Allies or bystanders? : the involvement of spinach seed microbiota in the suppression of Globisporangium ultimum damping-off

Seeds mark the onset of plant life and can be used in agriculture to deliver not only desirable plant traits to a new plant generation, but desirable microbiota as well. With seed microbiota aiding seed germination and plant fitness, it is becoming clear that seeds are equipped with both nutrients for early seedling growth and beneficial seed microbiota. Given the need to provide farmers with healthy seeds while chemical pesticides are being phased out, the seed industry has an interest in making use of the potential benefit of such microorganisms. This thesis focused on the role of seed microbiota in seed and seedling disease suppression to provide insights on the following knowledge gaps: (i) understanding the extent to which seed microbiota may play a role in seed and seedling disease suppression, (ii) identifying specific microbial actors that are involved in safeguarding seed and seedling health in the absence of chemical products and (iii) exploring methodologies that would integrate microbial applications in the development of sustainable seed health strategies. I addressed these knowledge gaps by formulating the following research questions: (i) Can seed microbiota confer disease suppression? (ii) Are there specific seed microbiota linked with the suppressing effect? (iii) Are these microorganisms culturable and ubiquitous? In chapter 2, I took the first step to understand whether seed microbiota involved in disease suppression by tackling the proof-of-concept: seed microbiomes can be beneficial for seed and seedling health by conferring disease suppression. In chapter 3, I zoomed in on the spinach – Globisporangium ultimum pathosystem to explore spinach seed microbiome characteristics linked to suppressiveness against damping-off caused by this pathogen, which was previously known as Pythium ultimum. In chapter 4, I worked with the microbiota of two suppressive spinach seed lots using amplicon sequencing and culture-dependent techniques. I investigated what fraction of the total microbial community per seed lot was culturable. Overall, the results presented in these three experimental chapters can be considered as a starting point for understanding the involvement of seed microbiota in seedling disease suppression and provide information for stipulating ways in which seed microbiota could become integrated in the development of sustainable seed health strategies. This is discussed in chapter 5, where I also comment on the importance of sample preprocessing prior to DNA extraction, sample representativeness and developmental stage of the seeds used, for the results of a seed microbiome study. The chapter also includes a description of possible future research directions. Additionally, I highlight the importance of my work from a scientific and societal perspective. The most indisputable impact of this work is the funding of a follow-up public-private partnership project which will also investigate links between seed health and seed microbiota. Finally, I am confident that my work demonstrated that: (i) microorganisms exist and may manifest as part of seed microbiomes, (ii) seed microbiota can be active and influential and (iii) learning about seed microbiota encourages their preservation.