinformatics: Under stress plants are able to "cry for help" and recruit beneficial microbes. You will develop new data analysis and computational tools in order to analyse and intergrate multi-omics data (transcriptomics, metabolomics and metagenomics).
  • Publications


    • Zancarini, A., Westerhuis, J. A., Smilde, A. K., & Bouwmeester, H. J. (2021). Integration of omics data to unravel root microbiome recruitment. Current Opinion in Biotechnology, 70, 255-261.



    • Echenique-Subiabre, I., Zancarini, A., Heath, M. W., Wood, S. A., Quiblier, C., & Humbert, J-F. (2018). Multiple processes acting from local to large geographical scales shape bacterial communities associated with Phormidium (cyanobacteria) biofilms in French and New Zealand rivers. Scientific Reports, 8.


    • Zancarini, A., Echenique-Subiabre, I., Debroas, D., Taib, N., Quiblier, C., & Humbert, J-F. (2017). Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France. Scientific Reports, 7.


    • Zhu, L., Zancarini, A., Louati, I., De Cesare, S., Duval, C., Tambosco, K., ... Humbert, J-F. (2016). Bacterial Communities Associated with Four Cyanobacterial Genera Display Structural and Functional Differences: Evidence from an Experimental Approach. Frontiers in Microbiology, 7.


    • Zancarini, A., Lépinay, C., Burstin, J., Duc, G., Lemanceau, P., Moreau, D., Munier-Jolain, N., Pivato, B., Rigaud, T., Salon, C., & Mougel, C. (2013). Combining molecular microbial ecology with ecophysiology and plant genetics for a better understanding of plant-microbial communities interactions in the rhizosphere. In F. J. de Bruijn (Ed.), Molecular microbial ecology of the rhizosphere Wiley-Blackwell.
    • Zancarini, A., Mougel, C., Terrat, S., Salon, C., & Munier-Jolain, N. (2013). Combining ecophysiological and microbial ecological approaches to study the relationship between Medicago truncatula genotypes and their associated rhizosphere bacterial communities. Plant and Soil, 365(1-2), 183-199.


    • Zancarini, A., Mougel, C., Voisin, A-S., Prudent, M., Salon, C., & Munier-Jolain, N. (2012). Soil Nitrogen Availability and Plant Genotype Modify the Nutrition Strategies of M. truncatula and the Associated Rhizosphere Microbial Communities. PLoS ONE, 7(10).


    • Contesto, C., Milesi, S., Mantelin, S., Zancarini, A., Desbrosses, G., Varoquaux, F., ... Touraine, B. (2010). The auxin-signaling pathway is required for the lateral root response of Arabidopsis to the rhizobacterium Phyllobacterium brassicacearum. Planta, 232(6), 1455-1470.


    • Martinière, A., Zancarini, A., & Drucker, M. (2009). Aphid transmission of cauliflower mosaic virus: the role of the host plant. Plant Signaling & Behavior, 4(6), 548-50.
    This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list.
  • Ancillary activities
    • No ancillary activities