Biology subjects

Dupuy, L. X.

Publications and source records attributed to Dupuy, L. X..

14 recordsLinked to original sources

bioRxiv2026

Root responses to mechanical heterogeneity are shaped by pore geometry and root-soil biomechanics

Mechanical limitations to root growth occur when pressure exerted by turgor within root cells is counteracted by excessive resistance of the surrounding soil as well as by that of the cell walls. In a natural soil, however, heterogeneity allows roots to find paths of least resistance, though the governing principles behind this process have yet to be identified. Here, we combined artificial substrates, high-throughput live imaging, advanced image analysis, and mechanical modelling to uncover the principles governing the ability of a root to penetrate or deflect from zones of high mechanical impedance within a heterogeneous substrate. Our findings show that root responses to substrate heterogeneity can be accurately predicted from the pore-matrix geometry when both the mechanical properties of the substrate and those of the roots are known. Consequently, a crucial step toward understanding the physical limitations to root growth may lie in a detailed characterisation of soil mechanical properties.

plant biology↗

bioRxiv2026

Motile bacteria collectively transport soil water during host colonisation

Nutrient availability in soil is temporally and spatially heterogeneous, and, as a result, microbial migration is critical for many species. The nature of microbial movement in soil, however, is unknown due to a lack of observations and experimental data. We developed live-imaging and image-analysis techniques to track the movement of single cells through soil to elucidate how Bacillus subtilis utilises pore space during the early root colonisation. The study reveals that the bacterium can modify fluid pathways to create streams, even at low bulk cell density. The phenomenon was influenced by pore structure, distance from the root and the viscosity of the soil solution. By generating macroscopic fluid motion, bacteria may also be able to travel faster and farther than individually, while limiting energy expenditure.

microbiology↗

bioRxiv2026

How motile bacteria move water in soil

Although rhizosphere microbiomes are known to enhance plants resistance to water stress, it is believed that only fungi actively contribute to the transport and uptake of water. We investigated the biomechanical impact of bacterial motility on water transport in soil by combining surface tension measurements and water infiltration experiments in soil microcosms. We observed that flagellar-based motility in the of the rhizobacteria Bacillus subtilis cells reduces the apparent surface tension of fluids by up to 15%. The effect reported depends on cell density and swimming speed, confirming its biomechanical origin, and was able to accelerate water infiltration and rewetting of soil. We conclude that Bacillus subtilis facilitates soil water transport through the deformation of air water interfaces in pores. SignificanceWater and light limitations to photosynthesis rarely occur simultaneously enabling plants in arid environments to allocate a greater proportion of assimilated carbon to belowground growth, particularly to rhizodeposition. Using microbial activity to convert chemical energy into mechanical work within soil pores offers a major opportunity for improving water use efficiency in agriculture, especially as farming shifts from polluting, energy-intensive mineral fertilisers toward resilient biological fertilisation alternatives.

biophysics↗

bioRxiv2026

Growth under constraints: root tip development controls trade-offs between speed and mechanical efficiency

Relationships between root tip development--particularly tip shape--are thought to play a key role in enabling plants to overcome soil mechanical resistance. However, correlations between root tip morphology and the ability to penetrate compact or hard soils have remained inconsistent. This study applies a new quantitative framework to growth kinematics data from six plant species, analysing the trade-offs between frictional energy loss, growth stability, and reduced root elongation rates. A shorter root elongation zone can reduce the fraction of the mechanical energy lost to friction, but this is done at the expense of the elongation rate. A sharper tip or increased radius can help roots maintain the elongation rate at no energetic cost, but these strategies come with the cost of growth instability (tortuous roots) and decrease in specific root length respectively. During establishment, root strategies may therefore occupy a 2-dimensional trait space in which the mechanical efficiency of growth is balanced against the explorative-exploitative trade-off. HighlightsGrowth and form of root tips explain how plants overcome mechanical resistance from the soil Trade-offs link the energy lost by friction, growth stability and elongation rate of roots Larger roots allow faster growth independently of these trade-offs New framework formalises plants strategies to acquire soil resources List of symbols O_TBL View this table: org.highwire.dtl.DTLVardef@2df502org.highwire.dtl.DTLVardef@130848eorg.highwire.dtl.DTLVardef@4ec7deorg.highwire.dtl.DTLVardef@23e5eeorg.highwire.dtl.DTLVardef@ccaae7_HPS_FORMAT_FIGEXP M_TBL C_TBL

