Eco-technological potential of salinity-driven functional specialization in Indian solar salterns revealed by integrated culturomics and whole-metagenome profiling

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Abstract
Solar salterns are environmentally stable yet biologically extreme ecosystems that serve as vital models for understanding and managing hypersaline environments, including industrial saline effluents. Despite their ecological and biotechnological significance, Indian solar salterns remain functionally underexplored. In this study, we integrated culture-dependent isolation with whole-metagenome sequencing to investigate microbial community assembly, functional specialization, and eco-technological potential across four geographically distinct Indian salterns. Physicochemical analyses revealed pronounced spatial variation in salinity, pH, and electrical conductivity, which together strongly structured microbial communities. Metagenomic sequencing generated between 4.84 and 8.68 Gb of raw data across individual site, yielding between 429,420 and 669,991 predicted genes in high-salinity locations. Taxonomic reconstruction demonstrated archaeal dominance at extreme salinity, particularly among Euryarchaeota, whereas comparatively moderate salinity sites supported more balanced bacterial–archaeal assemblages. Alpha diversity patterns indicated higher richness in Tamil Nadu and Rajasthan, while Gujarat exhibited reduced evenness consistent with environmental filtering. Culture-dependent approaches recovered 42 halophilic and polyextremophilic isolates, primarily affiliated with Halobacteriaceae and Bacillaceae, complementing the broad taxonomic detection of these lineages inferred from metagenomic data. Functional annotation revealed extensive enrichment of genes involved in ion transport, energy production, osmoprotectant biosynthesis, and DNA repair, reflecting an adaptive mechanism critical for survival in high-salinity industrial processes. Amino acid metabolism genes exceeded 25,000 hits in selected sites, and replication and repair genes reached 32,554 in Gujarat, indicating heightened stress-response activity. Secondary metabolite biosynthetic gene clusters, including pathways for novel antimicrobial peptides, terpene, ribosomally synthesized and post-translationally modified peptide-like, and type III polyketide synthase pathways, were widely distributed, offering new biological control mechanisms for environments impaired by stress. Antimicrobial resistance signatures were limited and unevenly distributed across sites. These findings demonstrate that salinity acts as a dominant ecological filter driving both taxonomic composition and functional specialization in Indian solar salterns. By linking environmental gradients to adaptive genomic traits, this study establishes a functional baseline for hypersaline ecosystems.
Funding Information
  • King Abdullah University of Science and Technology (RFS #5974)
  • University of Delhi (IoE/2024-25/12/FRP and IoE/2025-26/12/FRP)

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