Antibiotic resistance genes detected in lichens: insights from Cladonia stellaris

Antibiotics are natural compounds produced by microorganisms that have long existed in ecosystems. However, the widespread clinical and agricultural use of antibiotics has intensified selective pressures on bacteria, leading to the proliferation of antibiotic resistance genes (ARGs). The increasing prevalence of these genetic elements in clinical and environmental settings now poses a major global health threat. While ARGs are well documented in anthropogenically influenced environments, their distribution and origins in remote ecosystems, such as boreal forests, remain poorly understood. Here, we investigate the occurrence, diversity and potential origins of ARGs in the boreal lichen Cladonia stellaris.

We conducted the first targeted assessment of ARGs in lichens by analysing 42 C. stellaris samples from northern and southern lichen woodlands in eastern Canada. Using high-throughput quantitative PCR, we screened for 33 ARGs and three mobile genetic elements (MGEs), quantifying their relative abundance. Bacterial community composition was characterized via 16S rRNA gene sequencing. Statistical analyses evaluated geographical patterns, co-occurrence between ARGs and bacterial taxa, and the influence of latitude on ARG distribution.

Ten ARGs conferring resistance to four antibiotic classes (aminoglycosides, beta-lactams, quinolones and sulfonamides), along with one MGE, were detected. The ARGs blaCTX-M-1, qnrB and qepA were highly prevalent, with qepA often surpassing 16S rRNA gene abundance. Only qnrB showed significantly higher abundance in southern samples. Latitude significantly influenced ARG profiles, whereas bacterial community composition did not.

Our findings demonstrate that C. stellaris harbours diverse ARGs in remote boreal ecosystems with limited anthropogenic influence. Proposed explanations for ARG presence include long-distance dispersal via bioaerosols and endogenous development within lichen microbiomes, yet these remain speculative. Future work incorporating bacterial isolation, whole-genome sequencing, metatranscriptomics, air sampling and metabolomic profiling is necessary to unravel the ecology and evolution of ARGs in natural habitats.