Region-specific patterns of soil bacterial communities' adaptation to hexachlorocyclohexane contamination

Hexachlorocyclohexane (HCH) is a persistent organochlorine pollutant whose attenuation at former production sites relies on microbial degradation. The canonical lin pathway, predominantly associated with Sphingomonadaceae, is considered the main aerobic route for HCH transformation, yet its environmental distribution remains limited. We investigated soil bacterial communities and enrichment-derived bacterial consortia from three historically contaminated sites in Germany, Italy, and Spain using HCH depletion assays, 16S rDNA metabarcoding, and functional inference, based on a curated BIOSYSMOdb dataset developed by the BIOSYSMO project. Based on the ASL-level functional inference, the Spanish samples uniquely encoded a complete lin pathway restricted to Sphingobium sp., whereas German and Italian communities harboured respectively partial (LinB-C) or single-step (LinB) modules. Despite these differences, efficient depletion of all HCH isomers occurred across all enrichment cultures. Core-microbiome and differential-abundance analyses identified several non-Sphingomonadaceae taxa, including Stenotrophomonas, Pseudomonas, Achromobacter, Pseudolabrys, and Cupriavidus, which consistently increased during selective enrichment and likely contribute to HCH depletion. Overall, our findings suggest that effective HCH degradation is not restricted to the canonical lin pathway nor to Sphingomonadaceae but it might be mediated also by diverse soil bacteria via alternative lin-independent mechanisms. These results broaden the known ecological and functional landscape of HCH biodegradation and support the exploration of non-Sphingomonadaceae taxa for bioremediation of legacy lindane-contaminated sites.