Microniche sampling of the microbiome in the Starlet Sea Anemone, Nematostella vectensis, reveals a compartment-specific dominance of Spirochetes

Microniche sampling can reveal highly specialized bacterial associations within the holobiont as well as facilitate identification of core microbial symbionts that would have otherwise been overlooked by bulk sampling methods. In this study, we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct body regions: the capitulum, mesenteries, and physa. This sampling design allowed us to uncover distinct bacterial community compositions between compartments, including the compartment-specific dominance of Spirochetes within the capitulum of N. vectensis. Bacteria from the Spirochaetaceae family made up 65.8% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. Spirochetes are known to play significant roles in nitrogen and carbon cycling as symbionts of other invertebrates. The capitulum community also exhibited significantly lower Alpha-diversity compared to the other two compartments, however Beta-diversity metrics between the compartments were inconclusive as to their distinctness. A phylogenetic analysis of the predominate Spirochete sequence recovered from N. vectensis showed higher similarity to Spirochaeta spp. recovered from the Pacific Oyster, Crassostrea gigas, the cold water coral, Lophelia pertusa, and the soft coral, Millepora sp., but not to a Spirochete previously recovered from N. vectensis. This suggests a flexible capitulum niche in N. vectensis open to different groups of Spirochaetales depending on the environmental circumstances of the association.

微生境采样能够揭示全共生体（holobiont）内高度特化的细菌共生关联，同时有助于识别常规批量采样方法会遗漏的核心微生物共生体。本研究以模式刺胞动物星状海葵（Nematostella vectensis）为研究对象，将其躯体形态划分为三个独立区域：口盘区（capitulum）、隔膜（mesenteries）与足盘区（physa），以此解析其分区特异性的微生物群落关联。该采样设计帮助我们揭示了不同躯体区域间显著分化的细菌群落组成，包括星状海葵口盘区中螺旋体类群的区域特异性优势。螺旋体科（Spirochaetaceae）细菌占口盘区群落组成的65.8%，而在隔膜与足盘区群落中占比仅分别为1.2%与0.1%。已知螺旋体类群作为其他无脊椎动物的共生体，在氮、碳循环中发挥重要功能。口盘区群落的α多样性（Alpha-diversity）亦显著低于另外两个躯体区域，但不同区域间的β多样性（Beta-diversity）指标无法明确证明其群落组成的独特性。对从星状海葵中获取的优势螺旋体序列进行系统发育分析，结果显示其与太平洋牡蛎（Crassostrea gigas）、冷水珊瑚（Lophelia pertusa）以及软珊瑚（Millepora sp.）中获取的螺旋体属（Spirochaeta spp.）序列相似度更高，而与此前从星状海葵中获取的螺旋体序列相似度较低。这表明星状海葵的口盘区生态位具有灵活性，可根据共生关联的环境条件接纳不同类群的螺旋体目（Spirochaetales）细菌。