Our research focusses on developing microfluidic or "organ-on-a-chip" technologies to probe the interplay between soil-dwelling organisms at the single cell level. This technique has a great potential to provide a unique view of biological events at the level of single organisms and cells by enabling precise environmental control, high-resolution dynamic imaging, the simulation of environmental complexity and affording quantitative information.

We are involved in projects positioned at the interface between bioengineering, microbiology and plant biology, including the study of bacterial-fungal interactions at the single cell level, the defence response of fungi upon predation by nematodes and the adaptation of plant roots towards environmental asymmetry.

Probing bacterial-fungal interactions at the single cell level

Scheme 1. (A) Bacterial-fungal interaction (BFI) device (scale bar, 5 mm), (B) 3D representation of BFI device, (C) bacterial-induced blebbing of hyphal cells (scale bar, 25 μm) and (D) fluorescence time-series illustrating the interaction of B. subtilis (green) with C. cinerea (red) (scale bar, 50 μm).

A diversity of interactions exist between fungi and other microorganisms, playing a central role in certain human infections, the biological control of plant diseases and the promotion of symbiotic activity. Yet, very little is known about fundamental fungal biology and the interplay between fungi and other microorganisms. Claire has developed novel microfluidic platforms for assessing and visualising the interaction between growing filamentous fungi and bacteria in collaboration with Prof. Markus Aebi (ETH Zürich). Implementation of the bacterial-fungal interaction (BFI) device revealed novel insights into the interaction of Bacillus subtilis with Coprinopsis cinerea, including bacteria-induced blebbing of hyphal cells and a dynamic polar attachment of B. subtilis cells to a specific subset of C. cinerea hyphae, suggesting a differential competence of fungal hyphae and thus differentiation of hyphae within a mycelium. These findings were published in Integrative Biology and various hypotheses with regard to the physical basis of this interaction are now being tested. As dynamic interactions between bacteria and fungi at the single cell level can now be monitored in real time, the location and quantification of antimicrobial production with both temporal and spatial resolution can be achieved, as well as the implementation of promoter-reporter fusion strains to study events such as quorum sensing of bacterial cells in bacterial-fungal interactions, for example. 

We are now using this tool to investigate so-called "fungal highways" (Prof. Pilar Junier, Université de Neuchâtel), fungal hyphae as a retention hot spot of phage transport (Dr Lukas Wick, Helmholz Centre for Environmental Research) and the defence response of fungi upon predation by nematodes (Dr Markus Künzler, ETH Zürich).

The dual-flow-RootChip

Scheme 2. Imaging and perfusion platform for Arabidopsis roots. (A) Pillar design for root guidance allowing symmetric or asymmetric perfusion of a root (B) 3D representation of device and (C) photograph of the device and a time-lapse series illustrating a growing A. thaliana root. Scale bar, 50 μm.

Plant roots are highly sensitive, growing in dynamic and heterogeneous environments and therefore responding to a variety of environmental stimuli. Yet, there exists a limited amount of information concerning the underlying molecular mechanisms that translate an environmental stimulus into a response and it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. As such, a new imaging and perfusion device for Arabidopsis roots was developed by Claire in collaboration with Dr Guido Grossmann (University of Heidelberg) – termed the dual-flow-RootChip – that provides guidance of the root tip and centring of the root within the chamber to allow symmetric or asymmetric perfusion of the root for investigations on root-environment interactions under simulated environmental heterogeneity. We revealed cell-autonomous adaption of root hair development under asymmetric phosphate perfusion, with unexpected repression in root hair growth on the side exposed to low phosphate and rapid tip-growth upregulation when phosphate levels increased. The asymmetric root environment further resulted in an asymmetric expression profile of RSL4, a key transcriptional regulator of root hair growth. Our findings, published in New Phytologist, demonstrate that roots can locally adapt to heterogeneous conditions in their environment at the physiological and transcriptional level. Being able to generate asymmetric micro-environments for roots will help further elucidate decision making processes in root-environment interactions.