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Aquaculture Environment Interactions

    AEI prepress abstract   -  DOI:

    Exploring video and eDNA metabarcoding methods to assess oyster aquaculture cages as fish habitat

    Renee Mercaldo-Allen, Paul Clark, Yuan Liu, Gillian Phillips, Dylan Redman, Peter J. Auster, Erick Estela, Lisa Milke, Alison Verkade, Julie M. Rose*

    *Corresponding author:

    ABSTRACT: Multi-tiered oyster aquaculture cages may provide habitat for fish assemblages similar to natural structured seafloor. Methods were developed to assess fish assemblages associated with aquaculture gear and boulder habitat using underwater video census combined with environmental DNA (eDNA) metabarcoding. Action cameras were mounted on 3 aquaculture cages at a commercial eastern oyster farm (cage) and among 3 boulders on a natural rock reef (boulder) from June to August 2017 in Long Island Sound, USA. Interval and continuous video recording strategies were tested. During interval recording, cameras collected 8-minute video segments hourly from 7 am to 7 pm on cages only. Continuous video was also collected for 2-3 hours on oyster cages and boulders. Data loggers recorded light intensity and current speed. Seawater was collected for eDNA metabarcoding on the reef and farm. MaxN measurements of fish abundance were calculated in video and seven fish species were observed. Black sea bass Centropristis striata, cunner Tautogolabrus adspersus, scup Stenotomus chrysops, and tautog Tautoga onitis were the most abundant species observed in both oyster cage and boulder videos. In continuous video, black sea bass, scup, and tautog were observed more frequently and at higher abundance on the cage farm, while cunner were observed more frequently and at higher abundance on boulders within the rock reef. eDNA metabarcoding detected 42 fish species at the farm and reef. Six species were detected using both methods. Applied in tandem, video recording and eDNA provided a comprehensive approach for describing fish assemblages in difficult to sample structured oyster aquaculture and boulder habitats.