A blue carbon eDNA marker reveals macroalgal signals from coastal to deep-sea sediments

Marine macroalgae play an important yet underrecognized role in coastal and benthic carbon cycling, with recent attention focusing on their contribution to blue carbon storage via detrital pathways. However, their ecological significance remains underrepresented in molecular monitoring studies, partly due to the absence of dedicated genetic markers for sedimentary detection. Here, we developed and validated a novel environmental DNA (eDNA) primer set, DSea-9, targeting a hypervariable region of the nuclear 18S rRNA gene optimized for macroalgal detection in marine sediments. The primer was designed by aligning over 7,000 macroalgal sequences and was evaluated through in silico PCR and in vitro amplification of 30 macroalgal species from Phaeophyceae, Rhodophyta, and Ulvophyceae. Field validation was performed on coastal and offshore sediment eDNA, with taxonomic assignments via PR2, SILVA, and NCBI databases. DSea-9 demonstrated high in silico coverage (>85–90%) and significantly improved the detection of macroalgal taxa such as Alaria and Palmaria, compared to conventional universal primers. Notably, DSea-9 enabled consistent detection of macroalgal DNA across a wide depth range, including the deepest sampled station (933 m), demonstrating its sensitivity to low-abundance DNA templates in offshore sediments. Overall, DSea-9 provides a sensitive and scalable tool for sedimentary eDNA monitoring of macroalgal biodiversity. Its application can contribute to refining biodiversity baselines, tracking macroalgal detritus dispersal, and strengthening the ecological representation of macroalgae in blue carbon assessments and sustainable marine management frameworks.