Description
Enregistrements de données
Les données de cette ressource données d'échantillonnage ont été publiées sous forme dune Archive Darwin Core (Darwin Core Archive ou DwC-A), le format standard pour partager des données de biodiversité en tant quensemble dun ou plusieurs tableurs de données. Le tableur de données du cœur de standard (core) contient 296 enregistrements.
3 tableurs de données dextension existent également. Un enregistrement dextension fournit des informations supplémentaires sur un enregistrement du cœur de standard (core). Le nombre denregistrements dans chaque tableur de données dextension est illustré ci-dessous.
Cet IPT archive les données et sert donc de dépôt de données. Les données et métadonnées de la ressource sont disponibles pour téléchargement dans la section téléchargements. Le tableau des versions liste les autres versions de chaque ressource rendues disponibles de façon publique et permet de tracer les modifications apportées à la ressource au fil du temps.
Versions
Le tableau ci-dessous naffiche que les versions publiées de la ressource accessibles publiquement.
Comment citer
Les chercheurs doivent citer cette ressource comme suit:
Pochon X, Bomati E (2026). Citizens of the Sea Pacific Rally 2024 – eDNA Metabarcoding Dataset (Bact16S, Uni18S, COI, mt16SMarVer3). Citizens of the Sea Charitable Trust. Sampling event dataset. Published via GBIF New Zealand IPT. https://doi.org/[DOI to be assigned on publication]
Droits
Les chercheurs doivent respecter la déclaration de droits suivante:
L’éditeur et détenteur des droits de cette ressource est Citizens of the Sea. Ce travail est sous licence Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0.
Enregistrement GBIF
Cette ressource a été enregistrée sur le portail GBIF, et possède lUUID GBIF suivante : 67a99753-e500-4156-a902-aacd3ba234f4. Citizens of the Sea publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec lapprobation du GBIF New Zealand.
Mots-clé
Samplingevent; eDNA; environmental DNA; metabarcoding; amplicon sequencing; ASV; DADA2; citizen science; ocean biodiversity; Pacific Ocean; southwest Pacific; marine bacteria; marine eukaryotes; metazoans; marine vertebrates; 16S rRNA; 18S rRNA; COI; mitochondrial 16S; harmful algal blooms; pathogens; sampling event; TorpeDNA; Specimen
Contacts
- Créateur ●
- Personne De Contact
- Science Lead
https://orcid.org/0000-0001-9510-0407
- Créateur ●
- Personne De Contact
- Executive Director
Couverture géographique
Southwest Pacific Ocean, covering the Pacific Rally 2024 sailing route between Aotearoa New Zealand, Tonga and Fiji. All samples were collected from surface waters (1–3 m depth) by 26 sailing vessels travelling opportunistically along rally routes. The sampling area encompasses both national Exclusive Economic Zone (EEZ) waters of Aotearoa New Zealand, Tonga and Fiji, and international high seas (Areas Beyond National Jurisdiction). Sampling spanned 20 degrees of latitude (36.6°S to 16.7°S) and 13 degrees of longitude (173.4°E to 186.0°E, equivalent to 174°W). Bounding Coordinates: West: 173.4 East: -174.0 (186.0°E) North: -16.7 South: -36.6
| Enveloppe géographique | Sud Ouest [-90, -180], Nord Est [90, 180] |
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Couverture taxonomique
N/A
| Kingdom | Archaea, Bacteria |
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| Phylum | Chloroflexi, Patescibacteria, Chlamydiota, Marinimicrobia (SAR406 clade), SAR324 clade(Marine group B), Fibrobacterota, NB1-j, Poribacteria, Pseudomonadota, Thermodesulfobacteriota, Myxococcota, Planctomycetota, Bacillota, Acidobacteriota, Margulisbacteria, Chloroflexota, Proteobacteria, Cyanobacteria, Cyanobacteriota, Campylobacterota, Candidatus Eremiobacterota, Desulfobacterota, Verrucomicrobiota, Balneolota, Thermoplasmatota, Nitrospinota, Dadabacteria, Gemmatimonadota, Fusobacteriota, Nanoarchaeota, Bacteroidota, PAUC34f, WPS-2, Actinobacteriota, Actinomycetota, Campilobacterota, Crenarchaeota, Firmicutes, Spirochaetota, Sumerlaeota, Bdellovibrionota |
