PhD thesis: Harnessing plant-microbiome interactions in the context of sustainable agriculture (2025)

Mutualistic plant-microbiome interactions are crucial for plant development and stress resilience, yet they have been disrupted by climate change and conventional agricultural practices. Traditional breeding programs, focused on yield and stress resistance under ideal conditions, have also overlooked the role of microbiomes in plant growth. This thesis emphasises integrating plant genotypes and soil microbiomes to reduce agriculture’s environmental impact and achieve sustainability. For the first time, we demonstrate that selecting cultivars with microbiome interactive traits is feasible and can produce high-performing crops that support microbiome-assisted agriculture. Furthermore, our findings highlight the role of soil biodiversity in shaping plant growth under well-watered, drought-stressed, and rewetting conditions. We also show that microbial communities influence root exudate profiles, with root metabolite-microbiome interactions regulating plant traits. Additionally, phages within the microbial community play a key role in regulating plants' coping with drought. In summary, this work underscores the importance of integrating microbiome science into breeding programs and agricultural management to unlock the full potential of plant-microbiome interactions, ensuring food security and environmental sustainability.