Marine Mammals’ Fauna Detection via eDNA Methodology in Pagasitikos Gulf (Greece)

Marine mammals are important ecological bio-indicators of marine ecosystems impacted by a plethora of anthropogenic and environmental threats. Genomics detects genetic variation, adaptation to environmental shifts, and susceptibility to diseases in marine mammal species. In this study, eDNA was utilized for the first time in the Pagasitikos Gulf over three consecutive years (2022–2024) in order to detect marine mammal species. Additionally, visual monitoring and eDNA results were compared to reveal the pros and cons of the two methodologies. The gulf was zoned into five different areas with respect to oceanographic features for sampling. DNA extraction was assessed by using a standard protocol of phenol–chloroform followed by PCR amplification using the 16S rRNA gene. A total of 5,209,613 highly filtered sequence reads were attributed to 108 species. Among these, Monachus monachus, Tursiops truncatus, and Ziphius cavirostris species were detected. This novel detection of Z. cavirostris in the relatively shallow waters of the Gulf of Pagasitikos raised the question of whether it was a random event or a new ecological trend. Z. cavirostris and M. monachus appeared to share the same marine areas within the gulf. In the era of the climate crisis, eDNA provides essential information on marine mammals’ ecological status, yields novel detections, and predicts behavioral changes essential to deep-diving species.