Comparative genomics of Cladosporium reveals limited evidence of selective pressure in soils historically contaminated with hexachlorocyclohexane and polychlorinated biphenyls

Hexachlorocyclohexane (HCH) and polychlorobiphenyls (PCB) are widespread halogenated organic contaminants (HOC). Although mycoremediation mainly focused on ligninolytic Basidiomycetes, polluted soils are often dominated by Ascomycetes, whose genomic basis for HOC transformation remain poorly understood. This study investigated the genomic basis of HOC degradation in six Cladosporium strains isolated from two historically polluted sites in France (PCB) and Italy (HCH). All strains significantly depleted PCB within 5 days (50–78%). HCH depletion after 15 days was strain-dependent: five strains depleted all isomers (10–50%), while one showed negligible activity. Depletion patterns did not align with the pollutant present at the isolation site, and pollutant depletion inversely correlated with glucose consumption. High-quality genomic assemblies (BUSCO '95%) were obtained via PacBio HiFi sequencing. These were annotated and compared with 12 publicly available Cladosporium genomes from non-polluted matrices. Comparative analyses based on Gene Ontology and CAZyme profiles revealed limited functional separation between strains from polluted and non-polluted sources. Variations in candidate HOC-related functions and amino-acid sequences were strongly associated with phylogenetic distance rather than isolation source, providing limited evidence of pollution-driven selective pressure. A strong, uniform pollution-driven genomic signature was not observed. This outcome is itself informative, indicating that the genetic potential for HOC transformation might be broadly distributed across the genus Cladosporium and shaped by phylogeny rather than being restricted to isolates from polluted sites. Obtained results hold applicability and environmental relevance, as they might widen the pool of strains that can be screened and optimized, supporting flexible bioprospecting strategies beyond heavily polluted hotspots.