Separating faces in ARMS metabarcoding improves marine biodiversity monitoring

Evento de muestreo Observación
Última versión publicado por OSU Pytheas el jun 19, 2026 OSU Pytheas
Fecha de publicación:
19 de junio de 2026
Publicado por:
OSU Pytheas
Licencia:
CC-BY 4.0

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Descripción

Monitoring marine biodiversity requires approaches that capture its full complexity through space and time. DNA metabarcoding coupled with Autonomous Reef Monitoring Structures (ARMS) is increasingly used for this purpose, yet most applications still pool all sessile fractions and rarely benchmark molecular ouputs against photographic observations. Here, we combined photographic analysis with cytochrome c oxidase I (COI) metabarcoding across ten north-western Mediterranean sites to test, compare, and refine ARMS-based monitoring protocols. We first optimized laboratory procedures (DNA extraction and polymerase choice) and applied the control-driven, replicate-aware VTAM pipeline to minimize false positives and ensure full traceability. We then conducted the first face-by-face comparison of α- and β-diversity between imaging and eDNA in which each individual ARMS face was metabarcoded separately rather than pooled.

Registros

Los datos en este recurso de evento de muestreo han sido publicados como Archivo Darwin Core(DwC-A), el cual es un formato estándar para compartir datos de biodiversidad como un conjunto de una o más tablas de datos. La tabla de datos del core contiene 330 registros.

también existen 2 tablas de datos de extensiones. Un registro en una extensión provee información adicional sobre un registro en el core. El número de registros en cada tabla de datos de la extensión se ilustra a continuación.

Event (core)
330
dnaDerivedData 
14180
Occurrence 
14180

Este IPT archiva los datos y, por lo tanto, sirve como repositorio de datos. Los datos y los metadatos del recurso están disponibles para su descarga en la sección descargas. La tabla versiones enumera otras versiones del recurso que se han puesto a disposición del público y permite seguir los cambios realizados en el recurso a lo largo del tiempo.

Versiones

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es OSU Pytheas. Esta obra está bajo una licencia Creative Commons de Atribución/Reconocimiento (CC-BY 4.0).

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: 17930d18-ba23-4954-95b0-c919b743086d.  OSU Pytheas publica este recurso y está registrado en GBIF como un publicador de datos avalado por GBIF France.

Palabras clave

Samplingevent; Occurrence; Observation

Contactos

Anne Chenuil
  • Originador ●
  • Punto De Contacto
IMBE
Marseille
Emese Meglecz
  • Originador ●
  • Punto De Contacto
IMBE
Marseille
Elyna Bouchereau
  • Originador
IMBE
Térence Legrand
  • Originador
MIO
Virgile Calvert
  • Originador
IMBE
Cécile Chemin
  • Originador
IMBE
Sandrine Chenesseau
  • Originador
IMBE
Dorian Guillemain
  • Originador
OSU PYTHEAS
José Miguel Gutiérrez Ortega
  • Originador
TAXON Estudios Ambientales
Anne Haguenauer
  • Originador
CNRS
Michèle Leduc
  • Originador
STARESO
Florent Marschal
  • Originador
IMBE
Christian Marschal
  • Originador
IMBE
Fatma Mirleau
  • Originador
IMBE
Marjorie Selva
  • Originador
IMBE
Laurent Vanbostal
  • Originador
OSU PYTHEAS
Frédéric Zuberer
  • Originador
OSU PYTHEAS
Pascal Mirleau
  • Originador
IMBE
Laetitia Plaisance
  • Originador
National Museum of Natural History, Smithsonian Institution
Vincent Rossi
  • Originador
MIO
Sandrine Ruitton
  • Originador
MIO
Vincent Dubut
  • Originador
ADENEKO

Cobertura geográfica

Mediterranean Sea - Western Basin http://marineregions.org/mrgid/4279

Coordenadas límite Latitud Mínima Longitud Mínima [42,443, 3,111], Latitud Máxima Longitud Máxima [43,689, 7,335]

Cobertura temporal

Fecha Inicial / Fecha Final 2018-03-05 / 2019-04-19

Datos del proyecto

Spatial structure and connectivity of marine populations for ecosystem management Innovative and standardized monitoring of marine biodiversity Biodiversity protection: a critical planetary challenge

Título SEAMOBB - Monitoring protocol for benthic marine biodiversity of rocky habitats

Personas asociadas al proyecto:

Anne Chenuil

Métodos de muestreo

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.

Área de Estudio North-western Mediterranean Sea; 2028-19
Control de Calidad 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.

Descripción de la metodología paso a paso:

  1. 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

Metadatos adicionales

Agradecimientos