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Detection of a non-indigenous marine macroalga (Acanthophora spicifera) with environmental DNA from surface seawater

Nichols, Patrick1; Sherwood, Alison1; Fraiola, Kaʻuaʻoa2; Ely, Taylor1; Hauk, Brian3; Counsell, Chelsie1; Porter, Megan1; Marko, Peter1

Published Nov 03, 2025 on Dryad. https://doi.org/10.5061/dryad.cfxpnvxjd

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Abstract

Non-indigenous species (NIS) have far-reaching economic, ecological, and cultural impacts to 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 coral reefs 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 was validated with species-specific primers targeting a 131 base-pair region of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene. Using environmental DNA (eDNA) collected from surface seawater samples, 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 modeling 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 Marine National Monument (PMNM), a world heritage site that is home to numerous endemic species. Thorough investigation of control samples, high-throughput sequencing data, and visual surveys suggests that the presence of A. spicifera eDNA within PMNM 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.