Morphological and genetic identifications of Spirulina based on 16S rRNA gene

Spirulina is a microalga with spiral or linear trichome shapes that has potential in industrial and food sectors due to its rich nutritional content. Spirulina can live in various aquatic habitats with different environmental conditions. Differences in cultivation environments can affect the morphological characteristics of Arthrospira due to phenotypic plasticity, making morphology-based identification prone to errors. Therefore, molecular identification using the 16S rRNA gene for phylogenetic analysis is necessary. This study aims to identify and analyze the genetic relationships of Spirulina from freshwater and brackish water based on 16S rRNA gene sequences. Freshwater Spirulina samples were taken from Bogor (BGR) and Yogyakarta (MRP), while brackish water Spirulina was taken from Jepara (JPR). DNA extraction was performed using the Zymo Research Quick-DNA Fungal/Bacterial Miniprep Kit, amplification of the 16S rRNA gene was conducted through PCR, followed by DNA sequencing. Phylogenetic analysis was carried out using MEGA11 to construct the phylogenetic tree. The morphology of strains BGR and MRP showed straight and thin filaments, whereas JPR had spiral and relatively long filaments. Sequencing analysis results showed that strains JPR and MRP had the closest homology similarity to Arthrospira sp. IAQUASC-C0001 with percentages of 99.34% and 99.12%, respectively. Meanwhile, Spirulina from BGR had the closest homology similarity to Arthrospira fusiformis strain AICB 668 with a percentage of 99.78%. Phylogenetic analysis indicated that strains BGR, JPR, and MRP are more closely related to Arthrospira than to Limnospira.