Microbial Degradation of Lignin Generates Iron-Binding Organic Ligands

Abstract The association of organic carbon (OC) with iron (Fe) minerals is a primary mechanism governing soil OC persistence, yet the molecular agents mediating Fe–OC binding remain poorly defined. In this study, we demonstrated that microbial degradation of lignin, one of the major contributors to soil OC, generates organic compounds with the potential to bind to Fe, with implications for mineral-associated carbon stabilization. Lignin samples were microbially degraded by Pseudomonas putida KT2440 for 30 days and subsequently reacted with FeCl3. Ultrahigh-performance liquid chromatography–high-resolution tandem mass spectrometry (UHPLC–HRMS/MS)-based analysis identified 494 distinct molecular features with MS/MS data, of which 21 were identified as lignin-derived Fe-binding ligands using Fe isotopologue-enabled metabolomics. Structural annotation of 15 identified ligands further elucidated the chemical nature of the lignin-derived compounds. Systematic meta-analysis of more than 20,000 public HRMS datasets revealed that related compounds occur in soil and aquatic organic matter across diverse ecosystems, ranging from grassland to Arctic tundra. Ion identity molecular networking (IIMN) further revealed additional putative ligands and structurally related transformation products. Altogether, our findings provide a molecular framework for investigating how microbially generated Fe-binding ligands may contribute to Fe–OC interactions and potentially, soil carbon stabilization under changing climate conditions.