Insights into the microbiome assembly during different growth stages and storage of strawberry plants
Abstract Background Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growt...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | Environmental Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40793-022-00415-3 |
| _version_ | 1811338871252713472 |
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| author | Expedito Olimi Peter Kusstatscher Wisnu Adi Wicaksono Ahmed Abdelfattah Tomislav Cernava Gabriele Berg |
| author_facet | Expedito Olimi Peter Kusstatscher Wisnu Adi Wicaksono Ahmed Abdelfattah Tomislav Cernava Gabriele Berg |
| author_sort | Expedito Olimi |
| collection | DOAJ |
| description | Abstract Background Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. Results Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (107–1010 marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. Conclusion Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety. |
| first_indexed | 2024-04-13T18:17:02Z |
| format | Article |
| id | doaj.art-68ecd8f2c2c246a7aea992a33a41043b |
| institution | Directory Open Access Journal |
| issn | 2524-6372 |
| language | English |
| last_indexed | 2024-04-13T18:17:02Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Environmental Microbiome |
| spelling | doaj.art-68ecd8f2c2c246a7aea992a33a41043b2022-12-22T02:35:38ZengBMCEnvironmental Microbiome2524-63722022-04-0117111510.1186/s40793-022-00415-3Insights into the microbiome assembly during different growth stages and storage of strawberry plantsExpedito Olimi0Peter Kusstatscher1Wisnu Adi Wicaksono2Ahmed Abdelfattah3Tomislav Cernava4Gabriele Berg5Institute of Environmental Biotechnology, Graz University of TechnologyInstitute of Environmental Biotechnology, Graz University of TechnologyInstitute of Environmental Biotechnology, Graz University of TechnologyInstitute of Environmental Biotechnology, Graz University of TechnologyInstitute of Environmental Biotechnology, Graz University of TechnologyInstitute of Environmental Biotechnology, Graz University of TechnologyAbstract Background Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. Results Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (107–1010 marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. Conclusion Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.https://doi.org/10.1186/s40793-022-00415-3Fragaria × ananassaMicrobiome assemblyFruit pathogensBacterial communitiesFungal communitiesAmplicon sequencing |
| spellingShingle | Expedito Olimi Peter Kusstatscher Wisnu Adi Wicaksono Ahmed Abdelfattah Tomislav Cernava Gabriele Berg Insights into the microbiome assembly during different growth stages and storage of strawberry plants Environmental Microbiome Fragaria × ananassa Microbiome assembly Fruit pathogens Bacterial communities Fungal communities Amplicon sequencing |
| title | Insights into the microbiome assembly during different growth stages and storage of strawberry plants |
| title_full | Insights into the microbiome assembly during different growth stages and storage of strawberry plants |
| title_fullStr | Insights into the microbiome assembly during different growth stages and storage of strawberry plants |
| title_full_unstemmed | Insights into the microbiome assembly during different growth stages and storage of strawberry plants |
| title_short | Insights into the microbiome assembly during different growth stages and storage of strawberry plants |
| title_sort | insights into the microbiome assembly during different growth stages and storage of strawberry plants |
| topic | Fragaria × ananassa Microbiome assembly Fruit pathogens Bacterial communities Fungal communities Amplicon sequencing |
| url | https://doi.org/10.1186/s40793-022-00415-3 |
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