Description
Data Records
The data in this sampling event resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 330 records.
2 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.
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.
Versions
The table below shows only published versions of the resource that are publicly accessible.
How to cite
Researchers should cite this work as follows:
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
Rights
Researchers should respect the following rights statement:
The publisher and rights holder of this work is OSU Pytheas. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF Registration
This resource has been registered with GBIF, and assigned the following GBIF UUID: 17930d18-ba23-4954-95b0-c919b743086d. OSU Pytheas publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF France.
Keywords
Samplingevent; Occurrence; Observation
Contacts
- Originator ●
- Point Of Contact
https://orcid.org/0000-0001-8141-7147
- Originator ●
- Point Of Contact
- Originator
- Originator
- Originator
- Originator
- Originator
- Originator
Geographic Coverage
Mediterranean Sea - Western Basin http://marineregions.org/mrgid/4279
| Bounding Coordinates | South West [42.443, 3.111], North East [43.689, 7.335] |
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Temporal Coverage
| Start Date / End Date | 2018-03-05 / 2019-04-19 |
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Project Data
Spatial structure and connectivity of marine populations for ecosystem management Innovative and standardized monitoring of marine biodiversity Biodiversity protection: a critical planetary challenge
| Title | SEAMOBB - Monitoring protocol for benthic marine biodiversity of rocky habitats |
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The personnel involved in the project:
Sampling Methods
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
Additional Metadata
| Acknowledgements |
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