Abstract:
Like all eukaryotes, plants are colonized by a diverse community of microorganisms which collectively form the plant microbiome. While some can cause diseases, the majority are either harmless or beneficial to the plant. These beneficial effects can range from enhanced growth, improved nutrient uptake, increased tolerance to stress, or resistance to pathogens. Although these effects have been studied intensely in recent years, we still have a poor understanding of which factors shape the complex plant microbiome, particularly under natural conditions. Improving our understanding of the plant microbiome and its impacts on plants will be important not only for advancing fundamental science but also for agriculture and crop protection. In the first chapter of my thesis, I introduce two main perspectives for studying the plant microbiome interactions. One focuses on how the microbiome affects the fitness and survival of plants, and their interactions with the environment. The other perspective shifts attention towards the microbiome itself, exploring which factors shape its composition and diversity, and how these factors interact. In the following chapters, I focused on the microbiome perspective, specifically investigating how host factors such as plant organ, plant age, and intraspecific genetic variation influence the composition and diversity of the plant microbiome. I worked with Lotus corniculatus, a widely distributed perennial legume that is commonly used as livestock forage, and as a nitrogen-fixer it impacts the nutrient dynamics of its ecosystems. Over four years, I sampled plants across multiple natural populations in southern Germany and sequenced their microbiomes (bacteria, fungi and eukaryotes) separately for the roots, shoots, flowers and seeds of each plant. I also genotyped all plants using ddRAD sequencing and determined their ages through herb chronology. Chapter III focuses on how plant-associated microbial communities differ across plant organs, with a gradual reduction in diversity from roots to shoots, and further into flowers and seeds. Building on this, Chapter IV shows that plant genotype further shapes both the diversity and composition of these communities, with certain taxa associated with specific genotypes. The genotype effects tended to be strongest and most consistent for plant-associated bacteria, with the largest plant genotype differences in the microbiome diversity of flowers and seeds. In contrast to plant genotype effects, I found less but still some evidence for an effect of plant age on microbiome diversity. The age of plants explained variation in fungi diversity, and it was associated with the abundance of several microbial taxa. To test specifically for genetic variation in pathogen resistance, I conducted a controlled growth chamber experiment in which I infected 20 natural accessions of L. corniculatus with the two pathogenic fungi Fusarium and Uromyces under different temperature and shade conditions. In Chapter V I present the results of this experiment, showing that the effects of both pathogens varied significantly across plant genotypes. Furthermore, while the interactions between plant genotypes and pathogens remained largely independent of the abiotic stressors, I observed a strong overall influence of environmental conditions on infection outcomes. These results show that intraplant variation among organs, or age, as well as intraspecific genetic variation influence the diversity and composition of plant-associated microorganisms, even in complex natural environments. In the future, this knowledge could support breeding programs not only in enhancing pathogen resistance but also in selecting plant genotypes that support beneficial microbe combinations. Such approaches could contribute to more effective strategies for managing both abiotic and biotic stress, increasing plant health and resilience in a rapidly changing world.
microbial ecology