Prokaryotic Diversity and Dynamics during Dinoflagellate Bloom Decays in Coastal Tunisian Waters

(1) Background: Harmful algal blooms (HABs) can negatively impact marine ecosystems, but few studies have evaluated the microbial diversity associated with HABs and its potential role in the fates of these proliferations. (2) Methods: Marine prokaryotic diversity was investigated using high-throughput sequencing of the 16S rRNA gene during the bloom declines of two dinoflagellates detected in the summer of 2019 along the northern and southern Tunisian coasts (South Mediterranean Sea). The species <i>Gymnodinium impudicum</i> (Carthage, Tunis Gulf) and <i>Alexandrium minutum</i> (Sfax, Gabes Gulf) were identified using microscopy and molecular methods and were related to physicochemical factors and prokaryotic compositions. (3) Results: The abundance of <i>G. impudicum</i> decreased over time with decreasing phosphate concentrations. During the <i>G. impudicum</i> bloom decay, prokaryotes were predominated by the archaeal MGII group (<i>Thalassarchaeaceae</i>), <i>Pelagibacterales</i> (SAR11), <i>Rhodobacterales,</i> and <i>Flavobacteriales</i>. At Sfax, the abundance of <i>A. minutum</i> declined with decreasing phosphate concentrations and increasing pH. At the <i>A. minutum</i> peak, prokaryotic communities were largely dominated by anoxygenic phototrophic sulfur-oxidizing <i>Chromatiaceae</i> (<i>Gammaproteobacteria</i>) before decreasing at the end of the survey. Both the ubiquitous archaeal MGII group and <i>Pelagibacterales</i> were found in low proportions during the <i>A. minutum</i> decay. Contrary to the photosynthetic <i>Cyanobacteria</i>, the photo-autotrophic and -heterotrophic <i>Rhodobacterales</i> and <i>Flavobacteriales</i> contents remained stable during the dinoflagellate bloom decays. (4) Conclusions: These results indicated changes in prokaryotic community diversity during dinoflagellate bloom decays, suggesting different bacterial adaptations to environmental conditions, with stable core populations that were potentially able to degrade HABs.