Ancient lakes, modern tools: Oxford Nanopore MinION reveals prokaryotic diversity in Salda Lake, a Jezero analog

Lake Salda is a magnesium-rich, alkaline lake that serves as an important analogue for carbonate-bearing paleoenvironments on Mars, yet comprehensive species-level characterization of its microbial communities remains limited due to methodological constraints of short-read sequencing approaches. In this study, we applied optimized DNA extraction protocols combined with full-length 16S rRNA gene sequencing using Oxford Nanopore Technologies (ONT) to investigate prokaryotic diversity at species-level in sediment, microbial mat, and water samples from Lake Salda. The optimized extraction strategy successfully overcame challenges associated with magnesium carbonate matrices and enabled high-quality sequencing across all sample types. Our results revealed diverse and habitat-specific microbial communities dominated by taxa involved in elemental cycling, including members of Pseudomonadota, Bacillota, Cyanobacteriota, and Actinomycetota. Alpha and beta diversity analyses demonstrated differences between water and benthic (sediment and microbial mat) communities, while benthic habitats exhibited comparable diversity patterns. Compared to previous short-read Illumina-based studies, full-length ONT sequencing provided improved taxonomic resolution at lower taxonomic levels, reducing taxonomic uncertainty and enabling clearer discrimination of bacterial lineages. These findings enhance our understanding of microbial community structure in alkaline carbonate systems and provide new insights into microbially mediated carbonate mineral formation. Moreover, this study highlights the value of nanopore sequencing for investigating extreme environments on Earth and contributes to the interpretation of potential biosignatures in Martian paleolake settings such as Jezero Crater.