| Class | Nitrososphaeria, Phycisphaerae, Balneolia, BD7-11, SGST604, Nanoarchaeia, Thermoplasmata, Thermoanaerobaculia, Bacteriovoracia, Saccharimonadia, Dadabacteriia, Bdellovibrionia, Verrucomicrobiia, Desulfuromonadia, Rhodothermia, Sumerlaeia, Anaerolineae, Subgroup 26, Verrucomicrobiae, Fusobacteriia, Sericytochromatia, Planctomycetes, Pla3 lineage, Lentisphaeria, Clostridia, KD4-96, Chlamydiae, Chlamydiia, vadinHA49, Nitrospinia, Kapabacteria, Polyangia, Ktedonobacteria, Oligoflexia, Polyangiia, Kiritimatiellia, Gracilibacteria, Kiritimatiellae, Pla4 lineage, ABY1, Holophagae, Campylobacteria, BD2-11 terrestrial group, JG30-KF-CM66, Parcubacteria, Dojkabacteria, Alphaproteobacteria, 028H05-P-BN-P5, Desulfobulbia, Leptospirae, OM190, Desulfarculia, Myxococcia, Actinobacteria, Bacteroidia, Dehalococcoidia, Incertae Sedis, Fibrobacteria, Bacilli, Gammaproteobacteria, Spirochaetia, Cyanobacteriia, Eremiobacteria, Vampirivibrionia, Acidimicrobiia |
Couverture temporelle
| Date de début / Date de fin | 2024-05-06 / 2024-12-03 |
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Données sur le projet
This dataset contains environmental DNA (eDNA) metabarcoding data collected during the Citizens of the Sea (CitSea) Pacific Rally 2024 citizen science voyage across the southwest Pacific Ocean. Between 6 May and 3 December 2024, a fleet of 26 sailing vessels collected surface water samples across more than 1.5 million km² of ocean between Aotearoa New Zealand, Tonga and Fiji, spanning 20 degrees of latitude (36.6°S to 16.7°S). Samples were collected using the TorpeDNA towable eDNA filtration device, which captures eDNA from surface waters while the vessel is underway at sailing speeds up to 12 knots. A total of 745 samples (including 78 field negative controls) were collected; after quality filtering, 708 samples were processed at Cawthron Institute (Nelson, Aotearoa New Zealand). Four metabarcoding assays were applied to each sample targeting distinct taxonomic groups: bacterial 16S rRNA V3-V4 (Bact16S), eukaryotic 18S rRNA V4 (Uni18S), mitochondrial cytochrome oxidase I (COI), and vertebrate-specific mitochondrial 16S rRNA (mt16SMarVer3). Paired-end sequencing was performed on Illumina NextSeq platforms across six sequencing runs. Bioinformatic processing used CUTADAPT and DADA2 for quality filtering and ASV generation, with taxonomic assignment against the SILVA, PR2, MIDORI and GenBank reference databases. After all quality filters, the final dataset comprised approximately 466 million high-quality reads and 34,197 unique amplicon sequence variants (ASVs) across 708 samples. The dataset documents a clear biogeographic gradient in community structure strongly correlated with sea surface temperature and chlorophyll-a concentration, the presence of putative harmful algal bloom (HAB)-forming microalgae and pathogenic bacteria across sampling latitudes, and the detection of 43 unique vertebrate taxa including five cetacean species, among them the IUCN Endangered sei whale (Balaenoptera borealis). This Darwin Core Sampling Event dataset contains 2,218 sampling events, 589,128 occurrence records, and extended measurement or fact (eMoF) records encoding read counts and target gene information per detection. Field negative controls are excluded from occurrence data. Raw sequence data are available upon request to Citizens of the Sea. Data are managed in accordance with the FAIR and CARE data principles, national research permits, and the Nagoya Protocol on access and benefit sharing.
