Comparative Assessment of Freshwater Biodiversity in Los Morales Reservoir (Madrid) Using eDNA Collected From Sponges and Water Filtration

ABSTRACT Biodiversity loss is occurring at a faster rate in freshwater ecosystems than in marine or terrestrial ones. Developing tools for biodiversity monitoring in freshwater environments is thus crucial for informing conservation policies. Environmental DNA (eDNA) can serve as a key tool for environmental management, offering valuable insights into ecosystem biodiversity. The use of sponges as natural eDNA collectors (i.e., “natural sampler DNA”, nsDNA) has emerged as an innovative approach, showing promising results. Although this concept was initially developed and explored in marine ecosystems, it is expected to be transferable to freshwater environments; however, no studies have yet tested this approach in such systems. The main goal of this study was to evaluate the effectiveness of the freshwater sponge Ephydatia muelleri as nsDNA in freshwater ecosystems. To achieve this, we used metabarcoding techniques targeting a region of the mitochondrial cytochrome c oxidase gene on tissue samples from E. muelleri (with and without host‐specific blocking primers), as well as on water filter samples from Los Morales Reservoir in Madrid, Spain. Our results indicate that both filters and sponge tissue recovered a substantial and comparable number of taxa (84 and 66, respectively), spanning nine phyla. A greater number of taxa was identified in filter samples, followed by sponge tissue samples when host‐blocking primers were used. However, different types of communities were recovered for each method, with zooplankton being more highly represented in filter samples. Therefore, the use of both methods is recommended to obtain a more realistic composition of the metazoan community. Finally, we highlight the potential of freshwater sponges as natural eDNA samplers and offer key considerations to improve their efficiency in future research.