Plant age and genotype explain variation in the microbiome of natural Lotus corniculatus populations

In natural populations, plants are associated with a huge diversity of bacteria, fungi and other microbes. There is usually substantial microbiome variation between different plant individuals and populations, and the drivers of this variation are still poorly understood, particularly in wild plants. Here, we were interested in the potential of plant genotype and plant age to explain intraspecific variation in the plant microbiome of Lotus corniculatus. In seven natural populations, we genotyped a total of 168 individuals over four years, determined their ages through growth ring analysis, and then sequenced their root, shoot, flower and seed microbiomes. We found that plant genotypes differed both in the diversity and composition of microbes, and that some microbial taxa were associated with particular plant 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. We found less 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. Our study indicates that the genotype of a plant and - to a lesser degree its age - influences the diversity and composition of plant-associated microbiota, even in complex natural environments. ImportanceThe plant microbiome plays a key role in important plant functions such as pathogen resistance, nutrient uptake, and stress tolerance. To fully understand these processes, it is essential to identify the factors that drive microbiome variation. Most research to date has focused on model or crop species under controlled conditions, leaving open questions about the drivers of microbiome diversity and composition in natural populations. In this multi-year field study, we examined how plant genotype and age shape the microbiomes of Lotus corniculatus. We show that the plant genotype strongly influences microbial diversity and composition, while plant age has subtler but still important effects, particularly on fungal communities. To our knowledge, this is the first study to link plant age with microbiome variation in natural populations. These findings demonstrate that plant traits can shape the microbiome even in complex natural environments.