AUTHOR=Koedooder Coco , Landou Etai , Zhang Futing , Wang Siyuan , Basu Subhajit , Berman-Frank Ilana , Shaked Yeala , Rubin-Blum Maxim 

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

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.879970

DOI=10.3389/fmicb.2022.879970

ISSN=1664-302X

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