Investigating the diversity and spatiotemporal dynamics of eukaryotic communities in hydrothermal vents at the Central Indian Ridge using environmental DNA metabarcoding

Deep-sea hydrothermal vent ecosystems along the Central Indian Ridge (CIR) are ecologically and biogeographically important; however, their biodiversity patterns remain poorly understood amid concerns over potential anthropogenic impacts. Here, we conducted the first comprehensive survey of eukaryotic community diversity across eight vent fields, including the newly discovered Saero and Maru, as well as a non-vent reference site unaffected by hydrothermal activity. Environmental DNA (eDNA) metabarcoding of seawater and sediment samples collected in 2023–2024, targeting the 18S rRNA V9 region, yielded 1,569 and 1,783 amplicon sequence variants (ASVs), representing 34 and 39 phyla and 78 and 85 classes, respectively. The results revealed high diversity and pronounced spatial heterogeneity in both sample types, with numerous unique ASVs at individual sites, suggesting potential local endemism. Notably, inactive vent fields displayed alpha diversity comparable to or exceeding that of active vents and the reference site, underscoring their ecological significance and the need for conservation. Community structures varied among vent fields, showing latitudinal organization along the CIR, and differed across years, particularly in diffuse vents, reflecting environmental and temporal influences. Seawater and sediment captured complementary aspects of community composition, highlighting the value of multi-substrate eDNA approaches for comprehensive biodiversity assessment. These findings establish a critical baseline for long-term monitoring and provide essential insights to guide conservation and management of CIR hydrothermal ecosystems. • First eDNA-based survey of eukaryotic diversity along the Central Indian Ridge • Both active and inactive vents showed high diversity and strong site-specificity • Community structures varied with vent geochemistry and sampling year • Seawater and sediment samples revealed distinct yet complementary communities