Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets

Microbiome
Peter KusstatscherTomislav Cernava

Abstract

Sugar loss due to storage rot has a substantial economic impact on the sugar industry. The gradual spread of saprophytic fungi such as Fusarium and Penicillium spp. during storage in beet clamps is an ongoing challenge for postharvest processing. Early detection of shifts in microbial communities in beet clamps is a promising approach for the initiation of targeted countermeasures during developing storage rot. In a combined approach, high-throughput sequencing of bacterial and fungal genetic markers was complemented with cultivation-dependent methods and provided detailed insights into microbial communities colonizing stored roots. These data were used to develop a multi-target qPCR technique for early detection of postharvest diseases. The comparison of beet microbiomes from six clamps in Austria and Germany highlighted regional differences; nevertheless, universal indicators of the health status were identified. Apart from a significant decrease in microbial diversity in decaying sugar beets (p ≤ 0.01), a distinctive shift in the taxonomic composition of the overall microbiome was found. Fungal taxa such as Candida and Penicillium together with the gram-positive Lactobacillus were the main disease indicators in the microbiom...Continue Reading

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Methods Mentioned

BETA
amplicon sequencing
PCR
electrophoresis
PCRs

Software Mentioned

- BLAST
FUNGuild
PERMANOVA
Primer
BLAST
QIIME
QIIME2

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