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Doctoral thesis2020Open access

Microbial community dynamics in the phyllosphere of leafy vegetables

Darlison, Julia

Abstract

Microbes interact with the phyllosphere creating a plant microbiota holobiont. From a food safety aspect the phyllosphere is especially important in leafy vegetables which are generally consumed raw. Plant-microbe interactions are complex, but well-known ecological concepts can be applied to explain the dynamics. 

The microbial communities in the phyllosphere of spinach, rocket and Swiss chard were studied in field and greenhouse studies in this thesis. We examined the impact of nitrogen fertiliser application to plants on the microbiota in the phyllosphere. The influence of nitrogen fertiliser on establishment of an invading human pathogen, Escherichia coli O157:H7 gfp+ and the role of the plant species and plant cultivar were investigated. We explored the succession of microbial communities on leafy vegetables. To identify the microbial communities, culture-independent methods (Illumina MiSeq after DNA extraction from the leaf surface) and culture dependent methods (viable count and identification of bacterial isolates with 16S rRNA sequencing) were used in combination with plant physiological measurements and weather monitoring.

Plant species, environmental factors and annual variations had selective effects on the microbial communities in the phyllosphere. Increasing nitrogen supply reduced microbial diversity, as did harvesting the leaves. The concept of prevention of invasion by high diversity was not confirmed for bacterial communities in the phyllosphere. Phyllosphere microorganisms are also of interest for possibly developing new efficient and sustainable methods in agriculture and horticulture, however, before microbiomes can be exploited, more knowledge is needed about how plants and microbes interact with the environment, management and post-harvest procedures.

Keywords

phyllosphere; microbiome; microbial community; metagenomics; food safety; E. coli O157:H7 gfp+; leafy vegetables; nitrogen fertiliser; ecology concepts

Published in

Acta Universitatis Agriculturae Sueciae
2020, number: 2020:66ISBN: 978-91-7760-650-5, eISBN: 978-91-7760-651-2 Publisher: Department of Biosystems and Technology, Swedish University of Agricultural Sciences