Hedera helix phyllobiome structure and (pan)genomic survey of bacterial isolates with regard to phytoremediation of airborne pollutants

Abstract

Air pollution, containing fossil fuel-related volatile organic compounds (VOCs), constitutes a major problem in most urban areas. Worldwide, more people die from exposure to air pollution than from malaria and HIV infection together. Many years of research show that plant–microbe interactions can be exploited to significantly enhance phytoremediation of contaminated environments. Microorganisms living on plant leaves constitute promising candidates to detoxify harmful VOCs and promote plant growth. Hedera helix, an evergreen plant known for its hardiness and climbing ability, proves to be an excellent host species in the context of phytoremediation of air pollution. We employed 16S rRNA gene amplicon-based metagenomics to characterize the taxonomic structure of phyllospheric microbial communities associated with H. helix. Further, we investigated 33 bacterial isolates from 8 different genera using culture-dependent approaches and whole genome sequencing. Our results indicate that the relative composition of the H. helix phyllobiome is similar to that of the model plant Arabidopsis thaliana. The presence of pathways related to detoxification of fossil fuel-related VOCs could be confirmed by genome-level analyses of bacterial isolates showing a high in vitro capacity to metabolize selected VOCs and promote plant growth. We provide an integrated description of the H. helix phyllobiome, including the identification of interesting bacteria with significant potential as inoculants in phytoremediation approaches.