The Southern Ocean surrounding Antarctica harbours some of the most pristine marine environments remaining, but is increasingly vulnerable to anthropogenic pressures, climate change, and invasion by non-native species. Monitoring biotic responses to cumulative impacts requires spatiotemporal baselines and ongoing monitoring - traditionally, this has been obtained by continuous plankton recorder (CPR) surveys. Here, we conduct a 3000 nautical mile environmental DNA (eDNA) transect from Hobart (Australia) to Davis Station (Antarctica). We evaluate eDNA sampling strategies for long-term open ocean biomonitoring by comparing two water volume and filter pore size combinations: large (12 L with 20 μm) and small (2 L with 0.45 μm). Employing a broad COI metabarcoding assay, we found the large sample/pore combination was better suited to open-ocean monitoring, detecting more target DNA and rare or low abundance species. Comparisons with four simultaneously conducted CPR transects revealed that eDNA detections were more diverse than CPR, with 7 (4 unique) and 4 (1 unique) phyla detections respectively. While both methods effectively delineated biodiversity patterns across the Southern Ocean, eDNA enables surveys in the presence of sea-ice where CPR cannot be conducted. Accordingly, 16 species of concern were detected along the transect using eDNA, notably in the Antarctic region (south of 60°S). These were largely attributed to hull biofouling, a recognized pathway for marine introductions into Antarctica. In a warming Southern Ocean, continued biomonitoring is vital for conserving Antarctic ecosystems. We advocate for the long-term implementation of eDNA metabarcoding alongside CPR surveys to facilitate ecosystem-based management of these vulnerable environments.
