Biology subjects

Patko, D.

Publications and source records attributed to Patko, D..

4 recordsLinked to original sources

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↗

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

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↗