Enhanced eDNA monitoring for detection of viable harmful algal bloom species using propidium monoazide

•PMA selectively binds to damaged DNA, reducing exDNA-related false positives for iDNA.•iDNA (PMA) monitoring has been shown to align relatively well with conventional microscopy, demonstrating its reliability.•Correlation of iDNA (PMA) with water quality parameters reveals eDNA-environment dynamics.•Effective HABs detection through iDNA monitoring in surface and lower water columns.•iDNA (PMA) monitoring enhances accuracy in detecting viable HABs for marine management. This study investigated the use of propidium monoazide (PMA) to improve the accuracy of environmental DNA (eDNA) monitoring by selectively detecting intracellular DNA (iDNA) from living cells, while excluding extracellular DNA (exDNA) from dead organisms. eDNA samples were collected from various depths off the coast of Tongyeong, South Korea, and analyzed alongside environmental factors, such as temperature, dissolved oxygen, turbidity, and nutrient levels. The results showed that PMA-treated iDNA provided a more accurate estimate of viable harmful algal bloom species (HABs) than total eDNA and DNase-treated iDNA. Strong correlations were found between iDNA (PMA) and environmental factors, particularly nutrient levels and turbidity, suggesting its effectiveness in biological environments. The iDNA (PMA) concentrations were higher in the surface and bottom layers, indicating that these layers were more indicative of living organisms in marine environments. The application of PMA in eDNA monitoring reduces false positives and enhances the detection accuracy of viable HAB species, representing a promising tool for real-time monitoring and management of marine ecosystems.