Dauer, D. M. Biological criteria, environmental health and estuarine macrobenthic community structure. Mar. Pollut. Bull. 26, 249–257 (1993).
Borja, A., Franco, J. & Pérez, V. A marine biotic index to establish the ecological quality of soft-bottom benthos within European estuarine and coastal environments. Mar. Pollut. Bull. 40, 1100–1114 (2000).
Rosenberg, R., Blomqvist, M., Nilsson, H. C., Cederwall, H. & Dimming, A. Marine quality assessment by use of benthic species-abundance distributions: a proposed new protocol within the European Union Water Framework Directive. Mar. Pollut. Bull. 49, 728–739 (2004).
Muxika, I., Borja, Á. & Bonne, W. The suitability of the marine biotic index (AMBI) to new impact sources along European coasts. Ecol. Indic. 5, 19–31 (2005).
Patrício, J., Neto, J. M., Teixeira, H., Salas, F. & Marques, J. C. The robustness of ecological indicators to detect long-term changes in the macrobenthos of estuarine systems. Mar. Environ. Res. 68, 25–36 (2009).
Kröncke, I. et al. Changes in North Sea macrofauna communities and species distribution between 1986 and 2000. Estuar. Coast. Shelf Sci. 94, 1–15 (2011).
Coates, D. A., Deschutter, Y., Vincx, M. & Vanaverbeke, J. Enrichment and shifts in macrobenthic assemblages in an offshore wind farm area in the Belgian part of the North Sea. Mar. Environ. Res. 95, 1–12 (2014).
Worm, B. et al. Impacts of biodiversity loss on ocean ecosystem services. Science 314, 787–790 (2006).
Thrush, S. F. et al. Changes in the location of biodiversity–ecosystem function hot spots across the seafloor landscape with increasing sediment nutrient loading. Proc. Biol. Soc. 284, 1471–2954 (2017).
Lam-Gordillo, O., Baring, R. & Dittmann, S. Ecosystem functioning and functional approaches on marine macrobenthic fauna: A research synthesis towards a global consensus. Ecol. Indic. 115, 106379 (2020).
Lobo, J., Shokralla, S., Costa, M. H., Hajibabaei, M. & Costa, F. O. DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities. Sci. Rep. 7, 15618 (2017).
Hering, D. et al. Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Resour. 138, 192–205 (2018).
Grosse, M., Capa, M. & Bakken, T. Describing the hidden species diversity of Chaetozone (Annelida, Cirratulidae) in the Norwegian Sea using morphological and molecular diagnostics. ZooKeys 1039, 139–176 (2021).
Hablützel, P. et al. DNA-based monitoring of Non-Indigenous Species. Pilot Report (Interreg North Sea Region GEANS, EU, 2023).
Bucklin, A., Steinke, D. & Blanco-Bercial, L. DNA barcoding of marine metazoa. Ann. Rev. Mar. Sci. 3, 471–508 (2011).
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. & Willerslev, E. Towards next‐generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 21, 2045–2050 (2012).
Aylagas, E., Borja, A., Irigoien, X. & Rodriguez-Ezpeleta, N. Benchmarking DNA metabarcoding for biodiversity-based monitoring and assessment. Front. Mar. Sci. 3, 96 (2016).
Derycke, S. et al. Detection of macrobenthos species with metabarcoding is consistent in bulk DNA but dependent on body size and sclerotization in eDNA from the ethanol preservative. Front. Mar. Sci. 8 (2021).
Van den Bulcke, L. et al. DNA metabarcoding on repeat: Sequencing data of marine macrobenthos are reproducible and robust across labs and protocols. Ecol. Indic. 150, 110207 (2023).
Rey, A., Basurko, O. C. & Rodriguez-Ezpeleta, N. Considerations for metabarcoding-based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments. Ecol. Evol. 10, 2452–2465 (2020).
Bucklin, A. et al. Toward a global reference database of COI barcodes for marine zooplankton. Mar. Biol. 168, 78 (2021).
Leray, M. et al. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front. Zool. 10, 34 (2013).
Pawloski, J. et al. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Sci. Total Environ. 637, 1295–1310 (2018).
Cristescu, M. E. & Hebert, P. D. N. Uses and misuses of environmental DNA in biodiversity science and conservation. Annu. Rev. Ecol. Evol. Syst. 49, 209–230 (2018).
Weigand, H. et al. DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Sci. Total Envir. 678, 499–524 (2019).
