Seed tuber imprinting shapes the next-generation potato microbiome

Potato seed tubers are colonized and inhabited by soil-borne microbes, some of which can positively or negatively impact the performance of the emerging daughter plant in the next season. In this study, we investigated the intergenerational inheritance of microbiota from seed tubers to next-season daughter plants by amplicon sequencing of bacterial and fungal microbiota associated with tubers and roots of two seed potato genotypes produced in six different fields. We observed that field of production and potato genotype significantly affected the seed tuber microbiome composition and that these differences persisted during winter storage of the seed tubers. When seed tubers from different production fields were planted in a single trial field, the microbiomes of daughter tubers and roots of the emerging plants could still be distinguished according to the field of origin of the seed tuber. Remarkably, we found little evidence of direct vertical inheritance of field-unique microbes from the seed tuber to the daughter tubers or roots. Hence, we hypothesize that this intergenerational memory is imprinted in the seed tuber, resulting in differential microbiome assembly strategies depending on the field of production of the seed tuber.