Abstract
Summary Elucidation of the potential roles of single‐celled eukaryotes (protists) in ecosystem function and trophodynamics in hydrothermal vent ecosystems is reliant on information regarding their abundance, distribution and preference for vent habitats. Using high‐throughput 18S rRNA gene sequencing on a diverse suite of hydrothermally influenced and background water samples, we assess the diversity and distribution of protists and identify potential vent endemics. We found that 95% of the recovered sequences belong to operational taxonomic units (OTUs) with a cosmopolitan distribution across vent and non‐vent habitats. Analysis of ‘vent only’ OTUs found in more than one vent sample and co‐occurrence network analysis comparing protist groups to extremophilic reference organisms suggest that the most likely vent endemics are infrequently encountered, potentially in low abundance, and belong to novel lineages, both at the phylum level and within defined clades of Rhizaria and Stramenopila. Potential endemism is inferred for relatives of known apusomonads, excavates and some clades of Syndiniales. Similarity in community composition among samples was low, indicating a strong stochastic component to protist community assembly and suggesting that rare endemics may serve as a reservoir poised to respond to changing environmental conditions in these dynamic systems.