Application of environmental DNA as a tool for detecting intertidal habitat use by forage fish

Abstract

Many coastal forage fish species spend most of their life history using the water column, but some species such as Pacific Sand Lance (Ammodytes personatus) and Surf Smelt (Hypomesus pretiosus) have a requirement for intertidal sediments for spawning and or burying. Detection of suitable but typically uncommon intertidal habitats for spawning has historically relied on extensive visual surveys for eggs from large sand samples. In the present study, we developed and validated two new non-destructive qPCR-based tools for detecting Sand Lance and Surf Smelt eDNA from small sand samples. A total of 279 composite transect sand samples were collected from 101 beaches and were tested for eDNA sample integrity using the IntegritE-DNATM test. Initial testing showed that all but 42 of 46 samples passed after an inhibitor clean-up step. Of the 101 beaches sampled 275 times, there were 111 detections of Sand Lance on 52 beaches, and there were 13 detections of Surf Smelt on 10 beaches. One hundred and eighty-one samples were paired with visual egg counts and 76 (42%) of these tested positive for Sand Lance while 9 of 132 (7%) samples tested positive for Surf Smelt. For the 27 paired samples with two or more Sand Lance eggs visually detected there was a significant positive correlation (r = 0.694, p = 0.0001) with eDNA copies per liter suggesting that a larger Sand Lance presence is easily and reliably detected using eDNA. The methods and approaches described herein will serve as a foundation for broad application of eDNA approaches for forage fish species that utilize intertidal benthic habitats.