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<p>Cyanobacteria are key components of freshwater ecosystems and serve as ecological indicators due to their sensitivity to environmental changes. Accurate taxonomic classification of cyanobacteria remains challenging because of high morphological variability and hidden genetic diversity<b>.</b> In this study, we aimed to resolve the taxonomy of 11 cyanobacterial strains isolated from temple ponds in South India using a polyphasic approach integrating molecular and structural analyses. We combined 16S rRNA gene sequencing, in-silico restriction digestion, and RNA secondary structure analysis to infer phylogenetic relationships and confirm species identities. Phylogenetic analysis, incorporating sequences of reference type strains from GenBank, delineated clades with close affinity to <i>Chroococcus turgidus</i>, <i>C. minutus</i>, and <i>Synechococcus elongatus</i>, showing moderate-to-high bootstrap support, despite the limited resolution of ~ 540&#xa0;bp 16S rRNA fragments. Structural and restriction-based profiling revealed strain-specific polymorphisms consistent with reference/type sequences, enhancing molecular discrimination. To our knowledge, this is the first molecular-level characterization of cyanobacteria from culturally significant temple pond ecosystems using a comprehensive polyphasic framework<b>.</b> These findings underscore the value of molecular tools for precise freshwater cyanobacterial taxonomy and their application in environmental monitoring and aquatic biodiversity assessment.</p>

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Polyphasic taxonomic resolution of freshwater cyanobacteria from temple ponds using 16S rRNA sequencing, structural modeling, and restriction analysis

  • 期刊论文

  • 发表日期：

    2026年1月23日

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  • Nisha Banu Babulal,
  • Asraf Sithikka Rasheed,
  • Rajesh Kannan Velu,
  • Thajuddin Nooruddin

摘要

Cyanobacteria are key components of freshwater ecosystems and serve as ecological indicators due to their sensitivity to environmental changes. Accurate taxonomic classification of cyanobacteria remains challenging because of high morphological variability and hidden genetic diversity. In this study, we aimed to resolve the taxonomy of 11 cyanobacterial strains isolated from temple ponds in South India using a polyphasic approach integrating molecular and structural analyses. We combined 16S rRNA gene sequencing, in-silico restriction digestion, and RNA secondary structure analysis to infer phylogenetic relationships and confirm species identities. Phylogenetic analysis, incorporating sequences of reference type strains from GenBank, delineated clades with close affinity to Chroococcus turgidus, C. minutus, and Synechococcus elongatus, showing moderate-to-high bootstrap support, despite the limited resolution of ~ 540 bp 16S rRNA fragments. Structural and restriction-based profiling revealed strain-specific polymorphisms consistent with reference/type sequences, enhancing molecular discrimination. To our knowledge, this is the first molecular-level characterization of cyanobacteria from culturally significant temple pond ecosystems using a comprehensive polyphasic framework. These findings underscore the value of molecular tools for precise freshwater cyanobacterial taxonomy and their application in environmental monitoring and aquatic biodiversity assessment.