Investigating fine-scale breeding habitat use by amphibians in a continuous wetland using environmental DNA

Designing effective conservation plans to protect species from extinction requires a better understanding of their ecology. Conventional methods used to investigate habitat use are time consuming, and detectability of cryptic species is often insufficient. Environmental DNA (eDNA)-based approaches now provide an alternative for ecosystems monitoring and assessment. Nevertheless, to our knowledge, such methods have never been applied to investigate habitat use at a fine scale in a continuous wetland environment. Here, we used an eDNA metabarcoding approach to characterize the breeding habitat use of local amphibian species in a wet meadow expanse along the southern shore of Lake Neuchatel, Switzerland. We retrieved DNA from six out of the seven species expected to be present. We tested the influence of six abiotic environmental variables on overall species communities as well as individual species occurrences. We showed that the main factor structuring species communities was water temperature, and that the distribution of three amphibian species was associated with several environmental variables. Our results indicate that the eDNA approach is a promising tool to study species ecology at a small scale in continuous wetland habitats.