Aligning Molecular and Microscopy Methods for Biofouling Detection of Farmed Kelp ( Alaria esculenta and Saccharina latissima )

ABSTRACT

Kelp farming in the North Atlantic is emerging as a new sustainable source of food, feed, nutraceuticals and biostimulants. Kelp biofouling by epibiont taxa, including bryozoans, hydrozoans, amphipods, bivalves, and gastropods, is a key constraint in kelp yield and quality. The planktonic stages of these species belonging to meroplankton precede visible settlement on seaweed fronds. Thus, the precise taxonomic detection of the planktonic stage and the identification of the temporal lag with the biofouling stage could help form an early warning signal helping farmers plan harvesting times. To achieve this, monthly samples of plankton and kelp fronds were collected from a Scottish kelp farm during a kelp production period (September 2021–July 2022). The taxonomic identity of kelp biofouling epibionts was established by microscopy and DNA‐barcoding. The taxa were then traced in the plankton samples using both microscopy counts and eDNA‐metabarcoding. COI barcoding identified 14 kelp epibiont species, sharpening the morphological classification which only reached the class or genus level. Plankton microscopy confirmed two of these at the genus level while plankton eDNA metabarcoding recovered 9 of the 14 species and detected an additional 14 taxa. Microscopy counts of hydromedusae, bryozoan cyphonautes, and bivalve larvae peaked in the plankton 2 weeks before the maximum coverage on Saccharina latissima fronds. Metabarcoding and microscopy counts frequently identified different peak months for the same taxa. Depth‐stratified frond surveys revealed that kelp segments located deeper within the water column supported the highest levels of hydrozoan colonization, indicating either depth‐related colonization processes, kelp age‐related exposure effects, or UV avoidance. The results indicate that the combination of molecular diagnostics and conventional microscopy improves the sensitivity and specificity of biofouling detection, facilitating earlier and more informed farm management decisions.