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

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.

Oyster aquaculture cages provide fish habitat similar to natural structure with minimal differences based on farm location

“…Growing anecdotal and scientific evidence suggests that aquaculture gear may provide valuable habitat and ecosystem services for fish (e.g., Ferriss et al, 2021;Mercaldo-Allen et al, 2021;Shinn et al, 2021;Theuerkauf et al, 2021). Off-bottom cages, deployed on the seafloor but elevated several inches off the substrate, are increasingly employed for shellfish aquaculture along the eastern seaboard.…”

“…Off-bottom cages, deployed on the seafloor but elevated several inches off the substrate, are increasingly employed for shellfish aquaculture along the eastern seaboard. These cages produce more oysters on a smaller spatial footprint than traditional on-bottom cultivation methods where oysters are grown on the seafloor (e.g., Walton et al, 2013;Archer et al, 2014;Scuderi and Chen, 2019;Mercaldo-Allen et al, 2021). Multi-tiered cages hold oysters on shelves in mesh bags or inside stacked trays and create physical structures with high vertical relief.…”

“…The scale of aquaculture operations, and the number, proximity and footprint of gear on the seafloor may influence the habitat value conferred by shellfish farms (Dumbauld et al, 2009). Cage size and configuration varies, affecting the amount of added structure, for example, standard shelf and bag cages (1.22 x 0.91 x 0.61 m) typically hold 3 shelves with oysters, but much larger cages are also used by shellfish growers, having as many as 20 stacked trays, and could contribute even higher relief habitat (Mercaldo-Allen et al, 2020;Mercaldo-Allen et al, 2021). Clusters of farms within the same region can provide contiguous patches of habitat that support movement of transient species (Erbland and Ozbay, 2008).…”

“…Small, rugged, waterproof digital or "action" cameras (Struthers et al, 2015) offer a relatively low cost and easy way to collect high quality video that is readily accessible to researchers and citizen scientists alike (e.g., Florisson et al, 2018;Zarco-Perello and Enrıquez, 2019;Ulrich and Bonar, 2020). Recently these video methods have been extended to aquaculture gear and naturally occurring habitat (e.g., Muething et al, 2020;Ferriss et al, 2021;Mercaldo-Allen et al, 2021;Shinn et al, 2021).Video recording of fish interactions with aquaculture gear and natural structure can reveal how fish species at various life history stages use these habitats, produce indices of fish abundance, discern patterns of community composition, identify habitatspecific behaviors and visualize provision of ecosystem services. However, video analysis is extremely labor-intensive, and this recent research has had spatial and/or temporal limitations that constrained the conclusions that could be drawn from the data.…”

Environmental DNA reveals fine‐scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft‐ and hard‐bottom habitats

“…BRUVS offer an opportunity in this regard, as the video systems can be rapidly deployed at the exact location where eDNA is being sampled, while the bait may attract individuals in the vicinity that were also captured in the eDNA signal. Comparisons between eDNA and BRUVS have so far focused on biodiversity and community assessments (Boussarie et al, 2018; Jeunen, Lamare, et al, 2020; Marques et al, 2021; Mercaldo‐Allen et al, 2021; Stat et al, 2019), yet potential correlations between species‐specific qPCR detection and abundances recorded from BRUVS remain, to the best of our knowledge, untested.…”