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PhD position "The biophysics of microbial communities on (and in) leaves"

100%, Zurich, temporary

The Environmental Microfluidics Group of Prof. Roman Stocker in the Institute of Environmental Engineering is seeking a dynamic and motivated doctoral student for a project on the biophysics of microbial communities on (and in) leaves. The position is funded by a recently awarded Swiss National Centre of Competence in Research (NCCR) grant on Microbiomes and will be based in the laboratory of Prof. Roman Stocker (ETH).

Project background

Leaves represent environments with extremely interesting ‘biophysical characteristics’ for the development of microbial communities. First, leaves are highly structured, with topography that includes venations and stomata, providing both potential niches for different bacterial communities and structures that shape the movement of water and the hydrodynamic forces on bacteria. Second, leaves experience unique wetting conditions, with thin films of water often governed by surface tension, evaporation and rain, causing leaching of nutrients via the cuticle, subjecting microbial communities to harsh and often transient conditions, likely eliciting specific adaptations of leaf microbiomes. Third, leaves provide an environment between the ‘outside’ and the ‘inside’ of the plant, with stomata representing the interface, where chemicals abound, defense systems are at play, and different microbial communities interact.

Job description

The aim of this project will be to be able to ‘see’ these dynamics. By combining the extensive knowledge that the group of Prof. Julia Vorholt has accrued on leaf communities – including among others a set of 224 reference strains that have partially shown to be genetically manipulatable – with Prof/ Stocker’s group’s skills in microscopy, microfluidics and image analysis, the student will be able to understand – by directly visualizing them – the processes that occur on the surface of leaves. These include in particular the spatial distribution of bacteria, their movement, the effect of flow on them, the interaction among diverse species, the role of chemical signals from the plant on these processes, and the exchange between outside and inside. The student will pursue three models. Ideally, he/she will be able to directly visualize most of these processes on actual leaves. This is very challenging, because microscopy on the leaves has not been attempted before except for snapshots in epifluorescence to obtain static pictures of microbial distribution. We aim, instead, for a fully dynamic characterization of processes of the relevant timescales, based on our expertise with these approaches in other environments (e.g. marine particles). In a second approximation, and in particular if the first approach is not successful, the student will fabricate microfluidic imprints (e.g., out of PDMS) of actual leaves: this will exclude certain processes from being faithfully modeled (e.g. plant defense systems), but will allow others to be accurately quantified (e.g., fluid flow and cell migration). Finally, simple microfluidic reconstructions of fundamental features of the plant surface (e.g. microchannels with similar topographies to the leave’s venation) can be used for longer-term, high-accuracy experiments, for example on the interaction between different microbial species.

Your profile

The successful candidate will have a strong quantitative background, and a focus on experimental work. He/she will have the unique opportunity to learn, develop and apply a range of cutting-edge experimental techniques, including a suite of advanced microscopy techniques, microfluidic technology, and state-of-the-art image analysis. The student will be advised primarily by Prof. Stocker, though in close collaboration with Prof. Julia Vorholt. The student will also benefit from interacting with a PhD student in Prof. Vorholt's lab who is working on tagging leaf strains and will identify bottlenecks and dynamics upon leaf colonization via qPCR/BarSeq. The student will have the opportunity to work in a cutting-edge, fast-paced research environment, to interact with researchers from many different disciplines, to learn about fundamental biophysical and ecological processes in microorganisms and to interact with world-class collaborators.

ETH Zurich

ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find our university to be a place that promotes independent thinking and an environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we work together to develop solutions for the global challenges of today and tomorrow.
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We look forward to receiving your online application including a CV, full transcripts from undergraduate studies (both Batchelor and Masters), a brief (1-2 page) statement of research interests, and at least 2 (preferably 3) letters of reference. Review of applications will begin on January 4, 2021, with the position to start as early as March 1, 2021, or as soon as filled. Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered.

For questions regarding the position, please contact Dr. Francesco Carrara by email at (no applications).

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