Citizens of the Sea: Pacific Rally 2024 eDNA Metabarcoding Dataset

Registros de Dados

Os dados deste recurso de evento de amostragem foram publicados como um Darwin Core Archive (DwC-A), que é o formato padronizado para compartilhamento de dados de biodiversidade como um conjunto de uma ou mais tabelas de dados. A tabela de dados do núcleo contém 296 registros.

Também existem 3 tabelas de dados de extensão. Um registro de extensão fornece informações adicionais sobre um registro do núcleo. O número de registros em cada tabela de dados de extensão é ilustrado abaixo.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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]

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é Citizens of the Sea. This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 67a99753-e500-4156-a902-aacd3ba234f4.  Citizens of the Sea publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por GBIF New Zealand.

Palavras-chave

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

Contatos

Cobertura Geográfica

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

Cobertura Taxonômica

N/A

Cobertura Temporal

Dados Sobre o Projeto

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.

O pessoal envolvido no projeto:

Métodos de Amostragem

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.

Descrição dos passos do método:

1. 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.

Citações bibliográficas

1. 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
2. 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

Metadados Adicionais