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Development of a coastal species characterization approach using environmental DNA (eDNA) using the marker Mifish (12S)
Species characterization by environmental DNA (eDNA) is a method that allows the use of DNA released into the environment by organisms from various sources (secretions, faeces, gametes, tissues, etc.). It is a complementary tool to standard sampling methods for the identification of biodiversity. This project provides a list of fish and marine mammal species whose DNA has been detected in water samples collected between 2019 and 2021 using the mitochondrial marker MiFish (12S). The surveys were carried out in the summer of 2019 (July 14-18) and (July 30 - August 5), in the fall of 2020 (October 27-28) and in the summer-fall of 2021 (May 31 - June 3 ) and (August 24-25) between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 1-50 meters depth in 91 stations, with 1 to 3 replicates per station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissues or PowerWater extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. The libraries were prepared either by Génome Québec (2019, 2020) or by the Genomics Laboratory of the Maurice-Lamontagne Institute (2021), then sequenced on a NovaSeq 4000 PE250 system by Génome Québec. The bioinformatics analysis of the sequences obtained was carried out using an analysis pipeline developed in the genomics laboratory. A first step made it possible to obtain a table of molecular operational taxonomic units (MOTU) using the cutadapt software for the removal of the adapters and the R package DADA2 for the filtration, the fusion, removal of chimeras and compilation of data. The MOTUs table was then corrected using the R package metabaR to eliminate the tag-jumping and take contaminants into consideration. Samples showing a strong presence of contaminating MOTUs were removed from the dataset. The MOTUs were also filtered to remove all remaining adapter sequences and also retain only those of the expected size (around 170 bp). Finally, taxonomic assignments were made on the MOTUs using the BLAST+ program and the NCBI-nt database. Taxonomic levels (species, genus or family) were assigned using a best match method (Top hit), with a threshold of 95%. Only assignments at the level of fish and marine mammals were considered, and the taxa detected were compared to a list of regional species, and corrected if necessary. The species detections of the different replicas have been combined. The file provided includes generic activity information, including site, station name, date, marker type, assignment types used for taxa identification, and a list of taxa or species. The list of taxa has been verified by a biodiversity expert from the Maurice-Lamontagne Institute. This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Data Program under the Oceans Protection Plan. This initiative aims to acquire baseline environmental data that contributes to the characterization of significant coastal areas and supports evidence-based assessments and management decisions to preserve marine ecosystems. Data were also published on SLGO platform : https://doi.org/10.26071/ogsl-2239bca5-c24a
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Development of a coastal species characterization approach using environmental DNA (eDNA) using the marker COI
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Species characterization by environmental DNA (eDNA) is a method that allows the use of DNA released into the environment by organisms from various sources (secretions, faeces, gametes, tissues, etc.). It is a complementary tool to standard sampling methods for the identification of biodiversity. This project provides a list of invertebrates species whose DNA has been detected in water samples collected at 2018 using the marker COI. The surveys were carried out in the summer of 2018 from August 11 to 14, between Forestville and Godbout (Haute-Côte-Nord). Sampling was carried out between 9-52 meters depth in 40 stations with one sample par station. Two liters of water were filtered through a 1.2 µm fiberglass filter. DNA extractions were performed with the DNeasy Blood and Tissue extraction kit (Qiagen). Negative field, extraction and PCR controls were added at the different stages of the protocol. Libraries at the COI locus were prepared by Genome Quebec and sequenced on an Illumina MiSeq PE250 system. The bioinformatics analysis of the sequences obtained was carried out using an in-house analysis pipeline as reported in Bourret et al. 2022. A first step made it possible to obtain a molecular operational taxonomic unit table (MOTU) using the cutadapt software for the removal of the adapters and the DADA2 R package for the filtration, fusion, chimera removal and data compilation. The MOTUs table was subsequently corrected by taking into account the negative controls, where the number of observations in the latter was removed from the linked samples. Singleton MOTUs have also been removed. Finally, the taxonomic assignments were carried out on the MOTUs using the IDTAXA classifier (present in the DECIPHIER R package) using a training set trained on the COI reference bank for Golf St-Laurent (GSL-rl v1.0, https://github.com/GenomicsMLI-DFO/MLI_GSL-rl) and a threshold of 40. Detections with an “Unreliable due to gaps” category were reported at the genus level only. The file provided includes generic activity information, including site, station name, date, marker type, assignment types used for taxa identification, and a list of taxa or species. The list of taxa has been verified by a biodiversity expert from the Maurice-Lamontagne Institute. This project was funded by Fisheries and Oceans Canada's Coastal Environmental Baseline Data Program under the Oceans Protection Plan. This initiative aims to acquire baseline environmental data that contributes to the characterization of significant coastal areas and supports evidence-based assessments and management decisions to preserve marine ecosystems. Data are also available on SLGO platform : https://doi.org/10.26071/ogsl-cd4c205b-f63b
Taxonomic composition of environmental DNA acquired by filtration from the St. Regis River, New York
