MD.20.007 – Impact of root microbiome dynamics on plant health

Route: Measuring and detecting: anything, anytime, anywhere

Cluster question: 005 What role do micro-organisms play in ecosystems and how can we use them to improve health and the environment?

Plant-root microbiota consist of entangled webs of interactions formed by countless micro-organisms playing crucial roles in nutrient acquisition and plant resistance to biotic and abiotic stresses. As plant growth and health is highly dependent on these root-associated microbes, understanding the factors that determine the structure and function of plant-root microbiomes are of great scientific and practical value. However, it is not yet known how the variation over time within or between different individuals and species influences plant health or the onset (and progression) of disease. We investigate how root microbiome diversity and structure influence plant resistance against fungal and oomycete pathogens, in order to build a predictive framework of soil and plant health. Measuring microbiome structure and plant health over time, the proposed research encapsulates three specific goals: (1) to produce detailed soil and root microbiome profiles (using long-read DNA barcodes); (2) to investigate the link between root microbiome dynamics and plant disease progression in relation to biotic and abiotic stress; and (3) to develop a predictive framework for the relationship between root microbiome structure and ecosystem health (using advanced network analysis and machine learning). We focus on three different crop systems: sugar beet and both indoor-cultivated and outdoor-cultivated flower bulbs. In the context of agroecosystems, the research directly links to the NWA question: What is the role of micro-organisms in ecosystems, and how can we use this for health and environments? Through the combination of biological, technological, and analytical expertise of the research consortium members we are poised to make great advances in our knowledge of root microbiome dynamics and its effects in various crop species. These insights help to better understand the form and function of microbiomes in general, and will generate new hypotheses for empirical, experimental, and theoretical work on competition, adaptive immunity


Bacteria, biodiversity, DNA sequencing, Fungi, plant health

Other organisations

BaseClear, Jheronimus Academy of Data Science, KAVB, Leiden University (LEI), Stichting IRS, University of Amsterdam, University of Applied Science Leiden, Westerdijk Institute


Organisation Naturalis Biodiversity Center
Name Dr. Vincent Merckx