Northeast Pacific eelgrass fish communities characterized by environmental DNA represent local diversity and show habitat specificity

Fish biodiversity is an important indicator of ecosystem health and a priority for the National Park Service in Drakes Estero, a shallow estuary within Point Reyes National Seashore, Marin County, California. However, fish diversity has yet to be described following the removal of oyster aquaculture infrastructure within Drakes Estero from 2016 to 2017. We used environmental DNA (eDNA) to characterize fish biodiversity within Drakes Estero. We amplified fish eDNA with MiFish primers and classified sequences with a 12S rRNA reference database. We identified 110 unique operational taxonomic units (OTUs, at 97% similarity) within the estuary from 40 samples across 4 sites. From these 110 OTUs, we identified 9 species and 13 taxonomic groups at the genus, family, order, or class level within the estuary. Species-level assignments are limited by a lack of representative sequences targeted by the MiFish primers for 42% of eelgrass fishes in our region that we identified from a literature review in the Northeast Pacific (NEP) from Elkhorn Slough to Humboldt Bay. Despite this limitation, we identified some common Drakes Estero fishes with our eDNA surveys, including the three-spined stickleback (Gasterosteus aculeatus), Pacific staghorn sculpin (Leptocottus armatus), surfperches (Embiotocidae), gobies (Gobiidae), and a hound shark (Triakidae). We also compared fish biodiversity within the estuary with that from nearby Limantour Beach, a coastal site. Limantour beach differed in community composition from Drakes Estero and was characterized by high relative abundances of anchovy (Engraulis sp.) and herring (Clupea sp.). Thus, we can distinguish estuarine and non-estuarine sites (<10 km away) with eDNA surveys. Further, eDNA surveys accounted for greater fish diversity than seine surveys conducted at one site within the estuary. Environmental DNA surveys will likely be a useful tool to monitor fish biodiversity across eelgrass estuaries in the Northeast Pacific, especially as reference databases become better populated with regional species.