Preliminary Study into the Application of Metabolomics in Soil Discrimination

Soil metabolomics involves the comprehensive analysis of small-molecule metabolites (≤1.5 kDa) in soil and how these are influenced by environmental processes, offering a promising approach for soil characterization. Although soil metabolomics has been applied in studying various soil processes, it remains a relatively underexplored field within the broader metabolomics discipline, underscoring the need for further research. This study aims to characterize the soil metabolome across contrasting soil sites to evaluate the discriminative capacity of metabolomics and its potential as a soil quality indicator. Metabolites were extracted from soil samples using methanol and dichloromethane, and subsequently analyzed using an Agilent 1260 Infinity II liquid chromatography–mass spectrometry (LC-MS) platform. A total of 307 metabolites were positively identified, including steroids, saponins, amino acids, organothiophosphorus compounds, and fatty acids. Multivariate statistical analyses, including Partial Least Squares Discriminant Analysis (PLS-DA), loading plots, Variable Importance in Projection (VIP) scores, Significance Analysis of Microarrays (SAM), and heat maps successfully discriminated soil samples from four distinct sites. Prolyl-hydroxyproline (ID 1817) emerged as the most influential discriminant metabolite, with a top VIP score of approximately 2.62, and is proposed as a potential biomarker for soil differentiation. These findings highlight the utility of soil metabolomics as a powerful tool for assessing soil quality and environmental variation.