Molecular Detection and Diversity of Marine Harmful Algal Bloom Species in Nigerian Coastal Waters

Harmful algal blooms (HABs) represent an escalating threat to marine ecosystem health, fisheries, and public safety globally, yet their molecular diversity and detection remain poorly characterised in Nigerian coastal waters. This study applied molecular methods to detect and characterise harmful algal bloom species in the coastal waters of Lagos, Delta, and Rivers States. Water samples were collected monthly over twelve months from nearshore and offshore transects. Environmental DNA was extracted, and HAB species were identified using targeted PCR with species-specific primers and high-throughput metabarcoding of the 18S rRNA gene V4 region. Paralytic shellfish toxin and domoic acid concentrations were measured using enzyme-linked immunosorbent assay. Physicochemical variables were related to HAB occurrence using generalised additive modelling. A total of 14 HAB species were molecularly confirmed, including Alexandrium minutum, Pseudo-nitzschia multiseries, Gymnodinium catenatum, and Karenia mikimotoi. Several species were recorded for the first time in Nigerian waters based on molecular evidence. Alexandrium minutum was detected year-round at all offshore stations. Domoic acid was detected at concentrations exceeding European Union regulatory limits in shellfish sampled adjacent to two bloom events. Sea surface temperature and nitrate concentrations were the strongest environmental predictors of Pseudo-nitzschia abundance. The study demonstrates that molecular monitoring significantly exceeds microscopy in HAB species detection sensitivity and recommends its adoption as the national standard for HAB surveillance. Keywords: harmful algal blooms, molecular detection, metabarcoding, Nigeria, paralytic shellfish toxins.