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The effect of climate-relevant temperature shifts on leaf microbiota colonization

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  • Full or part time
    Dr M Agler
    Dr D Vassao
    Prof J Gershenzon
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

About This PhD Project

Project Description

Background: Plant leaves are colonized by diverse microorganisms, including bacteria, fungi and other microorganisms. Usually, plant immunity limits microbial growth but given the right conditions and microbiota, aggressive growth may lead to disease (often referred to as the pathobiome). It is increasingly clear that microbial interactions can play important roles in this balance by altering colonization patterns1–3. For example, leaf symbionts can manipulate plant defenses, allowing growth of devastating non-host pathogens4. With climates warming significantly in the next decades, there is increasing interest in how temperature affects plant-pathogen interactions, with recent work showing strong influence on pathogen virulence5. However, we have little understanding of the effects of relevant temperatures in natural systems and how this will influence microbe-microbe interactions. We hypothesize that it will play roles in balance of the commensal leaf microbiota.

Project Description: Winters in Europe are expected to warm relatively quickly, possibly affecting winter annual plants like the model Arabidopsis thaliana before other species. We are studying 5 A. thaliana populations in Jena, Germany that have low intra- and high inter-population diversity, including diverse leaf aliphatic glucosinolate profiles. We are working to understand how bacteria in these local populations are adapted to their hosts and identifying taxa that drive aggressive colonization. Here, we will investigate how winter temperatures and hosts together affect these interactions, utilizing gnotobiotic systems with plants and bacterial strains isolated from the 5 populations. In collaboration with the Vassao and Gershenzon labs, we will investigate the role of aliphatic glucosinolate-derived metabolites in interactions between bacteria and other leaf-associated microorganisms. We aim to understand how temperature affects bacterial degradation of glucosinolate-derived metabolites, and in turn how it will influence the development of leaf pathobiomes.

Candidate profile:

An MSc (or equivalent) in natural sciences (Microbiology, Biochemistry, Genetics) or biotechnology
Excellent background in microbial ecology, microbiology, biochemistry and/or plant science
Experimental design and analytical methods
Knowledge of a programming language (R, perl, python) and Unix-based computational tools is advantageous but not required
Enthusiasm to adapt new techniques to both lab and field work


Agler, M. T. et al. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation. PLoS Biol 14, e1002352 (2016).
Karasov, T. L. et al. The relationship between microbial biomass and disease in the Arabidopsis thaliana phyllosphere. bioRxiv 828814 (2019) doi:10.1101/828814.
Potnis, N. et al. Xanthomonas perforans colonization influences Salmonella enterica in the tomato phyllosphere. Appl. Environ. Microbiol. 80, 3173–3180 (2014).
Prince, D. C. et al. Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana. BMC Biol. 15, 20 (2017).
Huot, B. et al. Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis. Nat. Commun. 8, 1808–1808 (2017).

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