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

Peter Kusstatscher,Johann Maier,Gabriele Berg,Karsten Harms,Herbert Eigner,Tomislav Cernava,Christin Zachow

doi:10.1186/s40168-019-0728-0

Abstract

BackgroundSugar 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.ResultsThe 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 microbiome of decaying sugar beets. In contrast, the genera Plectosphaerella and Vishniacozyma as well as a higher microbial diversity in general were found to reflect the microbiome of healthy beets. Based on these findings, a qPCR-based early detection technique was developed and confirmed a twofold decrease of health indicators and an up to 10,000-fold increase of disease indicators in beet clamps. This was further verified with analyses of the sugar content in storage samples.ConclusionBy conducting a detailed assessment of temporal microbiome changes during the storage of sugar beets, distinct indicator species were identified that reflect progressing rot and losses in sugar content. The insights generated in this study provide a novel basis to improve current or develop next-generation postharvest management techniques by tracking disease indicators during storage.

Highlights

Sugar loss due to storage rot has a substantial economic impact on the sugar industry
The community structure was reconstructed with Sanger sequencing of 18S rRNA gene fragments from fungal isolates and Internal transcribed spacer (ITS) Illumina amplicon sequencing of total community Deoxyribonucleic acid (DNA) (Fig. 1)
Storage rot in stored sugar beets was shown to be accompanied by a change in microbial abundances

Summary

Introduction

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. Detection of shifts in microbial communities in beet clamps is a promising approach for the initiation of targeted countermeasures during developing storage rot. 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. Mainly by pathogenic or saprophytic fungi such as Fusarium, Penicillium, and Botrytis spp., leads to substantial sugar yield losses. The combined occurrence of microbial degradation, respiration of the beet root, synthesis of raffinose, and other causes can yield sugar losses of up to 50–60% during storage [16, 17]

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