Microeukaryotes are mainly composed of highly diverse and abundant protists, whose diversity and distribution in deep oceans have not been well studied. We investigated the vertical profiles of microeukaryotes throughout the water column down to abyssal sediments and their horizontal distribution over a distance of 1,300 km in the Western Pacific Ocean, using high throughput DNA sequencing. A distinct vertical distribution was detected for microeukaryote communities, which could be clustered into euphotic, aphotic and sediment groups. Nearly half of the operational taxonomic units detected in the sediment samples were also found in overlying water, indicating a frequent species exchange between seawater habitats and abyssal sediment habitats, which was similar to that observed for prokaryote communities. On the horizontal scaling side, a significant distance-decay relationship was found in the microeukaryote community. Furthermore, the major microeukaryotic groups revealed different distance-decay patterns which appeared to be significant for Dinoflagellata and Radiolaria, but insignificant for Ciliophora. Environmental selection contributed more to the variations in microeukaryote and Dinoflagellata communities than neutral processes, whereas neutral processes explained more variations in Radiolaria community. Generally, community variations explained by both processes were less than 30%, which was lower than that in coastal zones. These results imply that the complex distribution pattern within microeukaryote communities and more drivers, such as currents, water mass and biotic interactions, might contribute in shaping the distribution of microeukaryotes in the open ocean.

微型真核生物主要由高度多样化和丰富的原生生物组成，其在深海中的多样性和分布尚未得到很好的研究。我们使用高通量DNA测序技术研究了整个水柱中直至深海沉积物的微真核生物的垂直剖面及其在西太平洋1300公里距离内的水平分布。在微真核生物群落中检测到明显的垂直分布，可以将其分为富营养，无营养和沉积物类。在沉积物样品中检测到的近乎一半的业务分类单位也都在上覆水中发现，表明海水生境和深海沉积物生境之间的物种交换频繁，这与原核生物群落中观察到的相似。在水平缩放方面，在微真核生物群落中发现了显着的距离-衰减关系。此外，主要的微真核生物群体显示出不同的距离衰减模式，这对于Dinoflagellata和Radioraria而言似乎很重要，而对Ciliophora而言则无关紧要。与中性过程相比，环境选择对微型真核生物和恐龙鞭毛虫群落的贡献更大，而中性过程解释了放射虫群落的更多变异。通常，这两个过程所解释的群落变异小于30％，低于沿海地区。这些结果表明，微真核生物群落内部的复杂分布模式以及更多的驱动因素，例如洋流，水量和生物相互作用，可能有助于塑造微真核生物在远洋中的分布。