Corals house a variety of microorganisms which they depend on for their survival, including endosymbiotic dinoflagellates (Symbiodiniaceae) and bacteria. While cnidarian–microorganism interactions are widely studied, Symbiodiniaceae–bacteria interactions are only just beginning to receive attention. Here, we describe the localization and composition of the bacterial communities associated with cultures of 11 Symbiodiniaceae strains from nine species and six genera. Three-dimensional confocal laser scanning and electron microscopy revealed bacteria are present inside the Symbiodiniaceae cells as well as closely associated with their external cell surface. Bacterial pure cultures and 16S rRNA gene metabarcoding from Symbiodiniaceae cultures highlighted distinct and highly diverse bacterial communities occur intracellularly, closely associated with the Symbiodiniaceae outer cell surface and loosely associated (i.e., in the surrounding culture media). The intracellular bacteria are highly conserved across Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology. Our findings provide unique new insights into the biology of Symbiodiniaceae.

珊瑚内有多种微生物，它们赖以生存，包括内共生甲藻（Symbiodiniaceae）和细菌。虽然刺胞动物与微生物的相互作用得到了广泛的研究，但共生菌科与细菌的相互作用才刚刚开始受到关注。在这里，我们描述了与来自 9 个物种和 6 个属的 11 个 Symbiodiniaceae 菌株的培养相关的细菌群落的定位和组成。三维共聚焦激光扫描和电子显微镜显示细菌存在于共生菌科细胞内，并与其细胞外表面密切相关。来自共生菌科培养物的细菌纯培养物和 16S rRNA 基因元条形码突出了细胞内发生的独特且高度多样化的细菌群落，与共生藻科外细胞表面紧密结合，而松散结合（即在周围的培养基中）。细胞内细菌在 Symbiodiniaceae 物种中高度保守，表明它们可能参与 Symbiodiniaceae 生理学。我们的研究结果为共生菌科的生物学提供了独特的新见解。