Habitat differentiation is the essential force for shaping animal and plant biogeography. Distribution patterns of microeukaryotes, which are an assemblage of highly diverse and phylogenetically distant groups, across multiple marine habitats remain largely unknown. We hypothesize that microeukaryote communities vary across different types of marine habitats at the regional scale similar as macroorganisms, and they are shaped by multiple factors. Herein, we evaluated the microeukaryotic diversity and connectivity in sediments from intertidal flat through continental shelf to deep-sea floor, including habitats of deep-sea plain, seamount, and hydrothermal vent, using high-throughput DNA sequencing. Microeukaryote communities were clustered into their own sub-groups according to the types of the habitats, where the communities of abundant taxa tended to gather with nearby habitats, while the rare taxa were mainly shaped by the types of the habitats. The SourceTracker analysis showed that the most probable sources for each community composition, particularly for those from seamounts and hydrothermal vent, were identified unknown. The continental shelf and deep-sea plain showed a relatively larger fraction of sources from each other, indicating a stronger source-sink dynamic than that among other habitats. The habitat differentiation contributed more to community variations than the spatial variables and water depth did. Co-occurrence network analysis indicated more complex bio-interactions in the neritic zone, where Cercozoa might play fundamental roles in the stability of the community than those in the deep sea, where ciliates were more connected with other taxa. Altogether, our findings highlight that the microeukaryotic communities are clearly shaped by the habitat differentiation, and this study also identifies the most probable source of dispersal for each community of different habitats.

栖息地分化是塑造动植物生物地理学的重要力量。微型真核生物在多个海洋生境中的分布模式是高度多样且系统发育距离较远的群体的集合，目前尚不清楚。我们假设，微真核生物群落在不同类型的海洋生境中在区域尺度上与大型有机体相似，并且受多种因素影响。本文中，我们使用高通量DNA测序技术评估了潮间带穿过大陆架到深海底（包括深海平原，海山和热液喷口的栖息地）的沉积物中的微真核生物多样性和连通性。根据栖息地的类型，微型真核生物群落被分为各自的亚组，那里有丰富的生物分类群落聚集在附近的栖息地，而稀有生物分类主要是由栖息地的类型决定的。SourceTracker分析表明，每个社区组成的最可能来源，尤其是来自海山和热​​液喷口的那些来源，已被确定。大陆架和深海平原显示出彼此相对较大的来源，表明源库动态性强于其他生境。与空间变量和水深相比，生境的分化对群落变化的贡献更大。共现网络分析表明，与深海地区相比，地缘生物区的生物相互作用更为复杂，在该地区，角尾藻可能在社区稳定中起着根本性作用，纤毛虫与其他类群的联系更紧密。总而言之，我们的发现突出表明，微真核生物群落明显受到栖息地分化的影响，并且本研究还确定了不同栖息地的每个群落最可能的扩散来源。