説明
データ レコード
この sampling event リソース内のデータは、1 つまたは複数のデータ テーブルとして生物多様性データを共有するための標準化された形式であるダーウィン コア アーカイブ (DwC-A) として公開されています。 コア データ テーブルには、330 レコードが含まれています。
拡張データ テーブルは2 件存在しています。拡張レコードは、コアのレコードについての追加情報を提供するものです。 各拡張データ テーブル内のレコード数を以下に示します。
この IPT はデータをアーカイブし、データ リポジトリとして機能します。データとリソースのメタデータは、 ダウンロード セクションからダウンロードできます。 バージョン テーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。
バージョン
次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。
引用方法
研究者はこの研究内容を以下のように引用する必要があります。:
Chenuil A, Meglecz E, Bouchereau E, Legrand T, Calvert V, Chemin C, Chenesseau S, Guillemain D, Gutiérrez Ortega J M, Haguenauer A, Leduc M, Marschal F, Marschal C, Mirleau F, Selva M, Vanbostal L, Zuberer F, Mirleau P, Plaisance L, Rossi V, Ruitton S, Dubut V (2026). Separating faces in ARMS metabarcoding improves marine biodiversity monitoring. Version 1.0. OSU Pytheas. Samplingevent dataset. https://ipt.data-terra.org/resource?r=metabarcoding_faces&v=1.0
権利
研究者は権利に関する下記ステートメントを尊重する必要があります。:
パブリッシャーとライセンス保持者権利者は OSU Pytheas。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF登録
このリソースをはGBIF と登録されており GBIF UUID: 17930d18-ba23-4954-95b0-c919b743086dが割り当てられています。 GBIF France によって承認されたデータ パブリッシャーとして GBIF に登録されているOSU Pytheas が、このリソースをパブリッシュしました。
キーワード
Samplingevent; Occurrence; Observation
連絡先
https://orcid.org/0000-0001-8141-7147
- 最初のデータ採集者
- 最初のデータ採集者
- 最初のデータ採集者
- 最初のデータ採集者
- 最初のデータ採集者
- 最初のデータ採集者
地理的範囲
Mediterranean Sea - Western Basin http://marineregions.org/mrgid/4279
| 座標（緯度経度） | 南 西 [42.443, 3.111], 北 東 [43.689, 7.335] |
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時間的範囲
| 開始日 / 終了日 | 2018-03-05 / 2019-04-19 |
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プロジェクトデータ
Spatial structure and connectivity of marine populations for ecosystem management Innovative and standardized monitoring of marine biodiversity Biodiversity protection: a critical planetary challenge
| タイトル | SEAMOBB - Monitoring protocol for benthic marine biodiversity of rocky habitats |
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プロジェクトに携わる要員:
収集方法
Autonomous Reef Monitoring Structures (ARMS) were deployed by scuba divers at 12 sites distributed across three regions of the French Mediterranean coast (Figure 1) at depths of 16–22 m (Table 1). Units were immersed between 27 February and 7 April 2017 and retrieved between 5 March and 9 May 2018 (Table 1). Before dismantling and photographic documentation, each ARMS was kept in aerated seawater for 1 h to overnight. To remove vagile fauna, each plate was gently shaken prior to photography. After imaging, the sessile benthos was scraped from each face, preserved in 96 % ethanol, and stored in at +4°C until DNA extraction. Each ARMS consisted of nine superimposed plates (Figure 1), with an upper face (oriented upward) and a lower face (oriented toward the seafloor). In alternating inter-plate spaces, crossbars subdivided the gap into four compartments (see Pearman et al., 2020). Plate faces were designated by plate number and orientation (e.g. 1T, 2B, 2T … 9T, where “T” denotes the upward-facing surface and “B” the downward-facing surface). For subsequent statistical analyses, we grouped the 17 faces into five structural categories: • 9T, the uppermost face; • BC (bottom closed): faces 2B, 4B, 6B, 8B; • BO (bottom open): faces 3B, 5B, 7B, 9B; • TC (top closed): faces 1T, 3T, 5T, 7T; • TO (top open): faces 2T, 4T, 6T, 8T. This hierarchical face-type classification was used to test how fine-scale microhabitat influences community composition, and to evaluate whether grouping faces by structural categories before DNA extraction is an efficient approach for metabarcoding-based monitoring.
| Study Extent | North-western Mediterranean Sea; 2028-19 |
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| Quality Control | Sessile material scraped from ARMS plate faces was homogenized (~15 sec. in a blender), briefly rinsed, and transferred to clean 50 mL Falcon tubes filled with fresh 96 % ethanol. For DNA extraction, 1.5 mL of homogenate was used. To minimize cross-contamination, extractions were performed in individual tubes rather than in the 96-well plate format of the extraction kit (see Corse et al. 2017). DNA extractions and COI metabarcoding followed the protocol described by Thomasdotter et al. (2023), with the following key steps: (i) DNA was extracted using the NucleoSpin® Soil kit (Macherey-Nagel, Germany); (ii) the cytochrome c oxidase subunit I (COI) gene was amplified in triplicate PCRs with primers IIICRrevN (3′-GGNTGAACNGTNTAYCCNCC-5′) and HBR2d (5′-TAWACTTCDGGRTGNCCRAARAAYCA-3′), which include a heterogeneity spacer and 11–13 nucleotide sample-identifying tags, and target a broad spectrum of eukaryotic and algal phyla; (iii) a two-step tailed PCR generated paired-end, ready-to-load libraries; (iv) libraries were sequenced on an Illumina MiSeq using v2 chemistry (2 × 250 bp); and (v) a full series of negative and positive controls (two distinct mock communities) was incorporated. |
Method step description:
- For bioinformatic processing we used VTAM v0.2.0 (Validation and Taxonomic Assignment of Metabarcoding data; González et al., 2023), a pipeline specifically designed to leverage the presence of technical replicates and control samples (including negative controls and mock communities). The core principle of VTAM is to optimize parameter values across multiple filtering steps to maximize the removal of false-positive occurrences in control samples while retaining all expected variants (i.e., no false negatives in mock samples and the minimal possible number of false positives). Once optimized, these parameters are applied uniformly to all samples within the same sequencing library and run, under the rationale that parameter values validated on control samples are also appropriate for the corresponding experimental samples. The detailed protocol is availbale at : https://github.com/meglecz/seamobb_metabarcoding_pipeline
追加のメタデータ
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