Separating Faces in ARMS Metabarcoding Improves Marine Biodiversity Monitoring: A Comparison Across Protocols, Experimental Designs and Photographic Surveys
Abstract
Monitoring marine biodiversity requires approaches capable of capturing its spatial and temporal complexity. 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 outputs against photographic observations. Here, we combined photographic analysis with cytochrome c oxidase I (COI) metabarcoding across 10 north‐western Mediterranean sites to 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 traceability. We then conducted the first face‐by‐face comparison of α‐ and β‐diversity between imaging and eDNA, metabarcoding each ARMS face separately rather than pooling samples. Metabarcoding detected ~15× higher site‐level richness and revealed stronger correlations with geographic distance and environmental gradients—which stemmed from its finer taxonomic resolution—whereas photography provided complementary information on macro‐taxa and surface cover. For metabarcoding, processing each face separately yielded much higher richness and stronger β‐diversity–distance correlations than with the NOAA pooling protocol, demonstrating that pooling inflates sampling variance, weakening ecological signal. Grouping the 17 faces into five structural categories offered a more operational alternative while further increasing α‐diversity and strengthening β‐diversity correlations. Overall, our results show that retaining ARMS microhabitat structure is critical for maximizing metabarcoding performance. Using five structural sessile fractions per ARMS combined with a control‐driven bioinformatic workflow provides a reproducible, scalable framework for long‐term eDNA monitoring and early detection of biodiversity change.
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BibTeX
@article{chenuil2026separating,
title = {{Separating Faces in ARMS Metabarcoding Improves Marine Biodiversity Monitoring: A Comparison Across Protocols, Experimental Designs and Photographic Surveys}},
author = {Anne Chenuil and Elyna Bouchereau and Térence Legrand and Virgile Calvert and Cécile Chemin and Sandrine Chenesseau and Dorian Guillemain and José Miguel Gutiérrez Ortega and Anne Haguenauer and Michèle Leduc and Frédéric Legendre and Florent Marschal and Christian Marschal and Fatma Mirleau and Marjorie Selva and Laurent Vanbostal and Frédéric Zuberer and Pascal Mirleau and Laetitia Plaisance and Vincent Rossi and Sandrine Ruitton and Emese Meglécz and Vincent Dubut},
journal = {Molecular Ecology Resources},
year = {2026},
month = sep,
doi = {10.1111/1755-0998.70188},
url = {https://hal.science/hal-05761544v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Separating Faces in ARMS Metabarcoding Improves Marine Biodiversity Monitoring: A Comparison Across Protocols, Experimental Designs and Photographic Surveys
AU - Anne Chenuil
AU - Elyna Bouchereau
AU - Térence Legrand
AU - Virgile Calvert
AU - Cécile Chemin
AU - Sandrine Chenesseau
AU - Dorian Guillemain
AU - José Miguel Gutiérrez Ortega
AU - Anne Haguenauer
AU - Michèle Leduc
AU - Frédéric Legendre
AU - Florent Marschal
AU - Christian Marschal
AU - Fatma Mirleau
AU - Marjorie Selva
AU - Laurent Vanbostal
AU - Frédéric Zuberer
AU - Pascal Mirleau
AU - Laetitia Plaisance
AU - Vincent Rossi
AU - Sandrine Ruitton
AU - Emese Meglécz
AU - Vincent Dubut
PY - 2026
DA - 2026/09/11
JO - Molecular Ecology Resources
DO - 10.1111/1755-0998.70188
UR - https://hal.science/hal-05761544v1
AB - Monitoring marine biodiversity requires approaches capable of capturing its spatial and temporal complexity. 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 outputs against photographic observations. Here, we combined photographic analysis with cytochrome c oxidase I (COI) metabarcoding across 10 north‐western Mediterranean sites to 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 traceability. We then conducted the first face‐by‐face comparison of α‐ and β‐diversity between imaging and eDNA, metabarcoding each ARMS face separately rather than pooling samples. Metabarcoding detected ~15× higher site‐level richness and revealed stronger correlations with geographic distance and environmental gradients—which stemmed from its finer taxonomic resolution—whereas photography provided complementary information on macro‐taxa and surface cover. For metabarcoding, processing each face separately yielded much higher richness and stronger β‐diversity–distance correlations than with the NOAA pooling protocol, demonstrating that pooling inflates sampling variance, weakening ecological signal. Grouping the 17 faces into five structural categories offered a more operational alternative while further increasing α‐diversity and strengthening β‐diversity correlations. Overall, our results show that retaining ARMS microhabitat structure is critical for maximizing metabarcoding performance. Using five structural sessile fractions per ARMS combined with a control‐driven bioinformatic workflow provides a reproducible, scalable framework for long‐term eDNA monitoring and early detection of biodiversity change.
SN - 1755-098X
SN - 1755-0998
ER -