Comparing the performance variability of different eDNA primers in fish monitoring

Abstract

Environmental DNA technology develops rapidly in the field of biodiversity detection. Selecting appropriate primers may be one of the key questions. However, there is currently a lack of systematic studies on differences in primer detection efficiencies. This research investigates the efficiency of six universal primers (12S, 16S, 18S, MiFish, Cytb, and COI) in detecting fish species across diverse aquatic ecosystems using an environmental DNA approach. The research spans five study areas, representing marine, river, wetland, lake, and reservoir ecosystems. Illumina MiSeq sequencing and bioinformatics tools were employed for primer performance evaluation. Results indicate that MiFish consistently outperforms other primers, detecting the highest number of fish species across all ecosystems and exhibiting superior taxonomic coverage. Furthermore, marine ecosystems consistently show higher detection numbers across all primers. The absence of commonly identified species detected by all primers emphasizes the necessity of using multiple primers for a comprehensive assessment. This study provides valuable insights into the strengths and limitations of universal primers, highlighting the importance of primer selection for accurate eDNA-based fish monitoring. The findings contribute to the scientific basis for the comprehensive management of aquatic ecosystems, assisting researchers and ecosystem managers in screening suitable fish universal primers for eDNA methods. The study also calls for further research into factors influencing primer performance and encourages the refinement of primers to enhance biodiversity monitoring precision in various ecosystems.