Rhizophere microbiota harborng PCB degrading potential is associated to spontaneous plants in a polluted site

The SIN Caffaro is a large polluted site of national priority located in Italy, originated by the activities of a former chemical factory. The soil in the site presents a mixed contamination of halogenated persistent organic pollutants (PCBs, dioxins and furans), heavy metals and metalloids in variable concentrations, uneven distributed in the area and often exceeding the safety values. After the closure of the production plant, only the process of natural attenuation occurred in the SIN Caffaro soils. We aimed to explore the natural attenuation potential of the SIN Caffaro soil microbiota, focusing on the interactions between plants and associated bacteria. We studied the phylogenetic and functional diversity of the microbiome associated to three plant species naturally selected in the most contaminated area of the SIN Caffaro. The soil bacterial community was described by Illumina sequencing of the 16S rRNA gene, and a collection of rhizobacteria was established and tested for plant growth promotion (PGP) traits and bioremediation potential. The results showed that both the soil niche and the plant species shaped the composition of the resident microbiota, which was more strongly influenced by the plant species in the rhizosphere than in the soil surrounding roots. Hence, we can speculate that the “rhizosphere effect” was stronger than the high pollutant concentration in shaping the bacterial community structure. The microbiota selected in all the soil niches showed nevertheless a degrading potential, according to the PCR-based detection of the bphA gene, encoding for the biphenyl dioxygenase α subunit, in the soil metagenome. The cultivable microbiota in the rhizosphere of the different plant species showed highly similar phylogenetic and functional composition, in terms of PGP and bioremediation potential. A large part of the strains harbored the bphA gene and displayed catechol 2,3-dioxygenase and ACC deaminase activities, the latter considered a PGP trait contributing to plant tolerance to environmental stress. Overall, this work highlighted that spontaneous plant species differentially affect the rhizosphere bacterial community composition and harbor the intrinsic potential to sustain natural attenuation processes, further exploitable for rhizoremediation intervention at the SIN Caffaro.