High‐Resolution Longitudinal eDNA Metabarcoding and Morphological Tracking of Planktonic Threats to Salmon Aquaculture

ABSTRACT Salmonid aquaculture, a major component of the Northern European, North American, and Chilean coastal economies, is under threat from challenges to gill health, many of which originate from plankton communities. A first step toward mitigating losses is to characterize the biological drivers of poor gill health. Numerous planktonic taxa have been implicated, including toxic and siliceous microalgae, hydrozoans, and scyphozoans; however, rigorous longitudinal surveys of plankton diversity and gill health have been lacking. In the current study, we present and assess an exhaustive identification approach combining both morphological and molecular methods together with robust statistical models to identify the planktonic drivers of proliferative gill disease (PGD) and fish mortality. We undertook longitudinal evaluation at two marine aquaculture facilities on the west coast of Scotland using daily data collected during the 2021 growing season (March–October). Examining these two different sites, one sheltered and one exposed to the open sea, we identified potentially new, important, and unexpected planktonic drivers of PGD and mortality (e.g., doliolids and appendicularians) and confirmed the significance of some established threats (e.g., hydrozoans and diatoms). We also explored delayed or “lagged” effects of plankton abundances on gill health and undertook a comparison of environmental DNA (eDNA) metabarcoding and microscopy in their ability to identify and quantify planktonic species. Our data highlight the diversity of planktonic threats to salmonid aquaculture as well as the importance of using both molecular and morphological approaches to detect these. There is now an urgent need to expand systematic longitudinal molecular and morphological approaches across multiple sites and over multiple years. The resultant catalogue of main biological drivers will enable early warning systems, new treatments, and, ultimately, a sustainable platform for future salmonid aquaculture in the marine environment.