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Manipulating the plant phyllosphere microbiome for plant and environmental health

   School of Biological Sciences

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  Dr P Devlin, Prof A Devoto  No more applications being accepted  Competition Funded PhD Project (UK Students Only)

About the Project

Healthy plants, like all higher organisms, host an extensive commensal microbial community or microbiome. Non-pathogenic microbes in many cases benefit the host. In plants, both the leaf microbiome, the phyllosphere, and the root microbiome, the rhizosphere, contain a wide range of bacterial and fungal species, including some that have been shown to play a range of roles in disease prevention. Changes in the microbiome can, therefore, have important effects on plant health and microbial supplementation offers a real option for biological pesticides (fungicides) as part of a route to improved agricultural sustainability. However, understanding the rules of establishment of microbial supplements within the microbiome is currently a key knowledge gap, with many potential biological control agents failing to establish in the field under real agricultural conditions.

One area of particular interest in this respect is the dynamic nature of the microbiome. Microbial communities are subject to rapid change in composition, particularly true in the phyllosphere microbial community. The phyllosphere is the site of much fungal pathogenic invasion, making the phyllosphere microbiome key in defence. The phyllosphere is also a zone in which microbiome engineering can be relatively easily performed via application of synthetic communities (SynComs). Despite this, the phyllosphere has received much less focus than the rhizosphere.

This project will focus on characterising the dynamic nature of the phyllosphere microbiome. The composition of the phyllosphere microbial community is regulated by the exudates from the plant which are linked to plant metabolism. Our preliminary data provides strong evidence for circadian regulation of the phyllosphere microbiome, consistent with changes in plant metabolism providing an ideal system for examination the interaction mechanisms between plant and microbe. The project will fully characterise these dynamics via a metabarcoding approach to analyse the impact of time of day on the community structure and composition. Microbial community analysis will be combined with transcriptomic (RNAseq) and metabolomic (LC-MS) measurements, adding a strong interdisciplinary element. Application of SynComs generated from microbes isolated at specific times of day will also allow investigation of the importance of this regulation within the microbiome for establishment and this will be coupled with examination of the effectiveness of known biopesticides on plant health and resilience to pathogenic fungi when applied at different times of day.

There is an urgent need to fill the knowledge gap relating to biopesticide establishment in order to allow biopesticides to become a real alternative to chemical treatments. This project will have real impact in helping to address issues of environmental pollution as well as emerging pesticide resistance.

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Leggatt, E., Griffiths, A., Budge, S., Stead, A.D., Gange, A.C., Devlin, P.F., (2023) Addition of Arbuscular Mycorrhizal Fungi Enhances Terpene Synthase Expression in Salvia rosmarinus Cultivars. Life. 13, 315
Vincent S., Ebertz A., Spanu P.D., Devlin, P.F., (2022) Salicylic acid-mediated disturbance increases bacterial diversity in the phyllosphere but is overcome by a dominant core community. Front Microbiol. 13:809940
Ganie, S., Bhat, J. A. & Devoto, A., 2 (2021) The influence of endophytes on rice fitness under environmental stresses. Plant Mol Biol. 109, 447–467
Gadhave K.R.*, Devlin P.F.*, Ebertz A., Ross A., Gange A.C. (2018) Soil Inoculation with Bacillus spp. Modifies Root Endophytic Bacterial Diversity, Evenness, and Community Composition in a Context-Specific Manner. Microb Ecol. 76:741-50

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