Background: Mojave Desert springs are fragile ecosystems, hosting endemic plants and animals, which are threatened by the increasing human demand for water and climate change. To develop management practices that will protect the groundwater-dependent ecosystems at Mojave Desert springs, real-time, low cost biodiversity monitoring and assessments are required. Environmental DNA (eDNA) metabarcoding uses DNA shed from organisms (e.g. skin cells, feces, pollen, etc.) that is present in water, air, soil, or sediment samples to assess community composition. This approach can increase the detection sensitivity for rare and elusive species, compared to expensive and time-consuming conventional methods, which also require taxonomic expertise.

Aims: This study tests the effectiveness of eDNA techniques in capturing the observed Mojave Desert spring biodiversity in the winter and spring of 2019 at four distinct, naturally occurring springs. We also test the utility of sample types (water versus sediment) for capturing biodiversity.

Results: We found that each of the four Mojave Desert springs supports a unique biological community. Sediment samples contained the greatest biodiversity, but all sample types captured species observed in the field by humans or camera-traps. We also found no statistical difference in species richness captured in winter and spring except for the Cytochrome Oxidase I marker, for which winter had greater biodiversity.

Conclusion: This study supports the use of eDNA metabarcoding as an effective tool to mirror observation by human observers of ecological communities in desert springs. It demonstrates the importance of appropriately timing eDNA field sampling, primer selection, and using field-based surveys of wildlife and plants in addition to eDNA detection. This study also identified gaps in reference sequence databases for Mojave biodiversity and encourages collaboration of eDNA researchers with managers for effective conservation management plans.