Metagenome sequencing to unveil microbial community composition and prevalence of antibiotic and metal resistance genes in hypersaline and hyperalkaline Lonar Lake, India

[Display omitted] •Proteobacteria, Firmicutes and Bacteroidetes were abundant bacterial phyla.•Euryarchaeota was the abundant archaeal phyla.•Multidrug resistance and Beta-lactam genes were most abundant ARGs in the lake.•The lake resistome demonstrated fluoroquinolone and acriflavine resistance genes.•Arsenic, cobalt, cadmium, copper, and zinc resistance genes were abundant MRGs. Lonar Lake (India) is a hyperalkaline and hypersaline soda lake encompassing unique microbial composition and functions. This ecosystem has not been explored for taxonomic diversity and functional aspects (with emphasis on antibiotic and metal resistance genes) using whole metagenome sequencing for multiple years. Bacterial diversity analysis during year 2013, 2016, and 2018 depicted differences in the dominance of Proteobacteria, Firmicutes and Bacteroidetes. For archaeal diversity, a similar pattern persisted with higher abundance of Euryarchaeota. Functional metagenome analyses, indicated presence of antibiotic resistance gene (ARG) and metal resistance gene (MRG) profiles in the lake. A wider continuum of resistance genes with dominant ARG types as multidrug resistance efflux pumps and beta-lactams were also observed. The lake resistome demonstrated fluoroquinolone and acriflavine resistance genes indicating sewage water contamination in the lake. The MRGs linked with resistance to toxic metals (arsenic, cobalt, cadmium, copper, and zinc) and cation efflux protein CusA and cobalt-zinc-cadmium resistance protein revealed metal contamination. This study could be a baseline for understanding prevalence of antibiotic and metal resistance mechanisms resulting from various anthropogenic activities nearby lake, and find integrated approaches for conservation of the precious Lonar Lake ecosystem.