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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\n                    <jats:italic>c<\/jats:italic>\n                    oxidase I (COI) metabarcoding across 10 north\u2010western Mediterranean sites to compare and refine ARMS\u2010based monitoring protocols. We first optimized laboratory procedures (DNA extraction and polymerase choice) and applied the control\u2010driven, replicate\u2010aware VTAM pipeline to minimize false positives and ensure traceability. We then conducted the first face\u2010by\u2010face comparison of \u03b1\u2010 and \u03b2\u2010diversity between imaging and eDNA, metabarcoding each ARMS face separately rather than pooling samples. Metabarcoding detected ~15\u00d7 higher site\u2010level richness and revealed stronger correlations with geographic distance and environmental gradients\u2014which stemmed from its finer taxonomic resolution\u2014whereas photography provided complementary information on macro\u2010taxa and surface cover. For metabarcoding, processing each face separately yielded much higher richness and stronger \u03b2\u2010diversity\u2013distance 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 \u03b1\u2010diversity and strengthening \u03b2\u2010diversity 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\u2010driven bioinformatic workflow provides a reproducible, scalable framework for long\u2010term eDNA monitoring and early detection of biodiversity change.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.70188","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T13:22:22Z","timestamp":1789132942000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Separating Faces in\n                    <scp>ARMS<\/scp>\n                    Metabarcoding Improves Marine Biodiversity Monitoring: A Comparison Across Protocols, Experimental Designs and Photographic Surveys"],"prefix":"10.1111","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8141-7147","authenticated-orcid":false,"given":"Anne","family":"Chenuil","sequence":"first","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5925-7284","authenticated-orcid":false,"given":"Elyna","family":"Bouchereau","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9120-5153","authenticated-orcid":false,"given":"T\u00e9rence","family":"Legrand","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Universit\u00e9 de Toulon, CNRS, IRD, MIO  Marseille France"},{"name":"Ifremer, DYNECO\u2010Dynamiques Des \u00c9cosyst\u00e8mes C\u00f4tiers  Plouzan\u00e9 France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2942-8815","authenticated-orcid":false,"given":"Virgile","family":"Calvert","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5483-8103","authenticated-orcid":false,"given":"C\u00e9cile","family":"Chemin","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-1574-7743","authenticated-orcid":false,"given":"Sandrine","family":"Chenesseau","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorian","family":"Guillemain","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, CNRS, IRD, INRAE, OSU PYTHEAS  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0952-4444","authenticated-orcid":false,"given":"Jos\u00e9 Miguel Guti\u00e9rrez","family":"Ortega","sequence":"additional","affiliation":[{"name":"TAXON Estudios Ambientales S.L.  Alcantarilla Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2332-2929","authenticated-orcid":false,"given":"Anne","family":"Haguenauer","sequence":"additional","affiliation":[{"name":"CNRS, D\u00e9l\u00e9gation Provence et Corse  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mich\u00e8le","family":"Leduc","sequence":"additional","affiliation":[{"name":"STARESO Marine Station  Calvi, Corse France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6476-4183","authenticated-orcid":false,"given":"Fr\u00e9d\u00e9ric","family":"Legendre","sequence":"additional","affiliation":[{"name":"CEA Saclay\u2014CNRS UMR12, Laboratoire L\u00e9on Brillouin  Gif\u2010sur\u2010Yvette France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florent","family":"Marschal","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Marschal","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatma","family":"Mirleau","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marjorie","family":"Selva","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"Vanbostal","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, CNRS, IRD, INRAE, OSU PYTHEAS  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Zuberer","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, CNRS, IRD, INRAE, OSU PYTHEAS  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9654-6045","authenticated-orcid":false,"given":"Pascal","family":"Mirleau","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3375-4768","authenticated-orcid":false,"given":"Laetitia","family":"Plaisance","sequence":"additional","affiliation":[{"name":"National Museum of Natural History, Smithsonian Institution  Washington DC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7291-0415","authenticated-orcid":false,"given":"Vincent","family":"Rossi","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Universit\u00e9 de Toulon, CNRS, IRD, MIO  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4485-9979","authenticated-orcid":false,"given":"Sandrine","family":"Ruitton","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Universit\u00e9 de Toulon, CNRS, IRD, MIO  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7547-4858","authenticated-orcid":false,"given":"Emese","family":"Megl\u00e9cz","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5619-6909","authenticated-orcid":false,"given":"Vincent","family":"Dubut","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE  Marseille France"},{"name":"ADENEKO  Saint\u2010Girons France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041\u2010210X.12849"},{"key":"e_1_2_11_3_1","first-page":"218","volume-title":"PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods","author":"Anderson M. 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