- “MiCrop: Harnessing the second genome of plants: Microbial imprinting for crop resilience”. NWO Gravity Program. With University of Amsterdam, VU Amsterdam, Wageningen University, and NIOO-KNAW.
- “Innovation by nature: plant traits involved in maximizing growth and protective functions of root microbiota”; part of TTW Perspective Programme “Back to the Roots” (with Wageningen University, NIOO, Leiden University). Project members: Peter Bakker, Roeland Berendsen, Gilles Vismans, Pauline Trapet.
- “De weerbare plant”; with WUR Glastuinbouw en WUR-PRI. Project members: Saskia van Wees, Dharani Kamalachandran.
- “Unearthing beneficial microbe rhizosphere competence traits in vivo” NWO Green II project. Project members: Ronnie de Jonge, Juan José Sanchez Gil, Sanne Poppeliers, Bas Dutilh.
- “Selecting soybean-specific consortia of beneficial microbes for sustainable yield improvement” NWO Industrial Doctorate Program. Project members: Roeland Berendsen, Sietske van Bentum, Peter Bakker.
- “The potato microbiome and resilience”. Industrial funding from potato breeding companies. Project members: Roeland Berendsen, Peter Bakker, Ronnie de Jonge, Yang Song.