Abstract
Sambhar Salt Lake, situated in the state of Rajasthan, India is a unique temperate hypersaline ecosystem. Exploration of the salt lake microbiome will enable us to understand microbiome functioning in nutrient-deprived extreme conditions, as well as enrich our understanding of the environment-specific microbiome evolution. The current study has been designed to explore the Sambhar Salt Lake microbiome with a culture-independent multi-omics approach to define its metagenomic features and prevalent metabolic functionaries. The rRNA feature and protein feature-based phylogenetic reconstruction synchronously (R = 0.908) indicated the dominance of the archaea (Euryarchaeota) and bacteria (Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria). Metabolic reconstruction identified selective enrichment of the protein features associated with energy harvesting and stress tolerance (osmotic, oxidative, metal/metalloid, heat/cold, antibiotic, and desiccation). Metabolites identified with metabolome analysis confirmed physiological adaptation of the lake microbiome within a hypersaline and nutrient-deprived environment. Comparative metagenomics of the 212 metagenomes representing freshwater, alkaline, and saline ecosystem microbiome indicated the selective enrichment of the microbial groups and genetic features. The current study elucidates microbiome functioning within the nutrient-deprived harsh ecosystems. In summary, the current study harnessing the strength of multi-omics and comparative metagenomics indicates the environment-specific microbiome evolution.
Highlights
Sambhar Lake is the largest inland, hypersaline lake, situated at the semi-arid Aravalli schists of Rajasthan, India
Rarefaction curve analysis indicated that the curve reached toward attaining a plateau (Supplementary Figure 1). This analysis indicated the sufficiency of the current metagenomic data to provide a holistic overview of the salt lake microbiome
Sambhar Lake is the habitat of many microbes [Eubacteria (Sangeeta et al, 2016), Archaea (Upasani, 2008), and Alga (Arun and Singh, 2014)]
Summary
Sambhar Lake is the largest inland, hypersaline lake (salt content ∼30 g/L), situated at the semi-arid Aravalli schists of Rajasthan (longitude 75◦05 E, latitude 26◦58 N), India. Most of these studies were performed in isolation with the culture-dependent approach (Singh and Jha, 2016) They failed to explain microbial adaptation strategies (osmotolerance, oxidative stress tolerance, and metal/metalloid stress tolerance mechanisms), energy generation, and channelization processes in the salt lake microbiome. The evolution of such strategies by microbes is of utmost importance for their survival in such an extreme environment (Wood, 2015). The current study has been proposed to explore the Sambhar Salt Lake microbiome with a multi-omics approach to understand the microbiome functioning in such an extreme environment. All this information could be harnessed for various biotechnology applications
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