Fine Scale Depth Variation of eDNA Signatures: Informing Nearshore Coastal Marine Protected Area Monitoring

Keira Monuki, Zachary Gold and Paul H Barber, University of California, Los Angeles, Ecology and Evolutionary Biology, Los Angeles, CA, United States
To determine the effectiveness of marine protected areas (MPAs), comprehensive and standardized biodiversity monitoring is needed. However, current monitoring methods are costly, time-consuming, and can require extensive taxonomic expertise. Environmental DNA (eDNA) is a promising novel approach to rapidly and accurately survey biodiversity in marine ecosystems. However, key questions remain about the temporal, horizontal spatial and depth variation of eDNA signatures in nearshore marine environments, variation that could impact the utility of eDNA for marine ecosystem monitoring. This study examines eDNA signatures from sea water samples on three successive high tides from an offshore kelp forest along a depth gradient (0m, 1m, 5m, 9m, and 10m), as well as an adjacent beach habitat. These samples generated 21,045,099 reads and 19,721 amplicon sequence variants, representing 99 families, 178 genera, and 201 marine species. Both species richness and community assemblages varied across time, depth, and horizontal space. eDNA signatures varied on the order of hours, distinguished community differences on a vertical depth gradient of a few meters, and among samples from similar depths 137m apart. Furthermore, microhabitat depth preferences of marine vertebrates were reflected in the eDNA signatures, suggesting fine scale vertical sensitivity of this technique even in dynamic coastal marine environments. These results support the hypothesis that marine eDNA approaches are a highly localized snap shot of biodiversity, highlighting the need for increased temporal, horizontal spatial and depth sampling of eDNA approaches to accurately assess total marine biodiversity within nearshore MPAs.