Dive surveys and eDNA detect contrasting macroalgal community composition in Nova Scotia, Canada

Morphological identification of macroalgae can be time-consuming and species may be difficult to observe, collect, or identify, preventing detailed study on the distribution and ecology of many species. The use of eDNA in species surveillance and biodiversity assessments has gained considerable traction in studying macroalgae, as it provides an opportunity for increased sampling efficiency and a reduced reliance on taxonomic expertise for morphological identification. However, it is crucial to understand how eDNA tools may bias results of species diversity and detection and how these biases differ from traditional morphological surveys. The present study compared species composition and detection rates of dive quadrat collections with a combination of morphological identification and DNA barcoding (i.e., traditional survey methods) to two types of eDNA tools: quantitative polymerase chain reaction (qPCR) using four species-specific qPCR assays and metabarcoding using two metabarcoding markers. Metabarcoding detected nearly two times more species than traditional surveys; however, species overlap was as low as 19.2%, and some large conspicuous and ecologically important macroalgae were not detected by metabarcoding. This result suggests that metabarcoding uncovers a host of taxa largely distinct from dive surveys. Metabarcoding and qPCR proved capable of detecting target species even at very low abundances, but both showed a high incidence of false negatives. Results presented here support a combined approach leveraging the considerable strengths of eDNA in concert with species validation and abundance metrics provided by tradtional surveys.