Estuarine fishes associated with intertidal oyster reefs characterised using environmental DNA and baited remote underwater video

It has been widely shown that oyster reefs enhance local biodiversity and fisheries production. Therefore, in this study fish assemblages from oyster reefs were compared to sandy habitats using environmental DNA (eDNA) metabarcoding and baited remote underwater video. Fish diversity from eDNA was characterised using three metabarcoding assays - two that target the mitochondrial 16S region and one that targets the 12S region. Fish assemblages differed with each assay, as well as to that detected by BRUVs. Overall, 112 fish genera were identified, with 78 more genera detected using eDNA metabarcoding than those observed with BRUVs. Both eDNA and BRUVs resolved a higher number of fish genera associated with oyster reefs than with sand sites, and a different fish composition between habitats was also resolved using each method. Furthermore, eDNA was shown to be useful towards characterising the gamma diversity of the estuary, due to the intertidal nature and hydrodynamics of the system, as well as the alpha diversity associated with oyster reefs and sand sites.

已有大量研究证实，牡蛎礁（oyster reefs）可提升本地生物多样性与渔业产量。为此，本研究采用环境DNA（environmental DNA, eDNA）宏条形码技术与诱饵式远程水下视频（baited remote underwater video, BRUVs）两种方法，对比了牡蛎礁与沙质栖息地的鱼类群落组成。本研究通过三套宏条形码检测方案对eDNA检出的鱼类多样性进行解析：其中两套靶向线粒体16S区域，一套靶向线粒体12S区域。不同检测方案得到的鱼类群落组成存在差异，与BRUVs的检测结果亦不相同。整体而言，本次研究共鉴定出112个鱼类属，其中通过eDNA宏条形码技术检出的鱼类属数量较BRUVs多78个。eDNA与BRUVs均检出了更多与牡蛎礁相关的鱼类属，而非沙质栖息地；两种方法均解析出不同栖息地间鱼类群落组成的差异。此外，鉴于该系统具备潮间带特性与水动力特征，eDNA不仅可用于表征与牡蛎礁、沙质栖息地相关的α多样性（alpha diversity），还可用于解析河口湾的γ多样性（gamma diversity）。