Genomic complexity and evolutionary diversification of a novel cyanobacterium from coral reef ecosystems

Heterocyte-forming cyanobacteria play a critical role in carbon, oxygen, and nitrogen cycling in coral reef ecosystems. Despite their ecological significance and biomedical potential, our understanding of reef-associated cyanobacteria remains limited. This study described Aliinostoc maniaoense sp. nov., a novel heterocyte-forming cyanobacterium isolated from a tropical coral reef in the South China Sea. Morphologically, A. maniaoense exhibited filaments with loose structural arrangement, gas vesicle-bearing motile hormogonia, and cylindrical or irregularly shaped akinetes, distinguishing it from other members of the genus. Phylogenetic analyses confirmed its placement within Aliinostoc and demonstrated significant genetic divergence from previously described species. Genomic analysis revealed a complete nitrogen fixation gene cluster, whose phylogeny suggested ancient rearrangement or horizontal acquisition, likely reflecting ecological adaptation and the selective advantage of biological nitrogen fixation in nutrient-poor coral reef habitats. Additionally, A. maniaoense possessed an unusually high number of ribosomal operons, with notable variations in 16S23S internal transcribed spacer (ITS) secondary structures, highlighting the complexity of ITS-based taxonomy in cyanobacteria. In vitro bioactivity assays demonstrated potent cytotoxic effects against several cancer cell lines, underscoring its biomedical potential. Moreover, genome mining revealed biosynthetic gene clusters for nocuolin A and heterocyst glycolipids along with several uncharacterized secondary metabolite pathways, suggesting promising ecological and biotechnological applications. These findings expanded our understanding of cyanobacterial diversity in coral reefs and emphasized the importance of integrating morphological, molecular, and genomic approaches for accurate species classification and functional characterization.