Rhizocarpon geographicum lichen discloses a highly diversified microbiota carrying antibiotic resistance and Persistent Organic Pollutants tolerance

As rock-inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow on poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants and on the other hand secrete antimicrobial compounds. In addition, lichen-associated bacteria were described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spill and we combined 9 culturing methods with 16S rRNA sequencing to capture the largest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POP). Our study is a starting point to explore the ecological features of the lichen microbiota.