Breeding shapes the seed microbiome of future generations in Cucurbita pepo

Plant breeding does not only shape the plants characteristics, but also impacts the plant colonizing microbes. The Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) has a long tradition in the southern Austrian agriculture for oil production. We analyzed the microbiome of six genotypes (the complete pedigree of a three-way cross hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction of Enterobacteriaceae (40-83%). Additionally, potential plant beneficial bacterial taxa, including Bacillaceae, Burkholderiaceae and Pseudomonadaceae were found to be enriched in progeny seeds. Between cultivars more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Interestingly, mainly fungal communities in the soil were found to contribute to progeny seeds, while bacterial traits were mostly linked to sown seeds. Moreover, rhizosphere communities were assembled for the most part from soil. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin communities and represent the first steps into a microbiome-driven breeding for plant-beneficial microbes