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eDNA metabarcoding enriches traditional trawl survey data for monitoring biodiversity in the marine environment
Marine Protected Areas require comprehensive monitoring to ensure objectives are achieved; however, monitoring natural ecosystems at scale is challenged by the biodiversity it aims to measure. Environmental DNA (eDNA) metabarcoding holds promise to address this monitoring challenge. We conducted paired sampling at 54 sites for fish and invertebrate assemblages in the Northwest Atlantic using groundfish trawls and eDNA metabarcoding of benthic seawater using four genetic markers (12S rRNA, 16S rRNA, 18S rRNA, and CO1). Compared to trawling, eDNA detected similar patterns of species turnover, larger estimates of gamma diversity, and smaller estimates of alpha diversity. A total of 63.6% (42/66) of fish species captured by trawling were detected by eDNA, along with an additional 26 species. Of the 24 missed detections by eDNA, 12 were inevitable as they lacked reference sequences. Excluding taxa assigned to higher than species level and those without a species name, 23.6% (17/72) of invertebrate species captured by trawling were detected by CO1, which detected an additional 98 species. We demonstrate that eDNA is capable of detecting patterns of community assemblage and species turnover in an offshore environment, emphasizing its strong potential for a non-invasive, comprehensive, and scalable tool for biodiversity monitoring supporting marine conservation programmes. Cite this data as: Jeffery, N., Rubidge, E., Abbott, C., Westfall, K., Stanley, R. (2024): Data of: eDNA metabarcoding enriches traditional trawl survey data for monitoring biodiversity in the marine environment. Published: August 2024. Coastal Ecosystems Science Division, Fisheries and Oceans Canada, Dartmouth, N.S. https://open.canada.ca/data/en/dataset/43a91ba7-8025-4330-88db-db14022d729d
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Environmental DNA detections from deep seafloor habitats in the California Current Large Marine Ecosystem
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Environmental DNA (eDNA) metabarcoding may have utility in biodiversity surveys of marine environments, particularly for small, rare, or cryptic taxa that are more difficult to study using traditional methods (e.g., trawling and visual surveys). For this study, we used an eDNA metabarcoding approach to characterize biodiversity in the above-seafloor water column across three West Coast-based research cruises, focusing on understudied deep sea habitats (~800-3200 m). Approximately 100 eDNA seawater samples were collected during three research expeditions using Niskin bottles that were either mounted on remotely operated vehicles (ROVs, most samples) or using a conductivity/temperature/depth (CTD) rosette with niskin bottles. The research expeditions targeted deep seafloor habitats in the California Current Large Marine Ecosystem (CCLME) of potential biological/geological interest from three regions: Northern California, plus Northern and Southern Cascadia. Samples then underwent DNA extraction, amplification, and sequencing, as described in the methods. Taxonomy was assigned using the bioinformatic procedures described in the methods.
Using eDNA as a viable fish monitoring approach in Northern Gulf estuarine habitats
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A web-browser enabled (HTML) document and Excel file (Water quality parameters and DNA Sequence Reads) that contain detailed data used to inform results presented in publication. This dataset is associated with the following publication: Reschke, E., R. Ennis, and L. Harwell. Using eDNA as a viable fish monitoring approach in Northern Gulf estuarine habitats. ENVIRONMENTAL MONITORING AND ASSESSMENT. Springer, New York, NY, USA, 197: 1145, (2025).
2023 Environmental DNA (eDNA) Baseline to Monitor Intertidal Biodiversity in Waters Adjacent to Mixed Coarse Substrate Habitats Across the Boston Harbor Islands
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This data set contains environmental DNA (eDNA) data enumerating the presence of intertidal marine vertebrates, invertebrates, and macro algae collected across 5 islands with 10 sites in the Boston Harbor in 2023. This data was collected using water samples collected in association with other intertidal biodiversity monitoring protocols developed specifically for the mixed coarse substrate habitat found on the inner islands of Boston Harbor, including Gallops, Georges, Lovell (alternatively known as Lovells Island), Peddocks, and Thompson Island. Species were identified using an eDNA metabarcoding approach targeting the 12s (vertebrate) and 18s (invertebrate and macro algae) gene regions. Total read count scores for species detected are reported, with scores greater than 1 signaling a positive detection, and scores of 0 signaling no detection. Data included in this release was used to determine community composition and diversity metrics across high biodiversity and erosional sites for the 5 islands.
해양수산부 국가해양생태계종합조사 무척추동물
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국가해양생태계종합조사는 기존의 개별조사사업(연안습지기초조사, 해양생태계기본조사 등)을 하나로 통합하여 해양생태계의 종합적이고 장기적이며 체계적인 분석이 가능하도록 개편한 조사로, 2015년도 이후로 지속적인 모니터링을 통해 우리나라 전 연안의 생태계 기반 관리를 위한 기초자료 생산을 담당하고 있습니다. 국가해양생태계종합조사 무척추동물 서비스는 조사년도최소값, 조사년도최대값, 기본중점구분명, 조사항목명, 조사정선번호, 채집시작일자, 채집종료일자를 검색 조건으로 사용하여 조사년도, 사업구분코드, 조사사업구분코드, 기본중점구분명, 조사항목명, 조사정선번호, 조사정점번호, 조사방법명, 채집일자, 채집시분, 관측수심, 반복횟수 , 조간대내용, 문영문명, 강영문명, 목영문명, 과영문명, 속영문명, 종영문명, 아종영문명, 종약어영문명, 종명, 학명, 국명, 개체수, 습중량, 건중량, 피도율, 출현내용, 비고내용 데이터를 검색할 수 있습니다.
해양수산부 국가해양생태계종합조사 저서동물
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국가해양생태계종합조사는 기존의 개별조사사업(연안습지기초조사, 해양생태계기본조사 등)을 하나로 통합하여 해양생태계의 종합적이고 장기적이며 체계적인 분석이 가능하도록 개편한 조사로, 2015년도 이후로 지속적인 모니터링을 통해 우리나라 전 연안의 생태계 기반 관리를 위한 기초자료 생산을 담당하고 있습니다. 국가해양생태계종합조사 저서동물 서비스는 조사구분명, 조사년도최소값, 조사년도최대값, 기본중점구분명, 조사항목명, 조사정선번호, 채집시작일자, 채집종료일자를 검색 조건으로 사용하여 조사년도, 사업구분코드, 조사사업구분코드, 기본중점구분명, 조사항목명, 조사정선번호, 조사정점번호, 조사방법명 등의 데이터를 검색할 수 있습니다.
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