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Environmental DNA (eDNA) surveys have become important tools for monitoring aquatic biodiversity. Barcode sequencing of eDNA generates community profiles that, while potentially biased in both capture and amplification, can nonetheless yield high information content per unit cost. While factors affecting eDNA capture and amplification have been heavily studied, watershed-scale assessments of fish communities and our confidence in such have been less frequent. We performed an initial watershed-scale characterization of fish eDNA using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our bioinformatic approach included 1) direct estimation of sequencing error from unambiguous mappings (alignments) and simulation of error in taxonomic assignment under various mapping criteria; 2) binning of species based on inferred assignment error rather than by taxonomic rank; and 3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented for the St. Regis River, New York, United States, which supports a valuable recreational fishery and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. We found that 300 mL drawn through 25-mm filters yielded greater than 5 ng/µL DNA at most sites in August and September, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state-level checklist into 85 single-species bins and seven multispecies bins. Of 48 taxonomic bins actually observed in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants post-collection. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence.
Taxonomic composition of environmental DNA acquired by filtration from the St. Regis River, New York
공공데이터포털
Environmental DNA (eDNA) surveys have become important tools for monitoring aquatic biodiversity. Barcode sequencing of eDNA generates community profiles that, while potentially biased in both capture and amplification, can nonetheless yield high information content per unit cost. While factors affecting eDNA capture and amplification have been heavily studied, watershed-scale assessments of fish communities and our confidence in such have been less frequent. We performed an initial watershed-scale characterization of fish eDNA using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our bioinformatic approach included 1) direct estimation of sequencing error from unambiguous mappings (alignments) and simulation of error in taxonomic assignment under various mapping criteria; 2) binning of species based on inferred assignment error rather than by taxonomic rank; and 3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented for the St. Regis River, New York, United States, which supports a valuable recreational fishery and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. We found that 300 mL drawn through 25-mm filters yielded greater than 5 ng/µL DNA at most sites in August and September, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state-level checklist into 85 single-species bins and seven multispecies bins. Of 48 taxonomic bins actually observed in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants post-collection. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence.
국립해양생물자원관 해양생물종정보 서비스
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학명, 국명, 과명 등을 기준으로 해양생물 종의 분류체계 및 개요, 국내 분포, 생태 등의 상세정보를 제공하는 서비스입니다.
Detections of marine fauna using environmental DNA metabarcoding of seawater samples from the northern Gulf of America
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We sampled seawater from nine mesophotic reef sites in the Pinnacles Trend and DeSoto Rim areas in the northern Gulf of America in October 2022 to complement and inform restoration investments for coral communities. Four primer sets were used to amplify environmental DNA (eDNA) from seawater, targeting metazoans, eukaryotic plankton and protists, corals, and fishes. Across all markers, four Kingdoms were detected including Animalia, Chromista, Plantae, and Protista based on 11,793 amplicon sequence variants (ASVs). Within Kingdom Animalia, 11 Phyla containing 33 Classes were detected from the surface to the seafloor. Corals and fishes, which are of particular interest, were detected at all sites and in congruence with previous video sightings for the area.In some cases eDNA analyses were able to identify fish and coral to a lower taxonomic identification than was possible through video analyses. This study provides evidence that the addition of an eDNA component to habitat characterization and biodiversity assessments can provide essential information about ecosystem dynamics from the surface, through the water column, to the benthic community.
eDNA metabarcoding enriches traditional trawl survey data for monitoring biodiversity in the marine environment
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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
Coastal Environmental Baseline Program (Newfoundland Region), Placentia Bay Nearshore Fish Community Sampling
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This project was completed by the Coastal Environmental Baseline Program (Coastal and Freshwater Ecology Section) in the Newfoundland and Labrador Science Branch of Fisheries and Oceans Canada (DFO). The nearshore fish and invertebrate community was sampled annually in Placentia Bay at 14 sites for 5 years (2018 – 2022). The objective of this program was to collect data on juvenile fish (specifically Atlantic cod) communities and habitats within Placentia Bay. The sites and timing (October) were selected based on historical sampling. There were several data types collected during each of these sampling trips. Boat-based beach seining was used to collect data on fish and invertebrate diversity, abundance, distribution, and size. Visual transects were used to identify vegetation and substrate (habitat) types and proportions at seine sites. CTD profiles (temperature, conductivity, depth, and salinity) were obtained using a castaway CTD. Finally, eDNA samples were collected at each site (2018-2021) to obtain complementary information on the presence of juvenile fish and other species present. This record contains the geographic locations of the 14 sites, and information on the timing and type of data collected at each site.
