Abstract:
BACKGROUND : 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. 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 resistomemay comprise the ancestral gene diversity.
METHODS : We 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.
RESULTS : In 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.
CONCLUSIONS : ARGs 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.
Description:
Additional file 1: Table S1. Environmental factors of the 17 sampled
sites. Table S2. The selected ARGs chosen from noradab, including the
names, gene and ARG description, and ARG families. Figure S1. The
number of unique ARGs and number of unique AR hosts per site. Linear
model indicated in red and lowess in blue (Pearson’s correlation r = 0.89,
P = 1.62e-06). Figure S2. ARG host frequencies across sampled sites. The
number of different ARG hosts is indicated in green with the number of
unique ARG hosts displayed in red, axis on the left. The black line
represents the relative abundance, axis on the right. Figure S3. ARG
redundancy analysis. The only environmental factor to display a
significant impact was percentage N (P =0.024).
