Downy mildew-associated microbiomes

In this thesis, I have investigated microbiomes of plants that are under attack by obligate biotrophic pathogens that cause downy mildew disease. In particular, I have studied the phyllosphere bacterial communities of laboratory cultures of the downy mildews Hyaloperonospora arabidopsidis (Hpa) and Peronospora effusa (Pe) on their respective hosts Arabidopsis thaliana and Spinacia oleracea (henceforth Arabidopsis and spinach). Within these two pathosystems, we observed consistent enrichment of specific bacteria in distinct cultures (Chapters 2 and 4), and for the Arabidopsis system we demonstrated that the genomes of the specific bacteria enriched in distinct laboratory cultures across Europe were isogenic (Chapter 2). These bacteria were further shown to reach higher abundances in the phyllosphere upon Hpa infection (Chapter 2). Also in the rhizosphere, we observed increased colonization by downy mildew-associated bacteria on plants that were grown on soil that was conditioned by downy mildew-infected plants. This suggests that the downy mildew-associated microbes are part of a soil-borne legacy of disease that can be inherited by future generations of plants grown on the same soil (Chapter 3). Moreover, the microbes that are enriched in downy mildew-associated communities appear to be geared towards plant protection (Chapter 3), suggesting that their assembly is indeed directed by the host plant. Lastly, similarities were observed between Pe-associated microbiomes in laboratory cultures and naturally Pe-infected field-grown plants (Chapter 4), highlighting that these microbiomes are not only a laboratory phenomenon. Together, these findings suggest that phyllosphere bacterial communities of plants that are under downy mildew attack are modulated to benefit the plant, meaning that a plant’s cry for help towards the microbiome upon pathogen attack may be a contributing factor to phyllosphere microbiome assembly. Finally, these findings are discussed in a broader perspective in chapter 5, focusing on the mechanisms that may underly the recruitment/enrichment of specific bacteria in downy mildew-infected leaves.