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.

中文翻译：

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探索视频和 eDNA 元条形码方法来评估牡蛎养殖网箱作为鱼类栖息地

摘要：多层牡蛎养殖网箱可以为类似于自然结构海底的鱼类组合提供栖息地。开发了使用水下视频普查结合环境 DNA (eDNA) 元条形码评估与水产养殖设备和巨石栖息地相关的鱼类组合的方法。动作相机安装在商业东部牡蛎Crassostrea virginica 的3 个水产养殖网箱上2017 年 6 月至 8 月，美国长岛湾的农场（“笼子”）和天然岩礁（“巨石”）上的 3 块巨石。测试了间隔和连续视频录制策略。在间隔记录期间，摄像机仅在笼子上从 07:00 到 19:00 每小时收集 8 分钟的视频片段。还在牡蛎笼和巨石上收集了 2-3 小时的连续视频。数据记录器记录光强度和当前速度。收集海水用于在珊瑚礁和农场上进行 eDNA 元条形码编码。在视频中计算了鱼类丰度的 MaxN 测量值，并观察到了 7 种鱼类。黑鲈Centropristis striata、 cunner Tautogolabrus adspersus、 scup Stenotomus chrysops和tautog Tautoga onitis是牡蛎笼和巨石视频中观察到的最丰富的物种。在连续视频中，在网箱养殖场更频繁地观察到黑鲈、scup 和 tautog，并且观察到的丰度更高，而在岩礁内的巨石上观察到的频率更高，丰度更高。eDNA 元条形码在养殖场和珊瑚礁中检测到 42 种鱼类。使用这两种方法检测到六个物种。视频记录和 eDNA 的串联应用为描述难以采样的结构化牡蛎养殖和巨石栖息地中的鱼类组合提供了一种综合方法。