Identifying the general patterns of biogeography is vital for a better understanding of biological communities over space. However, there is a lack of well-understood biogeographic patterns of microbial communities in pelagic ecosystems. In this study, we simultaneously investigated archaeal, bacterial, and protist communities using metabarcoding in the deep Pacific Ocean. Our results showed that archaea, bacteria, and protists shared a depth–decay relationship of community similarity, indicating a decrease in community similarity with increasing differences in water depth. Environmental factors were more important than water depth in shaping this relationship, indicating that the sinking process, compared to environmental conditions, might be relatively minor in driving community variations across water columns. Our study suggests that the depth–decay relationship should be primarily examined in field investigations to better interpret the vertical dynamics of marine microbial communities, and more efforts are required to determine the mechanism underlying this important relationship.

biogeography,microbial community,metabarcoding,depth–decay relationship,Pacific Ocean