16S rDNA analysis of bacterial communities associated with the hyper accumulator Arabidopsis halleri grown on a Zn and Cd polluted soil

Having a glimpse of the relationships between the zinc and cadmium hyper accumulator Arabidopsis halleri and its rhizospheric bacteria may represent an interesting step towards the implementation of a rhizoremediation strategy based on this plant. Until now, these relationships remained unraveled. This work aimed to give some insights into the composition of the bacterial communities surrounding A. halleri when it grows on a soil harboring elevated amounts of zinc and cadmium, as well as into the influence that plant roots may exert on them. Industrial highly polluted soils containing different amounts of zinc and cadmium and surrounding A. halleri plants were sampled and their bacterial contents were harvested at various distances from A. halleri root system. Genetic diversity was assessed through DNA extraction, PCR amplification, 16S rDNA libraries construction, RFLP analysis and partial sequencing. Nine mini-libraries of hundred clones each were established and analyzed. Up to 481 independent clones were sequenced and identified at genus level. Twelve genera among 48 were found particularly well represented in the different sub-fractions analyzed. At class level, ten different classes were identified. Alpha-proteobacteria, Gamma-proteobacteria, Flavobacteria and Sphingobacteria were the main contributors to flora diversity. In the less polluted soil, roots proximity seems to affect negatively Alpha-proteobacteria and Flavobacteria and positively Gamma-proteobacteria. A rhizospheric selection limited to some specific genera was also observed when pollution raised. •Monitoring of the impact of metallic pollution on bacterial communities associated to Arabidopsis halleri roots.•Specific vector–enzyme association improves rDNA mini-libraries analysis by RFLP.•Sequencing data confirms diversity data and clone discrimination.•Major bacterial class and genera represented are identified.•Visible influence of pollution degree and roots vicinity on bacterial populations.