Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets
Abstract Background 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 micr...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | Microbiome |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s40168-019-0728-0 |
| _version_ | 1818870538420879360 |
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| author | Peter Kusstatscher Christin Zachow Karsten Harms Johann Maier Herbert Eigner Gabriele Berg Tomislav Cernava |
| author_facet | Peter Kusstatscher Christin Zachow Karsten Harms Johann Maier Herbert Eigner Gabriele Berg Tomislav Cernava |
| author_sort | Peter Kusstatscher |
| collection | DOAJ |
| description | Abstract Background 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. Results 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 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. Conclusion By 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. |
| first_indexed | 2024-12-19T12:08:37Z |
| format | Article |
| id | doaj.art-616f04287b4c42889ac4ff719855de5e |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-19T12:08:37Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-616f04287b4c42889ac4ff719855de5e2022-12-21T20:22:16ZengBMCMicrobiome2049-26182019-08-017111210.1186/s40168-019-0728-0Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beetsPeter Kusstatscher0Christin Zachow1Karsten Harms2Johann Maier3Herbert Eigner4Gabriele Berg5Tomislav Cernava6Austrian Centre of Industrial BiotechnologyAustrian Centre of Industrial BiotechnologySüdzucker AGSüdzucker AGAgrana Research & Innovation CenterInstitute of Environmental Biotechnology, Graz University of TechnologyInstitute of Environmental Biotechnology, Graz University of TechnologyAbstract Background 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. Results 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 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. Conclusion By 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.http://link.springer.com/article/10.1186/s40168-019-0728-0Beta vulgarisStorage rotIndicator speciesPhytopathogensBacterial microbiomeFungal microbiome |
| spellingShingle | Peter Kusstatscher Christin Zachow Karsten Harms Johann Maier Herbert Eigner Gabriele Berg Tomislav Cernava Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets Microbiome Beta vulgaris Storage rot Indicator species Phytopathogens Bacterial microbiome Fungal microbiome |
| title | Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets |
| title_full | Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets |
| title_fullStr | Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets |
| title_full_unstemmed | Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets |
| title_short | Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets |
| title_sort | microbiome driven identification of microbial indicators for postharvest diseases of sugar beets |
| topic | Beta vulgaris Storage rot Indicator species Phytopathogens Bacterial microbiome Fungal microbiome |
| url | http://link.springer.com/article/10.1186/s40168-019-0728-0 |
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