Biomonitoring planktonic threats to salmon aquaculture: morphological and eDNA metabarcoding data

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 towards 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 those. 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.