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 330 enregistrements.
2 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:
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
Droits
Les chercheurs doivent respecter la déclaration de droits suivante:
L’éditeur et détenteur des droits de cette ressource est OSU Pytheas. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.
Enregistrement GBIF
Cette ressource a été enregistrée sur le portail GBIF, et possède lUUID GBIF suivante : 17930d18-ba23-4954-95b0-c919b743086d. OSU Pytheas publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec lapprobation du GBIF France.
Mots-clé
Samplingevent; Occurrence; Observation
Contacts
- Créateur ●
- Personne De Contact
https://orcid.org/0000-0001-8141-7147
- Créateur ●
- Personne De Contact
- Créateur
- Créateur
- Créateur
- Créateur
- Créateur
- Créateur
Couverture géographique
Mediterranean Sea - Western Basin http://marineregions.org/mrgid/4279
| Enveloppe géographique | Sud Ouest [42,443, 3,111], Nord Est [43,689, 7,335] |
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Couverture temporelle
| Date de début / Date de fin | 2018-03-05 / 2019-04-19 |
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Données sur le projet
Spatial structure and connectivity of marine populations for ecosystem management Innovative and standardized monitoring of marine biodiversity Biodiversity protection: a critical planetary challenge
| Titre | SEAMOBB - Monitoring protocol for benthic marine biodiversity of rocky habitats |
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Les personnes impliquées dans le projet:
Méthodes déchantillonnage
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.
| Etendue de létude | North-western Mediterranean Sea; 2028-19 |
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| Contrôle qualité | 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. |
Description des étapes de la méthode:
- 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
Métadonnées additionnelles
| Remerciements |
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