Comprehensive multi-omics integration to unravel poplar molecular responses to a phenanthrene contamination gradient

Phytoremediation using trees has become popular due to its effectiveness and affordability, including for brownfield soils contaminated with polycyclic aromatic hydrocarbons (PAH). However, our understanding of how trees cope with exposure to PAHs is limited. In this study, we employed an innovative experimental design combining a contamination gradient of eight phenanthrene concentrations (0-2000 mg·kg⁻¹), a model PAH, with a comprehensive integrative multi-omics approach (transcriptomics, proteomics, and metabolomics) to study the physiological responses of poplar (Populus x canadensis). The objective was to identify molecular biomarkers from poplar roots and leaves. This pioneering setup generated large datasets: 27,561 transcripts, 6787 proteins, and 2799 metabolites for roots, and 26,079 transcripts, 8249 proteins, and 2239 metabolites for leaves. The datasets were integrated using the mixOmics package, highlighting a distinct response between the lowest and highest phenanthrene concentrations for roots and the combinaison of roots and leaves (tipping point at 400 mg.kg^-1), and between PHE-spiked and unspiked control for leaves. Different metabolic pathways were identified as plant biomarkers at low and high PHE concentrations. These biomarkers were specific for low and high toxicity, respectively. The most affected pathways were carbon fixation, oxidative phosphorylation, glycerolipid metabolism at low PHE concentrations, starch and sucrose metabolism, and aminoacyl-tRNA biosynthesis at high PHE concentrations. In total, 73 relevant biomarkers were identified from photosynthesis to flavonoid biosynthesis pathways. These results highlight the key molecular mechanisms triggered by poplar in response to PAH contamination and suggest molecular targets of interest for future ecotoxicity tests.