Abstract
BackgroundSoil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity.MethodsWe used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs.ResultsIn total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and β-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r = − 0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events.ConclusionsARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.
Highlights
Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms
We found that undecaprenyl pyrophosphate phosphatases (UppP) genes, which confer resistance to Bacitracin, were assigned to the three most abundant bacterial phyla in these communities, Bacteroidetes (9 antibiotic resistance gene (ARG)), Acidobacteria (7 ARGs) and Proteobacteria (3 ARGs), while a large proportion could not be assigned to a known taxonomic group (7 ARGs)
This is the first detailed metagenomic study of antibiotic resistance genes in remote, pristine soils that are naïve to anthropogenic antibiotic use
Summary
Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Antibiotic production and resistance have ancient origins (~ 2 Gyr: [1, 2]). The three major mechanisms of bacterial antibiotic resistance are broadly categorised as efflux pumps, resistance mutations and antibiotic inactivation strategies [6, 7]. Drug-specific efflux pumps have narrow ranges of antibiotic export mechanism and are specific to a particular antibiotic (e.g. in the removal of tetracycline [8]), whereas multidrug efflux pumps have broad specificity and confer resistance to multiple antibiotics. Common drug inactivation mechanisms in soil communities include β-lactamases, which hydrolyse β-lactam antibiotics such as penicillin [10, 11]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
