Anaerobic protists are diverse, ecologically important members of oxygen-depleted microbial communities, acting as grazers, nutrient cyclers, and partners in multi-domain associations, yet remain understudied relative to anaerobic prokaryotes. Ciliates are particularly abundant and diverse in these habitats, but their global diversity and distribution are largely unknown. Here, we conducted a meta-analysis of public 18S rDNA datasets, along with one dataset generated here, to assess the global diversity and ecology of marine anaerobic ciliates. Using a novel pipeline, we processed 2854 samples from 42 studies spanning 19 habitat types. We recovered 3196 anaerobic ciliate amplicon sequence variants (ASVs) across all described lineages. Based on clade-specific divergence thresholds derived from phylogenetic distances, 28.4%-46.3% of ASVs qualified as novel. Most sequences belonged to a poorly described plagiopylean clade, suggesting a large reservoir of undescribed diversity in this clade. Community comparisons revealed close phylogenetic similarities between some shallow-water and deep-sea assemblages, suggesting that shared redox conditions may shape communities more than water depth. Our results demonstrate that marine anaerobic ciliates are globally distributed, taxonomically diverse, and rich in novel lineages. This study provides a framework for leveraging environmental sequencing data to better understand the diversity and ecology of neglected protist lineages and under-sampled habitats.
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