Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus L.. Bacterial and fungal communities associated with sunflowers

Despite the important effects of root and rhizosphere microbial communities on plant health, we have only a basic understanding of the factors determining the assembly of these communities. Domestication of agricultural crops, and the corresponding changes in plant phenotype, could alter the diversity, composition, and function of plant-associated bacterial and fungal communities with potentially important implications for the health and environmental tolerances of crop plants. To investigate these potential domestication effects on microbial communities, we grew 33 sunflower (Helianthus annuus L.) strains (n = 5) in a common garden and assessed rhizosphere and root endosphere bacterial and fungal communities to evaluate whether the microbial communities varied as a function of strain identity and/or their level of domestication. We found that neither root nor rhizosphere bacterial communities strongly differed across sunflower strains, but the composition of rhizosphere fungal communities did differ across the sunflower strains. Similarly, rhizosphere fungal community composition was significantly affected by the extent of sunflower domestication, with the roots and the rhizosphere of more modern strains having lower relative abundances of putative fungal pathogens compared to the more ancestral (less domesticated) sunflower strains. While sunflower phenotypic characteristics strongly differed across the strains, they were only weakly related to bacterial and fungal community structure. We also assessed whether vertical transmission of the microbiome through seeds could explain the strain-specific differences in fungal communities and found that the seed-associated microbial communities strongly differed across strains. However, several lines of evidence suggest that there is minimal vertical transmission of fungi from seeds to the adult plants. Together, our results indicate the observed variation in sunflower root and rhizosphere microbial communities was not strongly determined by either environment or sunflower genotype alone, but rather by a combination of genetic and environmental factors. It will be important to recognize these drivers of belowground plant-associated microbial community assembly when attempting to understand plant health or when seeking to optimize microbial communities to improve crop yields.