October 8, 2024
Journal Article

Improved characterization of soil organic matter by integrating FT-ICR MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions

Abstract

Understanding of how soil organic matter (SOM) chemistry is altered in a changing climate has advanced considerably, however most SOM components remain unidentified, impeding the ability to characterize a major fraction of organic matter and predict what type of molecules, and from which sources, will persist in soil. We present a novel approach to better characterize SOM extracts, by integrating information from three types of analyses, and we deploy this method to characterize decaying root-detritus soil microcosms subjected to either drought or normal conditions. To observe broad differences in composition we employed direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FT-ICR MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectra cosine similarity scores to relate unknowns and library matches through molecular networks. This integrated approach allowed us to corroborate DI-FT-ICR MS molecular formulas using library matches, which included fungal metabolites and related polyphenolic compounds. We also inferred structures of unknowns from molecular networks, and improved LC-MS/MS annotation rates from ~5 to 35% by considering DI-FT-ICR MS molecular formula assignments. Under drought conditions, we found greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas, and lower average nominal oxidation state of carbon, suggesting reduced decomposition of SOM and/or microbes under stress. Our integrated approach provides a framework for enhanced annotation of SOM components that is more comprehensive than performing individual data analyses in parallel.

Published: October 8, 2024

Citation

DiDonato N., A. Rivas Ubach, W.R. Kew, N. Sokol, C.S. Clendinen, J.E. Kyle, and C. Martinez, et al. 2024. Improved characterization of soil organic matter by integrating FT-ICR MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions. Analytical Chemistry 96, no. 29:11699-11706. PNNL-SA-199596. doi:10.1021/acs.analchem.4c00184