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

Abstract

<i>Trichodesmium</i> 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 <i>Trichodesmium</i> in the Red Sea, based on metagenome-assembled genomes (MAGs) and <i>hetR</i> gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct <i>Trichodesmium</i> colonies (tufts, dense and thin puffs). <i>Trichodesmium thiebautii</i> (puffs) and <i>Trichodesmium erythraeum</i> (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both <i>T. thiebautii</i> and <i>T. erythraeum</i>, a single <i>T. thiebautii</i> 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 <i>Trichodesmium nobis</i> and <i>Trichodesmium miru</i>, respectively that likely occurred as single filaments. The <i>hetR</i> gene phylogeny further indicated that the genotype in clade IV could represent the species <i>Trichodesmium contortum</i>. Importantly, we show the presence of <i>hetR</i> paralogs in <i>Trichodesmium</i>, where two copies of the <i>hetR</i> gene were present within <i>T. thiebautii</i> genomes. This may lead to the overestimation of <i>Trichodesmium</i> diversity as one of the copies misidentified <i>T. thiebautii</i> as <i>Trichodesmium aureum</i>. Taken together, our results highlight the importance of re-assessing <i>Trichodesmium</i> taxonomy while showing the ability of genomics to capture the complex diversity and distribution of <i>Trichodesmium</i> populations.