Revealing Phylum-Specific Signatures in Intact Lipids: A Novel Biomarker Approach in Soil Biodiversity Research

Soil ecosystems harbor a vast diversity of organisms—ranging from microbes (bacteria, fungi, archaea) to meso- and macrofauna (e.g., protists, nematodes, mites, insects)—that collectively drive soil functions such as nutrient cycling, organic matter decomposition, and plant productivity. These processes depend on intricate interactions within the soil food web. Despite the acknowledged importance of meso- and macrofauna in maintaining soil health and mediating biogeochemical cycles, effective chemical proxies for these organisms remain constrained to specific groups, limiting their use in comprehensive soil biodiversity assessments.To address this gap, we applied a lipidomic approach to more than 80 single species spanning 26 phyla of soil biota, including Euryarchaeota (archaea), Proteobacteria and Actinobacteriota (bacteria), Ascomycota and Mucoromycota (fungi), Chlorophyta (algae), Arthropoda, Nematoda and Mollusca (meso- and macrofauna), and Tracheophyta (higher plants). Through high-resolution mass spectrometry and molecular networking, we identified more than 700 novel molecular lipid families within 12,000 lipid compounds, many lipid families being unique to specific phyla. These findings establish a robust framework for developing phylum-specific biomarkers and deepen our understanding of the soil food web. By focusing the current study on pure species, and by quantifying their content in the specific organisms, we enable biomass quantification across the whole soil food web and improve taxonomic resolution with phylum-specific chemical proxies, revealing distinct lipid signatures—such as ceramides in arthropods and cardiolipins in bacteria—that illustrate the metabolic specializations and ecological adaptations of these organisms.This integrative approach underscores lipidomics as a powerful tool for linking molecular-level data with taxonomy and allowing biomass quantitation across complete food webs. As global environmental pressures intensify, our findings pave the way for biomarker-driven strategies to monitor, conserve, and elucidate soil biodiversity, ultimately supporting the essential services that soil ecosystems provide.