Biology subjects

Subrahmaniam, H. J.

Publications and source records attributed to Subrahmaniam, H. J..

3 recordsLinked to original sources

bioRxiv2026

A transparent window into the rhizosphere: a simplified workflow for spatially resolved soil metabolomics

Root exudates play a central role in nutrient cycling, microbial recruitment, and plant-plant interactions, yet most experimental approaches for analyzing exudate chemistry rely on sterile hydroponic systems that poorly represent soil conditions. We present a low-cost, open-source, 3D-printed rhizobox platform and associated workflow that enable non-destructive root imaging and targeted rhizosphere soil sampling for LC-MS based metabolomics under realistic soil conditions. The design integrates a transparent removable window for repeated root observations, a defined soil volume to support spatially explicit sampling, and a blank-informed data-processing pipeline to distinguish plant-derived metabolites from soil and construction material background. We validated the system using the model plants Arabidopsis thaliana (Col-0) and Phragmites australis. We demonstrate reliable plant growth and consistent root development across the imaging window. We also show robust detection of species-specific rhizosphere metabolite profiles, with minimal variation in the vertical or temporal dimensions relative to the strong species effects. We further illustrate the application of the workflow in a factorial experiment manipulating social context (solo vs. conspecific pairs) and short-term heat stress in A. thaliana, showing that the approach is sensitive to treatment-associated changes in metabolite richness, diversity, and chemical composition in soil. The complete protocol, from rhizobox fabrication and assembly to soil extraction, LC-MS acquisition, and data curation can be implemented within 4-6 weeks using standard laboratory equipment and openly available design files. By combining ecological realism with analytical control, this workflow provides a broadly applicable method for quantifying rhizosphere metabolite dynamics across species, treatments, and spatial sampling zones, facilitating experimental studies of below-ground chemical processes in plant ecology.

plant biology↗

bioRxiv2024

Targeting the untargeted: Uncovering the chemical complexity of root exudates

The chemical complexity of root exudates has garnered significant attention in recent years, yet critical gaps remain in understanding the full scope of root exudate chemical variation across the plant kingdom. To address this, we conducted a systematic review of 57 studies, comprising 124 experiments, aimed at evaluating current methodologies and findings in untargeted root exudate chemical analysis. Our review revealed that hydroponic (44%) and soil-hydroponic hybrid (32%) sampling approaches, primarily utilising water as the collection medium, were the most common experimental setups. Liquid chromatography-mass spectrometry (LC-MS) was the predominant analytical technique used in 54% of the studies, followed by gas chromatography-mass spectrometry (GC-MS) in 31%. The average number of metabolites identified per analysis was 960, though the number of annotated metabolites varied considerably. Shikimates, phenylpropanoids, and carbohydrates were the most frequently identified classes, with their relative abundances varying widely. Several methodological challenges were highlighted, including inconsistencies in sampling techniques, underrepresentation of non-crop plants, and incomplete chemical annotation. To address these limitations, we propose a framework emphasising the need for representative exudate sampling, the use of multiple analytical approaches, the development of advanced bioinformatics tools, and the integration of these findings to enhance our understanding of root exudates and their ecological functions.

ecology↗

bioRxiv2024

Natural variation in root exudate composition in the genetically structured Arabidopsis thaliana in the Iberian Peninsula

O_LIPlant root exudates are involved in nutrient acquisition, microbial partnerships, and inter- organism signaling. Yet, little is known about the genetic and environmental drivers of root exudate variation at large geographical scales, which may help understand evolutionary trajectories of plants in heterogeneous environments. C_LIO_LIWe quantified natural variation in chemical composition of Arabidopsis thaliana root exudates in 105 Iberian accessions. We identified up to 373 putative compounds using ultra-high performance liquid chromatography coupled with mass spectrometry. We estimated broad-sense heritability of compounds and conducted a genome-wide association (GWA) study. We associated variation in root exudates to variation in geographic, environmental, life history, and genetic attributes of Iberian accessions. C_LIO_LIOnly 25 of 373 compounds exhibited broad-sense heritability values significantly different from zero. GWA analysis identified polymorphisms associated to 12 root exudate compounds and 26 known genes involved in metabolism, defense, signaling, and nutrient transport. The genetic structure influenced root exudate composition involving terpenoids. We detected five terpenoids related to plant defense significantly varying in mean abundances in two genetic clusters. C_LIO_LIOur study provides first insights into the extent of root exudate natural variation at a regional scale depicting a diversified evolutionary trajectory among A. thaliana genetic clusters chiefly mediated by terpenoid composition. C_LI

plant biology↗