On-field microbial community influences postharvest root rot in sugar beets

Sugar beets (Beta vulgaris L.) are grown in temperate regions and primarily used for sugar production. Due to limited capacities of the sugar refineries, sugar beets in Europe are stored after harvest for up to 60 days. Microbial degradation leads to sugar decrease during this time. To investigate disease impact on the microbiome level, bacterial and fungal community of field-grown as well as stored sugar beets was compared. Using a barcoded amplicon sequencing approach targeting bacteria and fungi, microbiome dynamics, differences, and potential functions were assessed. Moreover, microbial transmission from field-grown to stored sugar beets was investigated. Interestingly, the microbiome of beets affected by root rot in the field as well as in storage showed broad overlaps, and bioinformatics-based predictions indicated transmission of field microbiomes to the storage clamps. Root rot was accompanied by a loss in microbial diversity (Shannon index decrease of 5.5 to 4.5 (bacteria) and 4.5 to 3.5 (fungi)) as well as the replacement of Plectosphaerella and Vishniacozyma, as predominant species in healthy roots, with Penicillium, Candida, and Fusarium sp. in rotting beets. Furthermore, the Gram-positive Lactobacillus was the predominant bacterial genus in rotting beets. Along with taxonomic changes also a trophic specialization of the fungal community was observed. The overall findings can be implemented in new postharvest strategies following a microbiome-driven approach for biological treatments.