A new method for rapid detection and identification of fish parasites through whole-fish homogenization

Background : The global biodiversity crisis, driven by anthropogenic activities, signals the onset of the sixth mass extinction in Earth’s history. The biodiversity decline is particularly evident in freshwater ecosystems, where multiple species are at risk including several fish taxa. Given their integral role in fish health and ecosystem functioning, fish parasites are also of crucial importance. However, the detection and monitoring of these organisms remains challenging, due to methodological difficulties involved. Conventional methods for detecting fish parasites rely on morphological analyses, which are time-consuming, labor-intensive, and require specialized expertise. Here, we propose a new method involving whole-fish homogenization along with DNA-based identification of its parasite biota. Our goal was to validate whether the method is equally effective in terms of identification efficiency while also being more time-efficient than morphological parasite identification. Methods : For this, we collected and analysed five specimens of European eel ( Anguilla anguilla ) from the River Rhine in Germany, focusing on their helminth composition. The helminths were identified morphologically to the lowest possible taxonomic level, and then all the parasites as well asthe entire fish tissue were homogenized together using a commercial blender. Molecular identification of the parasites was based on morphological identification and conducted using parasite-specific primers. Results : Through morphological identification, we have determined that all eels were infected by at least one parasite taxon and in the process, we identified four helminth taxa belonging to Acanthocephala ( Pomphorhynchus sp.), Cestoda ( Bothriocephalus/Proteocephalus sp.), Monogenea ( Pseudodactylogyrus sp.) and Nematoda ( Anguillicola crassus ). After homogenization and through DNA-based identification, the parasite diversity did not fully reflect the morphology-based assessment. While we could detect most of the detected taxa, even at times where they were not detected morphologically, we did not reliably detect cestodes. This might point to several possible issues including incompatibility of used primers, species misidentification or insufficient amount of parasite DNA in the homogenate samples. Conclusions : Even though the method still requires optimization, it shows great promise for an efficient and accuratedetection of parasites in fish hosts. The employment of this method in biomonitoring campaigns could improve the reliability of parasite assessments, which could aid fish biodiversity conservation efforts.