Parasitic taxa are key to the vertical stratification and community variation of pelagic ciliates from the surface to the abyssopelagic zone.

Background: An increase in upper-ocean thermal stratification is being observed worldwide due to global warming. However, how ocean stratification affects the vertical profile of plankton communities remains unclear. Understanding this is crucial for assessing the broader implications of ocean stratification. Pelagic ciliates cover multiple functional groups, and thus can serve as a model for studying the vertical distribution and functional strategies of plankton in stratified oceans. We hypothesize that pelagic ciliate communities exhibit vertical stratification caused by shifts in functional strategies, from free-living groups in the photic zone to parasitic groups in deeper waters.

Results: 306 samples from the surface to the abyssopelagic zone were collected from 31 stations in the western Pacific and analyzed with environmental DNA (the V4 region of 18 S rDNA) metabarcoding of pelagic ciliates. We found a distinct vertical stratification of the entire ciliate communities, with a boundary at a depth of 200 m. Significant distance-decay patterns were found in the photic layers of 5 m to the deep chlorophyll maximum and in the 2,000 m, 3000 m and bottom layers, while no significant pattern occurred in the mesopelagic layers of 200 m - 1,000 m. Below 200 m, parasitic Oligohymenophorea and Colpodea became more prevalent. A linear model showed that parasitic taxa were the main groups causing community variation along the water column. With increasing depth below 200 m, the ASV and sequence proportions of parasitic taxa increased. Statistical analyses indicated that water temperature shaped the photic communities, while parasitic taxa had a significant influence on the aphotic communities below 200 m.

Conclusions: This study provides new insights into oceanic vertical distribution, connectivity and stratification from a biological perspective. The observed shift of functional strategies from free-living to parasitic groups at a 200 m transition layer improves our understanding of ocean ecosystems in the context of global warming.