Multitrophic plant-microbe interactions

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In nature, the roots of healthy and asymptomatic plants associate with a variety of microbes, including bacteria, fungi and oomycetes (i.e. the root microbiota), therefore forming complex microbial consortia that impact plant growth and productivity. In such multitrophic complexes microbes coexist and interact, forming physically and metabolically interdependent consortia that harbour properties that are distinct when compared to those of the constituent pars. Paradoxically, while microbiome studies investigating the complexity of microbial communities are abundant, systematic research capturing the diversity of microbes across individual classes is sparse. It is likely that both plant-microbe and microbe-microbe interactions are equally important in sculpting root-associated microbial assemblages in nature. However, it remains unclear whether cooperative or competitive interactions within or between microbial classes are important organizational determinants governing microbial colonization on plants and to which extent microbe-microbe interactions along the soil-root continuum can benefit the host. Understanding the organizational principles underlying the establishment of complex microbial consortia on plant roots as well as their functional impact on host health in nature remains challenging due to environmental noise. However, it is now conceivable to address these important ecological concepts by combining high-throughput microbial profiling methods, large-scale microbial species isolation, and microbiota reconstitution experiments with germ-free plants.



In the Multitrophic Plant-Microbe Interactions group, we aim at understanding the fundamental mechanisms that underlie the structure and the functions of multi-kingdom microbial consortia colonizing plant roots. By combining microbial community profiling data from natural A. thaliana populations, with the use of reference microbial culture collections and gnotobiotic plant systems, we dissect how both host-microbe and microbe-microbe interactions impact microbial community structure and plant health. We are also generating extensive microbial genome resources that will serve as key resources to identify the genetic determinants of microbial adaptation to plant roots and to interpret metatranscriptomic profiles of artificial microbial consortia.

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