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Detection of a Non‐Indigenous Marine Macroalga ( Acanthophora spicifera ) With Environmental DNA From Surface Seawater

Patrick K Nichols,Alison R. Sherwood,Kaʻuaʻoa M S Fraiola,Taylor D. Ely,Brian B. Hauk,C. Counsell,Megan L. Porter,Peter B Marko

Published 2025 in Aquaculture, Fish and Fisheries

ABSTRACT

Non‐indigenous species (NIS) have far‐reaching economic, ecological and cultural impacts on native biota. Early detection of nuisance species is crucial for preventing their widespread establishment and conserving threatened ecosystems. Acanthophora spicifera is a red alga that has successfully colonized tropical and subtropical waters around the globe, out‐competing native flora and fauna and is among the most common non‐indigenous algae of shallow Hawaiian coral reefs. To assist early detection and eradication efforts of NIS, we developed a qPCR assay for the non‐indigenous A. spicifera . Assay sensitivity and specificity were validated with species‐specific primers targeting a 131 base‐pair region of the ribulose‐1,5‐bisphosphate carboxylase/oxygenase large subunit ( rbc L) gene. Using environmental DNA (eDNA) collected from surface seawater samples across the Hawaiian Archipelago, we then estimated A. spicifera site occupancy across sites where its presence was visually confirmed, as well as a large number of sites where its presence is unknown. Through occupancy modelling of eDNA and opportunistic visual survey data, A. spicifera eDNA was estimated to be present at 17% of surveyed sites, including one in the remote Papahānaumokuākea National Marine Sanctuary (PNMS), a world heritage site that is home to numerous endemic species. Thorough investigation of control samples, high‐throughput sequencing data and visual surveys suggest that the presence of A. spicifera eDNA within PNMS is associated with an emerging colonization front in the region. Our results indicate that the eDNA assay is sensitive to the presence of A. spicifera and is a cost‐effective method for monitoring its distribution on impacted coral reefs.

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