Characterizing Variation in the Bacterial and Fungal Tare Soil Microbiome of Seed Potato

Abstract

For tuberizing crops such as potato (Solanum tuberosum), the geocaulosphere, or the thin zone of soil in contact with and influenced by the tuber, is a distinct habitat that exists between the potato and the soil environment. Geocaulosphere soil that remains associated with the tuber after harvest is called tare soil. However, beyond potato pathogens, the microbes present in tare soil are understudied. We used internal transcribed spacer and 16S metabarcoding to characterize the microbial communities present in 130 tare soils of commercially produced seed potato plantlets used for potato production in Oregon. In 2018 and 2019, tare soils were opportunistically sampled from seed potato plantlets that were collected from farmers in the Columbia Basin of Oregon. This sampling effort included seed tubers of 23 cultivars that had originated from 40 commercial seed farms in 11 states. We identified a core microbiome consisting of 61 bacterial and 26 fungal taxa, some of which are not common to the potato microbiome, and others which have been reported to either possess biocontrol activities, promote plant growth, or cause disease in potato. Seed grower farm accounted for the greatest amount of compositional variation among tare soil microbiome samples, with more similar communities found on seed tubers grown on farms near to each other. Learning which factors shape tare soil microbial community composition and whether those communities influence plant health are essential steps towards potato microbiome management.

Keywords

• amplicon sequencing
• bacteria
• core microbiome
• crop
• fungi
• geocaulosphere