A dual-flow RootChip enables quantification of bi-directional calcium signaling in primary roots

Kinetics of zoospores approaching a root using a microfluidic device

Phytophthora species are plant pathogens that cause considerable damage to agrosystems and ecosystems, and have a major impact on the economy. Infection occurs when their biflagellate zoospores move and reach a root on which they aggregate. However, the communication between the plant and the zoospores and how this communication modifies the behavior of the swimming zoospores is not fully understood. Here we use a microfluidic device incorporating a growing Arabidopsis thaliana root to study the real-time kinetics of Phytophthora parasitica zoospores approaching the root and accumulating (or aggregating) around a specific area called the elongation zone. We show that zoospore kinetics are modified only below a distance of a few hundred microns from the aggregation center, with a decrease in velocity coupled to an increase in the number of turns taken. Furthermore, we show that the rate of aggregation is constant throughout a one-hour experiment, and is dependent on zoospore density. This rate is consistent with the fact that zoospores randomly encounter the region close to the elongation zone, a result compatible with an absence of attraction beyond a few hundred microns. Finally, we show that in our configuration, this absence of attraction can be explained by a residual flow responsible for limiting the diffusion of the signal supposedly emitted by the root to a boundary layer of a few hundred microns.

Observing root growth and signalling responses to stress gradients and pathogens using the bi-directional dual-flow RootChip

Plants respond to environmental stressors with adaptive changes in growth and development. Central to these responses is the role of calcium (Ca2+) as a key secondary messenger. Here, the bi-directional dual-flow RootChip (bi-dfRC) microfluidic platform was used to study defence signalling and root growth. By introducing salinity as sodium chloride (NaCl) treatment via a multiplexed media delivery system (MMDS), dynamic gradients were created, mimicking natural environmental fluctuations. Signal analysis in Arabidopsis thaliana plants showed that the Ca2+ burst indicated by the G-CaMP3 was concentration dependent. A Ca2+ burst initiated in response to salinity increase, specifically within the stele tissue, for 30 seconds. The signal then intensified in epidermal cells directly in contact with the stressor, spreading directionally towards the root tip, over 5 minutes. Inhibition of propidium iodide (PI) stain transport through the xylem was observed following salinity increase, contrasting with flow observed under control conditions. The interaction of Phytophthora capsici zoospores with A. thaliana roots was also studied. An immediate directional Ca2+ signal was observed during early pathogen recognition, while a gradual, non-directional increase was observed in Orp1_roGFP fluorescent H2O2 levels, over 30 min. By adjusting the dimensions of the bi-dfRC, plants with varying root architectures were subjected to growth analysis. Growth reduction was observed in A. thaliana and Nicotiana benthamiana roots when exposed to salinity induced by 100 mM NaCl, while Solanum lycopersicum exhibited growth increase over 90 minutes at the same NaCl concentration. Furthermore, novel insights into force sensing in roots were gained through the engineering of displaceable pillars into the bi-dfRC channel. These findings highlight the vital role of controlling fluid flow in microfluidic channels in advancing our understanding of root physiology under stress conditions.

Counter-on-chip for bacterial cell quantification, growth, and live-dead estimations

Quantifying bacterial cell numbers is crucial for experimental assessment and reproducibility, but the current technologies have limitations. The commonly used colony forming units (CFU) method causes a time delay in determining the actual numbers. Manual microscope counts are often error-prone for submicron bacteria. Automated systems are costly, require specialized knowledge, and are erroneous when counting smaller bacteria. In this study, we took a different approach by constructing three sequential generations (G1, G2, and G3) of counter-on-chip that accurately and timely count small particles and/or bacterial cells. We employed 2-photon polymerization (2PP) fabrication technology; and optimized the printing and molding process to produce high-quality, reproducible, accurate, and efficient counters. Our straightforward and refined methodology has shown itself to be highly effective in fabricating structures, allowing for the rapid construction of polydimethylsiloxane (PDMS)-based microfluidic devices. The G1 comprises three counting chambers with a depth of 20 µm, which showed accurate counting of 1 µm and 5 µm microbeads. G2 and G3 have eight counting chambers with depths of 20 µm and 5 µm, respectively, and can quickly and precisely count Escherichia coli cells. These systems are reusable, accurate, and easy to use (compared to CFU/ml). The G3 device can give (1) accurate bacterial counts, (2) serve as a growth chamber for bacteria, and (3) allow for live/dead bacterial cell estimates using staining kits or growth assay activities (live imaging, cell tracking, and counting). We made these devices out of necessity; we know no device on the market that encompasses all these features.

Bi-directional Dual-flow-RootChip for Physiological Analysis of Plant Primary Roots Under Asymmetric Perfusion of Stress Treatments

Due to technical limitations, research to date has mainly focused on the role of abiotic and biotic stress-signalling molecules in the aerial organs of plants, including the whole shoot, stem, and leaves. Novel experimental platforms including the dual-flow-RootChip (dfRC), PlantChip, and RootArray have since expanded this to plant-root cell analysis. Based on microfluidic platforms for flow stream shaping and force sensing on tip-growing organisms, the dfRC has further been expanded into a bi-directional dual-flow-RootChip (bi-dfRC), incorporating a second adjacent pair of inlets/outlet, enabling bi-directional asymmetric perfusion of treatments towards plant roots (shoot-to-root or root-to-shoot). This protocol outlines, in detail, the design and use of the bi-dfRC platform. Plant culture on chip is combined with guided root growth and controlled exposure of the primary root to solute changes. The impact of surface treatment on root growth and defence signals can be tracked in response to abiotic and biotic stress or the combinatory effect of both. In particular, this protocol highlights the ability of the platform to culture a variety of plants, such as Arabidopsis thaliana, Nicotiana benthamiana, and Solanum lycopersicum, on chip. It demonstrates that by simply altering the dimensions of the bi-dfRC, a broad application basis to study desired plant species with varying primary root sizes under microfluidics is achieved. Key features Expansion of the method developed by Stanley et al. (2018a) to study the directionality of defence signals responding to localised treatments. Description of a microfluidic platform allowing culture of plants with primary roots up to 40 mm length, 550 μm width, and 500 μm height. Treatment with polyvinylpyrrolidone (PVP) to permanently retain the hydrophilicity of partially hydrophobic bi-dfRC microchannels, enabling use with surface-sensitive plant lines. Description of novel tubing array setup equipped with rotatable valves for switching treatment reagent and orientation, while live-imaging on the bi-dfRC. Graphical overview Graphical overview of bi-dfRC fabrication, plantlet culture, and setup for root physiological analysis.(a) Schematic diagram depicting photolithography and replica molding, to produce a PDMS device. (b) Schematic diagram depicting seed culture off chip, followed by sub-culture of 4-day-old plantlets on chip. (c) Schematic diagram depicting microscopy and imaging setup, equipped with a media delivery system for asymmetric treatment introduction into the bi-dfRC microchannel root physiological analysis under varying conditions.