NESP MaC Project 1.4 - Characterising values and identifying indicators and metrics of fish and benthic assemblages within the Capes region of the South-west Corner Marine Park (UWA)
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This record provides an overview of the NESP Marine and Coastal Hub bridging study - "Characterising values and identifying indicators and metrics of fish and benthic assemblages within the Capes region of the South-west Corner Marine Park". For specific data outputs from this project, please see child records associated with this metadata. Inventory surveys of Australian Marine Parks (AMPs) provide a broad description of the natural assets that exist in Commonwealth waters. These data can be further explored to identify biological indicators and metrics to cost-effectively monitor the AMPs and inform the AMP Monitoring Evaluation Reporting and Improvement (MERI) system. Historical surveys conducted under the NESP Marine Biodiversity Hub inventoried natural values and ecosystem components in selected AMPs. They developed and tested standardised survey techniques to allows scientists and park managers to identify and measure the status of natural values and ecosystem components. A recent Marine Biodiversity Hub survey conducted detailed bathymetric and visual sampling of key seafloor habitat and fish assemblages in the Capes region of South-west Corner Marine Park (Western Australia). This project analysed the Capes survey data to characterise and predict the broader distribution of natural values and ecosystem features, and to identify relevant indicators of fish and benthic assemblages for Park management. The results are presented alongside summaries of existing knowledge on natural, socio-economic, and cultural values, as well as human pressures. Recommendations include establishing national and international monitoring benchmarks and incorporating survey guidance from Traditional Owners. Outputs • Habitat annotations for AUV & drop camera imagery [dataset] • Geomorphic features map using existing fine-scale bathymetry of the Capes' National Park and Special Protection zones [dataset] • Habitat map using existing fine-scale bathymetry coverage (validated by drop camera surveys) [dataset] • Annotations of fish and shark size, abundance and diversity from stereo-BRUV deployments [dataset] • Science communication article for the Australian Marine Parks Science Atlas [written] • South-west Corner Marine Park survey report [written]
NESP MaC Project 1.4 - Characterising values and identifying indicators and metrics of fish and benthic assemblages within the Capes region of the South-west Corner Marine Park (UWA)
공공데이터포털
This record provides an overview of the NESP Marine and Coastal Hub bridging study - "Characterising values and identifying indicators and metrics of fish and benthic assemblages within the Capes region of the South-west Corner Marine Park". For specific data outputs from this project, please see child records associated with this metadata. Inventory surveys of Australian Marine Parks (AMPs) provide a broad description of the natural assets that exist in Commonwealth waters. These data can be further explored to identify biological indicators and metrics to cost-effectively monitor the AMPs and inform the AMP Monitoring Evaluation Reporting and Improvement (MERI) system. Historical surveys conducted under the NESP Marine Biodiversity Hub inventoried natural values and ecosystem components in selected AMPs. They developed and tested standardised survey techniques to allows scientists and park managers to identify and measure the status of natural values and ecosystem components. A recent Marine Biodiversity Hub survey conducted detailed bathymetric and visual sampling of key seafloor habitat and fish assemblages in the Capes region of South-west Corner Marine Park (Western Australia). This project analysed the Capes survey data to characterise and predict the broader distribution of natural values and ecosystem features, and to identify relevant indicators of fish and benthic assemblages for Park management. The results are presented alongside summaries of existing knowledge on natural, socio-economic, and cultural values, as well as human pressures. Recommendations include establishing national and international monitoring benchmarks and incorporating survey guidance from Traditional Owners. Outputs • Habitat annotations for AUV & drop camera imagery [dataset] • Geomorphic features map using existing fine-scale bathymetry of the Capes' National Park and Special Protection zones [dataset] • Habitat map using existing fine-scale bathymetry coverage (validated by drop camera surveys) [dataset] • Annotations of fish and shark size, abundance and diversity from stereo-BRUV deployments [dataset] • Science communication article for the Australian Marine Parks Science Atlas [written] • South-west Corner Marine Park survey report [written]
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