說明
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 330 筆紀錄。
亦存在 2 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。
此 IPT 存放資料以提供資料儲存庫服務。資料與資源的詮釋資料可由「下載」單元下載。「版本」表格列出此資源的其它公開版本，以便利追蹤其隨時間的變更。
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。:
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
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 OSU Pytheas。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF 註冊
此資源已向GBIF註冊，並指定以下之GBIF UUID: 17930d18-ba23-4954-95b0-c919b743086d。 OSU Pytheas 發佈此資源，並經由GBIF France同意向GBIF註冊成為資料發佈者。
關鍵字
Samplingevent; Occurrence; Observation
聯絡資訊
https://orcid.org/0000-0001-8141-7147
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地理涵蓋範圍
Mediterranean Sea - Western Basin http://marineregions.org/mrgid/4279
| 界定座標範圍 | 緯度南界 經度西界 [42.443, 3.111], 緯度北界 經度東界 [43.689, 7.335] |
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時間涵蓋範圍
| 起始日期 / 結束日期 | 2018-03-05 / 2019-04-19 |
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計畫資料
Spatial structure and connectivity of marine populations for ecosystem management Innovative and standardized monitoring of marine biodiversity Biodiversity protection: a critical planetary challenge
| 計畫名稱 | SEAMOBB - Monitoring protocol for benthic marine biodiversity of rocky habitats |
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參與計畫的人員:
取樣方法
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.
| 研究範圍 | North-western Mediterranean Sea; 2028-19 |
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| 品質控管 | 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. |
方法步驟描述:
- 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
額外的詮釋資料
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