Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to Assess Diversity.

are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Their blooms consist of a dynamic assemblage of subpopulations and colony morphologies that are hypothesized to occupy unique niches. Here, we assessed the poorly studied diversity of in the Red Sea, based on metagenome-assembled genomes (MAGs) and gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct colonies (tufts, dense and thin puffs). (puffs) and (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both and , a single genotype comprised both thin and dense puff morphotypes, and we hypothesize that this phenotypic variation is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to and , respectively that likely occurred as single filaments. The gene phylogeny further indicated that the genotype in clade IV could represent the species . Importantly, we show the presence of paralogs in , where two copies of the gene were present within genomes. This may lead to the overestimation of diversity as one of the copies misidentified as . Taken together, our results highlight the importance of re-assessing taxonomy while showing the ability of genomics to capture the complex diversity and distribution of populations.