High-resolution 3D mapping of rhizosphere glycan patterning using molecular probes in a transparent soil system

Abstract

Rhizospheres are microecological zones at the interface of roots and soils. Interactions between bacteria and roots are critical for maintaining plant and soil health but are difficult to study because of constraints inherent in working with underground systems. We have developed an in-situ rhizosphere imaging system based on transparent soils and molecular probes that can be imaged using confocal microscopy. We observed spatial patterning of polysaccharides along roots and on cells deposited into the rhizosphere and also co-localised fluorescently tagged soil bacteria. These studies provide insight into the complex glycan landscape of rhizospheres and suggest a means by which root / rhizobacteria interactions can be non-disruptively studied.

Exploring the roles of microbes in facilitating plant adaptation to climate change

“…biomass over time via hyperspectral cameras) than field experiments. In other mesocosms, transparent soil systems have been combined with molecular probes and fluorescently labeled bacteria to map microbial colonization and glycan distribution across plant development [ 75 ]. These experiments could be adapted for use in EcoPODs, which would enable researchers to not only track specific molecules involved in plant–microbe interactions, but also precisely measure how the transport and assimilation of these molecules correlates with environmental conditions.…”

Genetic Circuit Design in Rhizobacteria

“…Imaging of rhizobacterial fluorescence typically requires disruptive preparation of root samples [ 202 ], which can potentially perturb colonization patterns of soil-grown plants. Although live fluorescent imaging can be accomplished for plants grown in optically transparent soil [ 203 , 204 ], differences in chemical and physical properties of these synthetic systems may alter rhizobacterial colonization and plant growth when compared to natural soils. To address these limitations and build genetic circuits that report on rhizosphere dynamics in situ , reporters that function within soil environments are needed.…”

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

“…For example, root exudates increase the ability of soils to retain water (Carminati et al, 2010) but also reduce surface tension (Naveed et al, 2019), which is an important characteristic for the rewetting of the soil (Demie et al, 2010; Chaichi et al, 2015). Root exudates contain organic acids that reduce the pH of the soil (Dakora and Phillips, 2002; Jones et al, 2021; Lin et al, 2022), contain enzymes that break down organic materials, contribute to the mineralisation of nutrients (Richardson et al, 2009), and facilitate the solubilisation and transport of mineral elements to the plants (Dakora and Phillips, 2002). Root exudates also contain diverse polysaccharides and compounds with antimicrobial properties such as phenols, peptides, enzymes, amino acids, nucleotides, hormones, organic acids, fatty acids (Baetz and Martinoia, 2014; Steinauer et al, 2016; Sasse et al, 2018; Galloway et al, 2020).…”

“…In other cases, the combination of porous membranes with conventional microfluidics allows sampling root exudates at different places of the root trough time (Patabadige et al, 2019). Microfabrication techniques can be employed to mimic the structure of soil (Aufrecht et al, 2022; Walton et al, 2022) or the mapping of simple chemical changes like pH within the rhizosphere (Rudolph-Mohr et al, 2017; Jones et al, 2021; Patko et al, 2023), but the detection of specific molecules remain challenging.…”

“…Microfabrication techniques can be employed to mimic the structure of soil (Aufrecht et al, 2022;Walton et al, 2022) or the mapping of simple chemical changes like pH within the rhizosphere (Rudolph-Mohr et al, 2017;Jones et al, 2021;Patko et al, 2023), but the detection of specific molecules remain challenging.…”