| Titre | Citizens of the Sea: Pacific Rally 2024 eDNA Metabarcoding Dataset |
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| Identifiant | CitSeaPR24 |
| Description du domaine détude / de recherche | The CitSea Pacific Rally 2024 is the inaugural large-scale field campaign of the Citizens of the Sea programme, a non-profit citizen science initiative based in Aotearoa New Zealand. The campaign mobilised 26 volunteer sailing vessels to collect eDNA samples across more than 1.5 million km² of the southwest Pacific Ocean during the Island Cruising Pacific Rally. Sampling covered the open ocean routes between Aotearoa New Zealand, Tonga and Fiji from May to December 2024. The study area encompasses both coastal and open ocean environments spanning New Zealand EEZ waters, Tongan and Fijian EEZ waters, and international high seas. |
| Description du design | Sampling was conducted opportunistically by citizen scientist sailors rather than at pre-designated stations. Participants were trained to collect triplicate surface water samples sequentially at suitable locations during daylight hours (10 am – 2 pm) when weather and sea conditions permitted safe deployment. This flexible but standardised approach enabled scientifically valuable data collection across diverse oceanographic conditions while accommodating the safety and logistical needs of a volunteer sailing fleet. |
Les personnes impliquées dans le projet:
Méthodes déchantillonnage
Water samples were collected using the TorpeDNA towable eDNA filtration device (Pochon et al. 2024, Methods in Ecology and Evolution 15:60–68, Pochon et al; 2026, PeerJ 14:e21390 https://doi.org/10.7717/peerj.21390). A 47 mm nylon mesh filter (20 µm pore size; Merck Millipore) was inserted into the TorpeDNA end-cap and towed approximately 15 m behind the vessel for 5 minutes per replicate at sailing speeds of 5–12 knots. Immediately after recovery, filters were transferred using sterile forceps into 1.7 mL vials prefilled with PowerProtect™ preservation buffer (QIAGEN) and stored at 4°C on board. Samples were consolidated at drop-box locations in Nukuʻalofa (Tonga), Savusavu and Viseisei (Fiji), and shipped under chilled conditions to Cawthron Institute, Nelson, Aotearoa New Zealand. Field negative controls (blank filters processed identically) were collected throughout the campaign.
| Etendue de létude | Surface water eDNA sampling was conducted across the southwest Pacific Ocean between 6 May and 3 December 2024, covering the Pacific Rally sailing route between Aotearoa New Zealand, Tonga and Fiji. A total of 26 vessels participated, sampling opportunistically at the ocean surface (1–3 m depth) across more than 1.5 million km² of ocean, spanning latitudes 36.6°S to 16.7°S and longitudes 173.4°E to 174°W. Triplicate samples were collected per station during daylight hours under suitable sea conditions. |
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| Contrôle qualité | Field negative controls (n=78) and laboratory controls (n=5) were included throughout sample processing and used for contaminant removal. For 16S, only ASVs with ≥10 reads in ≥3 samples were retained; samples with <10,000 reads were removed. For 18S and COI, ASVs with ≥2 reads in ≥2 samples were retained; samples with <5,000 reads were removed. For mt16SMarVer3, only ASVs assigned to phylum Chordata were retained. |
Description des étapes de la méthode:
- Step 1 — DNA Extraction: DNA was extracted from each filter using the PowerSoil Pro Kit (QIAGEN) on a QIAcube HT automated extraction system following manufacturer protocols. Extraction negative controls (blank filters) were included in each high-throughput extraction batch. Step 2 — PCR Amplification: DNA extracts were PCR-amplified using four primer sets targeting distinct taxonomic groups. All primer sets were modified with Illumina overhang adapters. PCR reactions used MyFi Mix 2× Master Mix (Bioline) in 30 µL reaction volumes. (1) Bact16S: Klindworth 341F (CCTACGGGNGGCWGCAG) / 805R (GACTACHVGGGTATCTAATCC), 35 cycles, 53°C annealing (Klindworth et al. 2013, doi:10.1093/nar/gks808). (2) Uni18S: Zhan UNI18SF (AGGGCAAKYCTGGTGCCAGC) / UNI18SR (GRCGGTATCTRATCGYCTT), 37 cycles, 54°C annealing (Zhan et al. 2013, doi:10.1111/2041-210X.12037). (3) COI: Leray mICOIintF (GGWACWGGWTGAACWGTWTAYCCYCC) / jgHCO2198 (TANACYTCNGGRTGNCCRAARAAYCA), 40 cycles, 52°C annealing (Leray et al. 2013, doi:10.1186/1742-9994-10-34). (4) mt16SMarVer3: Valsecchi MarVer3F (AGACGAGAAGACCCTRTG) / MarVer3R (GGATTGCGCTGTTATCCC), 40 cycles, 55°C annealing (Valsecchi et al. 2020, doi:10.1002/edn3.72). All assays: initial denaturation 94°C 5 min; denaturation 94°C 30 s; elongation 72°C 45 s; final elongation 72°C 7 min. Step 3 — Library Preparation and Sequencing: Amplification products were normalised using SequalPrep Normalization Plates (Thermo Fisher Scientific) and dual-indexed with Nextera XT adapters (8 cycles, 55°C annealing). Indexed libraries were pooled, purified with AMPure XP beads (1.1× ratio), and quality-checked by Bioanalyzer (Agilent) and Qubit (Invitrogen). Paired-end sequencing was performed at Sequench Ltd (Nelson, Aotearoa New Zealand) on Illumina NextSeq 1000/2000 platforms using NextSeq 600-cycle P2 kits, spiked with 25–30% PhiX Control v3. Sequencing was conducted across six runs: COTS-24-001, COTS-24-002, COTS-24-003, COTS-24-004, COTS-25-03, COTS-25-04. Step 4 — Bioinformatic Processing: Raw fastq files were demultiplexed and primers removed using CUTADAPT v4.9 (no indels allowed; minimum overlap 15 bp). Sequences were quality-filtered and denoised using DADA2 v1.30; paired-end reads were merged with a minimum overlap of 10 bp. Chimeric sequences were removed using the DADA2 consensus method. Taxonomic assignment was performed using the RDP Naïve Bayesian Classifier against SILVA v138.2 (16S) and SILVA v132 / PR2 v5.0.0 (18S); the INSECT classifier against MIDORI UNIQUE (COI); and blastn/megablast against GenBank (COI, 18S, mt16S), with results merged using the biohelper R package. Nuclear mitochondrial DNA sequences (NUMTs) were removed from COI data using MetaMate. Contaminants were identified and removed using microDecon v1.0.2 with field and laboratory negative controls. Step 5 — Quality Control: Field negative controls (n=78) and laboratory controls (n=5) were included throughout sample processing and used for contaminant removal. For 16S, only ASVs with ≥10 reads in ≥3 samples were retained; samples with <10,000 reads were removed. For 18S and COI, ASVs with ≥2 reads in ≥2 samples were retained; samples with <5,000 reads were removed. For mt16SMarVer3, only ASVs assigned to phylum Chordata were retained.
Citations bibliographiques
- Pochon X, Urvois T, Quéméré E, Reynaud Y, Bomati E, Laroche O, Arnaud-Haond S, Trenkel VM, Baulier L, Boussarie G, Saenz-Agudelo P. 2026. TorpeDNA: a fit-for-purpose eDNA sampling device for marine biodiversity monitoring across applications and scales. PeerJ 14:e21390 https://doi.org/10.7717/peerj.21390
- Pochon, X., Laroche, O., von Ammon, U., & Zaiko, A. (2024). Filter no more: A modified plankton sampler for rapid in-water eDNA capture. Methods in Ecology and Evolution, 15, 60–68. https://doi.org/10.1111/2041-210X.14258
Métadonnées additionnelles
This dataset was produced as part of the Citizens of the Sea (CitSea) programme, a non-profit initiative pioneering the use of citizen science for ocean-scale marine biodiversity monitoring. Data collection and management follow the CitSea eDNA Data Management Protocol, which is aligned with the FAIR (findable, accessible, interoperable, reusable) and CARE (collective benefit, authority to control, responsibility, ethics) data principles. All sampling activities were conducted under national research permits. Data collected within the Exclusive Economic Zones of Tonga, Fiji and Aotearoa New Zealand are managed in consultation with the relevant national authorities in accordance with the Nagoya Protocol on access and benefit sharing. The dataset represents one of the largest open-ocean eDNA metabarcoding datasets produced to date and provides the first high-resolution multi-kingdom biodiversity baseline for the southwest Pacific Ocean. Future campaigns are planned in partnership with the Go East Rally 2026, The Ocean Race Europe 2026, The Ocean Race 2027 and the Vendée Globe 2028. For information about data access, raw sequence data requests, or collaboration enquiries, contact Citizens of the Sea at: info@citizensofthesea.org
| Remerciements | |
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| Introduction | |
| Objet |