eDNA-based metabarcoding of Red Sea mangrove Avicennia marina beds in Egypt

Mangroves play a vital role in stabilizing coastlines, supporting biodiversity, and delivering essential ecosystem services. To assess animal biodiversity within the grey mangrove Avicennia marina habitats along Egypt's Red Sea governorate's coast, seawater samples were collected for environmental DNA analysis from six key mangrove sites: 17 km and 40 km south of Safaga City, El-Sharm El-Bahary, Wadi El-Gemal, El-Qolaan, and Hamata. For comparison, eDNA was also obtained from two non-mangrove sites in the same region. The eDNA was analyzed via COI gene metabarcoding, and diversity metrics were used to compare habitats. Results revealed 13 fish species exclusive to mangroves, alongside diverse arthropods, poriferans, and cnidarians. Moolgarda sp. and Psettodes erumei were the most abundant fish species detected. Relative read abundances differed significantly between mangrove and non-mangrove sites, with some species exhibiting dual habitat use (e.g., transitioning between coral and mangrove systems). Notably, DNA from two marine alien species was also identified. This study underscores the high biodiversity supported by Red Sea mangroves, emphasizing their ecological and economic value. These findings can inform sustainable management strategies to protect these critical ecosystems for future generations.