Efficacy of environmental DNA metabarcoding in monitoring fish faunas in California estuaries and lagoons: a preliminary assessment

We evaluated the efficacy of environmental DNA (eDNA) metabarcoding in monitoring fish communities in California estuaries. Our goals included identifying spatial and seasonal faunal trends, comparing disparate systems, assessing similarity to known community data, and exploring limitations of the eDNA method. To this end, we surveyed fish communities from four estuaries and lagoons distributed in northern, central, and southern California across two seasons using eDNA from water samples. These surveys recovered 64 fish species across 36 families, with faunal assemblages reflecting known regional, local, and seasonal trends between estuaries. eDNA recovered communities similar to those described in literature, often recording more species than were reported in previous site-specific studies. Non-estuarine species recovered were attributable to identifiable exogenous sources of DNA, including wash-in of pelagics or transport in cattle feed. Results were further expanded by an amplicon sequence variant (ASV) based approach, which identified some limitations in taxonomic assignment, but also highlighted regional and temporal genetic diversity within Pacific staghorn sculpin ( Leptocottus armatus ) and steelhead trout ( Oncorhynchus mykiss ). Overall, eDNA presents an effective and efficient method for monitoring estuarine fish communities in California, and has potential to augment traditional sampling methods with finer-scale genetic data.