plant biology↗

bioRxiv2025

Modelling the influence of rhizodeposits on root water uptake

The chemical compounds produced by plant roots, referred to generally as rhizodeposits, affect several soil hydraulic properties. For example, the surface tension of soil water, and the contact angle between menisci and the pore surface. What remains less clear is how these effects manifest when considering soil water infiltration and retention, and the consequent impact on the availability of water for uptake by plant roots. By modifying the Richards equation, a novel model for soil water transport was developed which incorporates the influences of rhizodeposits. The finite-element method was used for simulations of model equations and calibration against experimental data was achieved through Bayesian optimisation. Numerical simulations from the calibrated model were used to investigate the effects of rhizodeposits on root water uptake under various precipitation regimes. It was found that the impact of rhizodeposits on the availability of water to the roots can be either positive or negative depending on precipitation regime and root system maturity. This, therefore, suggests that rhizodeposit characteristics require careful consideration when developing crops for improved water use efficiency and stress-resilience.

systems biology↗

bioRxiv2025

Root exudation facilitate water infiltration and rewetting of dry soil

The way plant roots facilitate water infiltration in soil may be just as important as the efficiency with which the root system in turn extracts it from the soil. Here we studied the mechanisms through which the root system facilitates water infiltration through a dry soil layer. Dye tracing experiments were conducted in model soil microcosms to characterise how root growth and exudation affects the permeability of dry layers of the model soil. Results showed that dissolved root exudates may be the primary facilitator of water infiltration, which may be linked to water surface tension. We conclude that in dry soil, root architecture and root exudation may combine to facilitate the infiltration of water and decrease the water lost by evaporation. These findings could enhance our understanding of the traits that provide drought resistance in crops.

plant biology↗

bioRxiv2024

MICROCOSM FABRICATION PLATFORM FOR LIVE MICROSCOPY OF PLANT-SOIL SYSTEMS

Biological processes in soil pores are critical to crop nutrition and productivity, but live observations of these processes at that scale have been difficult to accomplish. To address this challenge, we have developed new techniques for the fabrication of microcosms dedicated to live imaging of the rhizosphere which incorporate the ability to control water content in transparent soil. Chambers were assembled using poly(dimethyl siloxane) (PDMS) parts fabricated by injection moulding and subsequently joined to glass slides. The control of liquid fluxes in the microcosm was achieved by syringes passing through the PDMS parts or through custom made PDMS sponges. We then tested various low refractive index materials for the fabrication of transparent soils and carried out live microscopy using Fluorescence Light Sheet microscopy. The proposed fabrication techniques are modular and enabled the construction of a wide range of experimental systems, including split chamber systems for the control of water content in soil, heterogeneous distribution of water content, monitoring of dye tracers, and live observation of plant roots. Using the techniques, we show how plant roots increase water infiltration through increased permeability of dry soil layers. This study therefore establishes that material property control and microfabrication in model rhizosphere systems can greatly enhance our understanding of plant-soil interactions.

bioengineering↗

bioRxiv2023

Spatial and temporal detection of root exudates with a paper-based microfluidic device

Root exudates control critical processes in the rhizosphere, retaining water, selecting for beneficial microorganisms or solubilising nutrients prior to uptake by the plant. Analysing root exudation patterns however is challenging because existing methods are often destructive and unable to resolve spatial and temporal variations in the production of root exudates. Here, we present a paper-based microfluidic device with integrated colorimetric sensors for the continuous extraction of root exudates along plant roots. The microfluidic device used standard filter paper wax printer to create channels for water to carry the exudates towards the sensors. TiO2 nanotubes/alginate hydrogel-based sensors were used to analyse the glucose content of the root exudates of living plants. The study shows that the paper microfluidic substrate successfully extracts the released glucose from the root, and transfers it to the hydrogel-based sensor to be calorimetrically detected from independent sections of the root at different times, up to 7 days. The method was tested on two different wheat varieties Triticum aestivum (rgt Tocayo and Filon varieties), where significant differences in exudation patterns were recorded. The researchdemonstrates the feasibility of low cost technological solution for high precision screening and diagnostic of the biochemical composition of root exudates.

plant biology↗

bioRxiv2023

Construction and Characterisation of a Structured, Tuneable, and Transparent 3D Culture Platform for Soil Bacteria

2.We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms, Bacillus subtilis and Streptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare. 3. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/546105v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1123425org.highwire.dtl.DTLVardef@1d6cc3org.highwire.dtl.DTLVardef@1cf950aorg.highwire.dtl.DTLVardef@141dc0b_HPS_FORMAT_FIGEXP M_FIG C_FIG A step-by-step method for creating a tailored 3D culture medium for study of soil microbes. The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamics in situ by, for example, optical microscopy.

microbiology↗

bioRxiv2022

Can root systems redistribute soil water to mitigate the effects of drought?

