EndOMiX

France, as well as many countries over the world, has large polluted industrial sites contaminated by polycyclic aromatic hydrocarbons (PAH). Among remediation strategies, phytoremediation is considered as one of the most promising approach. The PAH biodegradation enhancement in the plant rhizosphere has been largely studied in the past. However, the direct enhancement of the PAH loss through plant uptake and in planta degradation was very little explored. Although PAH parent compounds are apparently detected at low concentration, various transformation and conjugation process generating PAH metabolites and derivatives have been proposed but never explored in complex plant system. Research effort is required to better understand the dynamic and fate of PAH in soils under plant influence and recently developed metabolomics tool could help identifying PAH-derivatives in plants. Plants are naturally colonized with a wide variety of microorganisms. While the role of the rhizosphere microbiome in PAH dissipation have been largely investigated, our knowledge regarding the endosphere microbiome remains limited. Bacterial and fungal endophytes are well known for their plant growth promotion (PGP) properties, and some of them are capable of degrading PAH, but the microbial PAH-degradation pathways and the physiological interactions with the plant have never been explored in planta. Although, positive biotic interactions between bacteria and fungi are well known, studies rarely focus on both at the same time. Consequently, the joint response of the plant and its endophytes to the PAH pollution need to be studied benefiting of the development of OMICs tools giving information on the cellular response at the genomic, transcriptomic, proteomic and metabolomics levels. In this context, the EndOMiX project will characterize the interactions between bacterial and fungal root endophytes and plants in the context of PAH-contaminated soils to unravel the fundamental molecular processes set up and thus make the most of phytoremediation. The 1st objective is to assess the impact of a PAH contamination gradient on the response of the plant and its microbiome, using combination of enzymatic and molecular omics tools. Data will help understanding how the pollution rate structures the diversity of microbial communities and modulates the metabolic activity of the plant and endophytes. As the fate of PAH in plants is still poorly understood, our 2nd objective is to identify, track, and localize the PAH parent compound and derivatives, in the rhizospheric soil, plant tissues and associated microbial biomass using 13C-labelled PAH and combining metabolomic tools and DNA-stable isotope probing to identify the microorganisms benefiting from this carbon source. The results will make it possible to propose scenarios concerning the fate of PAHs in soil-plant systems. The 3rd objective is to isolate bacterial and fungal endophytes under PAH stress and determine their functional traits (i.e. PGP and degradation of PAH). This part will provide a large bank of bacterial and fungal strains usable in phytoremediation. The last objective is to decipher, in simplified and controlled conditions, the role of the 3 partners (bacterium, fungus and plant) and the underlying functional mechanisms to reveal who is doing what, how and where, through the tracking of 13C-PAH. We will then fully understand the metabolic functioning of our system and reconstruct the major steps of PAH transformation in plants.