Biodiversity and antibiotic resistance profiling of a Triassic halite deposit in Northern Ireland

Kilroot salt mine, a Triassic halite deposit located in County Antrim, Northern Ireland, is the only hypersaline environment in the island of Ireland. We profiled the microbiome of this unstudied environment using conventional isolation approaches (with the addition of some augmented techniques) and metagenomics. Based on 16S rRNA gene sequencing, 89 extremely halophilic archaea from six known genera, and 55 halophilic and halotolerant bacteria from 19 genera were isolated. The archaea were highly similar to what has been previously isolated from other ancient halite deposits, and as expected, numerous genera were identified from metagenomic analysis which were not among the isolates, indicating the limitations of culture-based approaches. We also observed very high levels of antimicrobial resistance (AMR) among a selection of isolates from this ancient environment based on minimum inhibitory concentration (MIC) assays. A growing body of evidence suggests AMR is not a modern phenomenon, but that its origins are ancient, greatly predating modern antibiotic use, and implies that the halophiles obtained may provide reservoirs of AMR genes. Despite this, annotation of whole genome sequences and the metagenome identified few genes which would explain the highly resistant phenotypes, which may suggest that novel, as yet unidentified resistance mechanisms may be utilised by these microorganisms. Studying antibiotic resistance in environments that have had little or no exposure to anthropogenic antibiotic use provides a critical measure of the natural diversity of AMR, which has significant implications in our understanding of its prevalence and evolution.