Plants adapt both morphologically and physiologically in response to drought. This work considers another potential mechanism of plant drought resistance. Namely, the capacity of root systems to modify the hydraulic properties of surrounding soil, and extend the post-precipitation lifetime of water in the rooted zone. In studies of plant drought resistance, the effect of root-oriented preferential soil water transport is seldom considered, despite experimental evidence that it occurs. We developed a model for water transport through soil that incorporates preferential flow induced by a root system. Bayesian optimisation was employed to calibrate the model against experimental data, and the finite element method was used to obtain model simulations for the influence of different root architectures on post-precipitation water lifetime. When increasing preferential flow strength, simulations indicated a trade-off between evaporation and deep percolation losses. It was also observed that the soil surrounding root systems with a reduced gravitropic response, retained the most water following precipitation. This work provides new insight into the role of root system traits in plant drought resistance, and identifies potential crop phenotypes for improved water use efficiency.

systems biology↗

bioRxiv2021

In situ control of root-bacteria interactions using optical trapping in transparent soil

Bacterial attachment on root surfaces is an important step preceding the colonisation or internalisation and subsequent infection of plants by pathogens. Unfortunately, bacterial attachment is not well understood because the phenomenon is difficult to observe. Here we assessed whether this limitation could be overcome using optical trapping approaches. We have developed a system based on counter-propagating beams and studied its ability to guide Pectobacterium atrosepticum (Pba) cells to different root cell types within the interstices of transparent soils. Bacterial cells were successfully trapped and guided to root hair cells, epidermis cells, border cells and tissues damaged by laser ablation. Finally, we used the system to quantify the bacterial cell detachment rate of Pba cells on root surfaces following reversible attachment. Optical trapping techniques could greatly enhance our ability to deterministically characterise mechanisms linked to attachment and formation of biofilms in the rhizosphere.

microbiology↗

bioRxiv2021

Smart soils to observe hidden rhizosphere processes

Agriculture must reduce green-house gas emission and pollution, produce safer and healthier food, closer to home, reducing waste whilst delivering more diverse diets to a growing world population. Soils could enable this transformation, but unfortunately, they have a hugely complex and opaque structure and studies of its myriad of mechanisms are difficult. Here, the fabrication of smart soils for the screening of below-ground bio-processes is demonstrated. Particles were generated from fluoropolymer waste with functionalisation converting them into sensors able to report on key chemical dynamics. Tailored functionalization was obtained by radical terpolymerisation to improve growth conditions and sensing capabilities. The study demonstrates the potential for the development of accelerated genetic or agrochemical screens and could pave the way for improved models for rhizosphere dynamics.

plant biology↗

bioRxiv2021

Model predicts the impact of root system architecture on soil water infiltration.

There is strong experimental evidence that root systems substantially change the saturated hydraulic conductivity of soil. However, the mechanisms by which roots affect soil hydraulic properties remain largely unknown. In this work, we made the hypothesis that preferential soil moisture transport occurs along the axes of roots, and that this is what changes a soils saturated hydraulic conductivity. We modified Richards equation to incorporate the preferential flow of soil moisture along the axes of roots. Using the finite element method and Bayesian optimisation, we developed a pipeline to calibrate our model with respect to a given root system. When applied to simulated root systems, the pipeline successfully predicted the pore-water pressure profiles corresponding to saturated hydraulic conductivity values, observed by Leung et al. (2018), for soils vegetated with willow and grass. Prediction accuracy improved for root systems with more realistic architectures, therefore suggesting that changes in saturated hydraulic conductivity are a result of roots enabling preferential soil moisture transport along their axes. The model proposed in this work improves our ability to predict moisture transport through vegetated soil and could help optimise irrigation, forecast flood events and plan landslide prevention strategies.

systems biology↗

bioRxiv2021

Whole plant-environment microscopy reveals how Bacillus subtilis utilises the soil pore space to colonise plant roots

Our understanding of plant-microbe interactions in soil is limited by the difficulty of observing processes at the microscopic scale throughout plants large volume of influence. Here, we present the development of 3D live microscopy for resolving plant-microbe interactions across the environment of an entire seedling growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A tailor made dual-illumination light-sheet system acquired scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3 in size with as good as 5 m resolution at a rate of up to one scan every 30 minutes. The system tracked the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed towards the root cap, the point "first contact", before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand plant-microbe interactions.

plant biology↗