Temporal dynamics and tissue-specific variations of the blueberry phyllosphere mycobiome

Abstract

Highbush blueberry (Vaccinium corymbosum) is an economically important fruit-bearing woody perennial. Despite the importance of microbial communities to plant health, the aboveground (phyllosphere) microbiome of blueberry is understudied. The phyllosphere is exposed to varying conditions throughout a growing season. The fruit undergoes extensive physiological change across a season from bud to fruit. This study aimed to provide a temporal characterization of the blueberry phyllosphere across a growing season and a characterization of specific tissues and phenological stages. Blueberry branches were harvested every other week across 2 years and two locations during the development process of the blueberry fruits. The internal transcribed spacer regions were amplified from DNA extracts and sequenced to perform amplicon-based characterization of the fungal microbiome across time and plant tissue. Fungal communities showed changes in α-diversity depending on the week of harvest and tissue type. Early in the season, α-diversity was high, but it decreased in midseason when flowers developed into fruit. Later in the season, as the fruit ripened, α-diversity increased again. The β-diversity of the community changed across time and tissue types during plant development. Notable members of the identified core microbiome were members of the genus Alternaria, Peltaster, and Taphrina, as well as the pathogenic taxa Aureobasidium pullulans and Botrytis cinerea. This research provides background for future experimentation of understanding the microbial composition in the blueberry phyllosphere in relation to the infection court of pathogens (e.g. Colletotrichum fioriniae and B. cinerea) and the temporal components of blueberry plant health and management.

Acknowledgements

The authors would like to thank the Michigan blueberry growers and the Michigan Blueberry Commission who have supported this project. We also thank our program’s field manager Roger Sysak for collecting field samples throughout the duration of this project, as well as Dr. Greg Bonito for providing primers. For funding, we would also like to thank the USDA-SCRI project titled: ‘BLUE-DYNAMO: an interactive platform to deliver blueberry disease and horticultural management strategies for fruit rots’ Project number MICL20054. We also acknowledge funding from Michigan State University’s Project GREEEN. This project is also supported by USDA Hatch project MICL02617. Michigan State University and the plant pathology farms sampled in this study occupy Anishinaabe lands ceded in the 1819 Treaty of Saginaw. The Southwest Michigan Research and Extension Center occupies Anishinaabe lands ceded in the 1821 Treaty of Chicago.

Author contributions

S.L.S. performed sample collection, sample processing, data analysis and interpretation, and manuscript preparation. T.D.M. and S.L.S. both participated in manuscript editing and study design. T.D.M. participated in project management in support of this research.

Data availability

Raw sequencing data generated for this study can be found in the NCBI SRA archive as Bioproject PRJNA1161654. Code is available at https://github.com/szymanskishay/blueberrytimecourse/

Conflict of interest statement

The authors report no conflicts of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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