Between Abyss and Hadal: Metabarcoding reveals distinct meiofauna community patterns in North-Pacific trenches

Hadal trenches are extreme and dynamic environments, yet their meiofauna diversity and biogeographic connectivity remains poorly resolved. This study compared abyssal and hadal meiofauna communities from two trench systems in the Northern Pacific, the Aleutian Trench and the Kuril-Kamchatka Trench, using CO1 metabarcoding as the primary genetic marker, with the 18S V1V2 marker as an exploratory comparison. With CO1 five higher meiofauna taxa were retained, being dominated by Crustacea and Nematoda. In comparison, V1V2 additionally detected rare taxa, such as Tardigrada, Gastrotricha and Loricifera. Across both trench systems, abyssal samples exhibited significantly higher observed and expected OTU richness, diversity and evenness than hadal samples. Ordination analyses revealed a clear separation between abyssal and hadal communities, with CO1 capturing a more distinct depth-related gradient but still present in V1V2. The majority of CO1 OTUs (∼84%) were restricted to a single region-habitat group, showing a strong spatial turnover in community composition. Yet a subset of Copepoda OTUs occurred across both trench systems and habitats. Indicator analysis identified OTUs associated with habitats and regions, predominantly linked to copepod lineages from the CCZ, but also including Zosimeidae from the Aleutian Trench. Haplotype networks suggested a mixture of shared and trench restricted variants. Overall, meiofaunal communities were primarily structured by depth (abyssal vs. hadal), with additional regional-specific signals. CO1 proved generally more robust in detected habitat related patterns compared to V1V2 and also showed a higher success regarding legacy samples.