Ronnie de Jonge
Microbial (meta)genomics of plant-associated microbes
Beneficial microbes provide plants with important services, such as enhanced mineral uptake, nitrogen fixation, growth promotion and biocontrol, and thus contribute to plant health. Alike their pathogenic counterparts, they can be recognized by the plant immune system through detection of their common microbe associated molecular patterns or MAMPs, thereby triggering basal immunity. Thus, successful colonization depends on active interference with the plant immune system. Plants in turn need to distinguish between beneficial and pathogenic microbes to facilitate only those that are advantageous. Such establishment of plant-microbe symbioses requires the exchange of specific signaling molecules to fine tune immunity and promote colonization.
Understanding the molecular mechanisms of plant – microbe interactions are at the heart of our investigations. In order to understand how microbes, be it pathogenic or beneficial, interact with the plant we make extensive use of sequencing data and comparative, evolutionary genomics as well as transcriptomics approaches. Secreted small molecules play an important role in many such interactions and we have recently revealed the genetic basis of cercosporin (a small polyketide toxin) biosynthesis and self-resistance in the sugar beet pathogen Cercospora beticola (https://doi.org/10.1101/100545). Also plants make use of small organic molecules to interact with their surrounding microbes, and we investigate how exudation of such molecules directs microbiome assemblage in and around the root. To do this we use metagenome sequencing and comparative genomics, transposon mutagenesis as well as high-throughput heterologous expression in alternative host microbes.
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