Consistent effects of independent domestication events on seed microbiome assembly

Plant domestication has been decisive in the development of human societies. However, the consequences of plant domestication at the ecosystem level are still poorly understood. Among different organisms that live in association with plants, microbial communities exert important biological and ecological functions. Whether and how plant domestication changed plant-microbe interactions remains difficult to prove but could have important repercussions for sustainable agriculture. In this study, we investigate whether there is a domestication effect on plant-microbe interactions and the processes that drive the assembly of the microbiome in wild and domesticated plants. To achieve this, we focused on Phaseolus, which is one of the few plant genera that have undergone four independent domestication events within two species (Phaseolus vulgaris and Phaseolus lunatus), providing us with a replication of an event lasting thousands of years. We specifically examined the effect of domestication on seed-associated microbial communities, as the seed is a plant compartment that has been subject to large phenotypic changes during domestication, making it an ideal candidate to test a domestication effect on the microbiome. We analysed the seed bacteriome of wild accessions of P. vulgaris and P. lunatus and accessions derived from all four domestication events and observed evidence of a common domestication effect on the seed microbiome, which can be explained, at least partially, by domesticated plant phenotypes. Our results provide evidence of a coordinated evolution of domesticated plant phenotypes and seed microbiome assembly leading to a reduction in selective forces during plant domestication. Processed data is available from GitHub (https://github.com/RSO9192/Consistent-effects-of-independent-domestication-events-on-seed-microbiome) as well as instructions to process raw reads submitted to ENA (folder ENA_instructions)