Citizens of the Sea: Pacific Rally 2024 eDNA Metabarcoding Dataset

資料紀錄

此資源sampling event的資料已發佈為達爾文核心集檔案（DwC-A），其以一或多組資料表構成分享生物多樣性資料的標準格式。 核心資料表包含 296 筆紀錄。

亦存在 3 筆延伸集的資料表。延伸集中的紀錄補充核心集中紀錄的額外資訊。 每個延伸集資料表中資料筆數顯示如下。

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版本

以下的表格只顯示可公開存取資源的已發布版本。

如何引用

研究者應依照以下指示引用此資源。:

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]

權利

研究者應尊重以下權利聲明。:

此資料的發布者及權利單位為 Citizens of the Sea。 This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC 4.0) License.

GBIF 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: 67a99753-e500-4156-a902-aacd3ba234f4。  Citizens of the Sea 發佈此資源，並經由GBIF New Zealand同意向GBIF註冊成為資料發佈者。

關鍵字

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

聯絡資訊

地理涵蓋範圍

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

分類群涵蓋範圍

N/A

時間涵蓋範圍

計畫資料

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.

參與計畫的人員:

取樣方法

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.

方法步驟描述:

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.

引用文獻

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

額外的詮釋資料