Fish communities in Baltic Sea coastal bays; using eDNA metabarcoding to assess vertical profile and traditional method comparison

Abstract Fish communities in the coastal Baltic Sea are currently monitored using passive fishing gears, such as gillnets. In recent years, eDNA approaches have gained popularity for fish detection thanks to their non-invasive nature, faster processing, and more precise identification, although such methods have been underutilized in comprehensive fish community assessments in the Baltic Sea. This study reports fish diversity using eDNA metabarcoding within different depth profiles for the first time in temperature-stratified coastal bays in the Baltic Sea, while also offering some comparison with traditional net-based approaches. Comparing samples above and below the thermocline revealed exclusivity in fish species at both depths, emphasizing the importance of vertical sampling in capturing a comprehensive understanding of fish distribution patterns in such systems. Results indicated that eDNA captured more fish taxa per sample compared to gillnet sampling, with similar or higher fish diversity, although variations occurred between bays. This study highlights the importance of incorporating eDNA metabarcoding, alongside traditional survey methods, to aid assessment of fish communities in aquatic environments.