The Trichoplax H2 holobiont: a simple animal and its two intracellular symbionts

The Placozoa are an enigmatic group of simple marine metazoans where all taxa harbor intracellular bacteria. Despite four decades of research, the bacterial identities, their location and their roles remain elusive. Here we show that the placozoan Trichoplax H2 is associated with two intracellular bacteria. We detected the symbionts and reconstructed their physiology using metagenomic and metatranscriptomic evidence from the same single-animal specimens. One symbiont forms a new genus in the Midichloriaceae (Rickettsiales) and correlative fluorescent labelling and 3-D electron microscopic tomography showed that it inhabits the rough ER in the fiber-cells. It has mutualistic traits and occurs worldwide as we could detect it in 10% of all aquatic tag sequencing datasets. The second symbiont is an intracellular bacterium from the Margulisbacteria, a phylum-level clade previously only identified from DNA sequencing and not known to form intracellular associations. It resides in the digestive ventral epithelial cells, uses lipids digested by the host and has the physiological capacity to supplement the placozoan nutrition. Our single-individual approach revealed that this cultivable placozoan host forms a tripartite symbiosis and provides experimental access to microbial dark matter – a rickettsiales that inhabits a novel niche within eukaryote cells and an intracellular margulisbacterial symbiont.

扁盘动物门（Placozoa）是一类神秘的简单海洋后生动物类群，所有已知类群均携带胞内共生细菌。尽管已有四十年的研究历程，这类细菌的分类学身份、定植位点与功能仍未明晰。本研究证实，扁盘动物Trichoplax H2与两种胞内细菌存在共生关联。我们通过同一单一个体标本的宏基因组学与宏转录组学数据，成功检测到这些共生菌并重构了其生理特征。其中一种共生菌属于立克次氏体目（Rickettsiales）的米氏立克次体科（Midichloriaceae），代表一个全新的属；通过关联荧光标记与三维电子显微镜断层成像分析，证实其定植于纤维细胞的粗面内质网中。该菌具备互利共生特征，且分布广泛——我们在10%的水生标签测序数据集中均检测到了该菌。第二种共生菌属于马古利斯细菌门（Margulisbacteria），该门级演化支此前仅通过DNA测序被发现，从未被证实可形成胞内共生关系。该菌定植于宿主的腹面消化上皮细胞内，可利用宿主消化的脂质，并具备为扁盘动物宿主补充营养的生理能力。本研究采用单个体分析方法，揭示了这株可培养扁盘动物宿主与两种共生菌构成的三重共生关系，同时为研究微生物暗物质提供了实验模型：一类栖息于真核细胞内全新生态位的立克次氏体目细菌，以及一种胞内马古利斯细菌共生体。