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Aquaculture Environment Interactions

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AEI 13:277-294 (2021)  -  DOI: https://doi.org/10.3354/aei00408

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

Renee Mercaldo-Allen1, Paul Clark1, Yuan Liu1,2, Gillian Phillips1,2, Dylan Redman1, Peter J. Auster3, Erick Estela1, Lisa Milke1, Alison Verkade4, Julie M. Rose1,*

1NOAA Fisheries, Northeast Fisheries Science Center, Milford Laboratory, 212 Rogers Avenue, Milford, CT 06460, USA
2A.I.S. Inc., 540 Hawthorn Street, North Dartmouth, MA 02747, USA
3University of Connecticut Department of Marine Sciences & Mystic Aquarium, 1080 Shennecossett Road, Groton, CT 06340, USA
4NOAA Fisheries, Greater Atlantic Regional Fisheries Office, Habitat Conservation Division, 55 Great Republic Drive, Gloucester, MA 01930, USA
*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 Crassostrea virginica 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 min video segments hourly from 07:00 to 19:00 h on cages only. Continuous video was also collected for 2-3 h 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 7 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.


KEY WORDS: Oyster aquaculture cages · Boulders · Rock reef · Video · eDNA · Environmental DNA · MaxN · Finfish


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Cite this article as: Mercaldo-Allen R, Clark P, Liu Y, Phillips G and others (2021) Exploring video and eDNA metabarcoding methods to assess oyster aquaculture cages as fish habitat. Aquacult Environ Interact 13:277-294. https://doi.org/10.3354/aei00408

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