Bergsten, J. et al. The effect of geographical scale of sampling on DNA barcoding. Syst. Biol. 61(5), 851–69 (2012).
Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Sayers, E. W. GenBank. Nucleic Acids Res. 44 (2016).
Leray, M., Knowlton, N., Ho, S. L., Nguyen, B. N. & Machida, R. J. GenBank is a reliable resource for 21st century biodiversity research. Proc. Natl. Acad. Sci. USA 116(45), 22651–22656 (2019).
Ratnasingham, S. & Hebert, P. D. N. BOLD: The Barcode of Life Data System (www.barcodinglife.org). Mol. Ecol. Notes 7, 355–364 (2007).
Locatelli, N. S., McIntyre, P. B., Therkildsen, N. O. & Baetscher, D. S. GenBank’s reliability is uncertain for biodiversity researchers seeking species-level assignment for eDNA. Proc. Natl. Acad. Sci. USA 117, 32211–32212 (2020).
Collins, R. A. et al. Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes. J. Fish Biol. 99(4), 1446–1454 (2021).
Pentinsaari, M., Ratnasingham, S., Miller, S. E. & Hebert, P. D. N. BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries? PLoS One 15(4), e0231814 (2020).
Emeis, K. C. et al. The North Sea – A shelf sea in the Anthropocene. J. Mar. Syst. 141, 18–33 (2015).
Moullec, F. et al. Identifying and addressing the anthropogenic drivers of global change in the North Sea: a systematic map protocol. Environ. Evid. 10, 19 (2021).
Daewel, U., Akhtar, N., Christiansen, N. & Schrum, C. Offshore wind farms are projected to impact primary production and bottom water deoxygenation in the North Sea. Commun. Earth Environ. 3, 292 (2022).
Hebert, P. D. N., Cywinska, A., Ball, S. L. & DeWaard, J. R. Biological identifications through DNA barcodes. Proc. Roy. Soc. B: Biol. Sci. 270, 313–321 (2003).
Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3(5), 294–299 (1994).
Geller, J. B., Meyer, C. P., Parker, M. & Hawk, H. L. Redesign of PCR primers for mitochondrial Cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Mol. Ecol. Res. 13(5), 851–861 (2013).
Barco, A., Raupach, M. J., Laakmann, S., Neumann, H. & Knebelsberger, T. Identification of North Sea molluscs with DNA barcoding. Mol. Ecol. Resour. 16, 288–297 (2016).
Laakman, S., Boos, K., Knebelsberger, T., Raupach, M. J. & Neumann, H. Species identification of echinoderms from the North Sea by combining morphology and molecular data. Helg. Mar. Res. 70, 18 (2016).
Raupach, M. J. et al. The application of DNA barcodes for the identification of marine crustaceans from the North Sea and adjacent regions. PLoS ONE 10(9), e0139421 (2015).
Beermann, J. et al. Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida). Sci. Rep. 8, 6893 (2018).
Ratnasingham, S. & Hebert, P. D. N. A DNA-based registry for all animal species: The Barcode Index Number (BIN) System. PLoS ONE 8(7), e66213 (2013).
Christodoulou, M. et al. A taxonomically reliable DNA barcode reference library for North Sea macrobenthos. https://doi.org/10.6084/m9.figshare.28408385.
Obst, M. et al. Marine long-term biodiversity assessment suggests loss of rare species in the Skagerrak and Kattegat region. Mar. Biodivers. 48, 2165–2176 (2017).
Derycke, S. et al. DNA-based monitoring of soft sediments. Pilot 1 Report (Interreg North Sea Region GEANS, EU, 2023).
Herman, P. M. J., Stolte, W. & van der Heijden, L. Summary presence/absence maps of macro-endobenthos in the greater North Sea, based of nearly 100,000 samples from 65 assembled monitoring data sets. EMODNET biology data product, https://www.emodnet-biology.eu/data-catalog?module=dataset&dasid=6617 (2020).
Zettler, M. L. et al. An annotated checklist of macrozoobenthic species in German waters of the North and Baltic Seas. Helgol. Mar. Res. 72, 5 (2018).
Estoup, A., Largiader, C., Perrot, E. & Chouruout, D. Rapid one-tube DNA extraction for reliable PCR detection of fish polymorphic markers and transgenes. Mol. Mar. Biol. Biotechnol. 5(4), 295–298 (1996).
Layton, K. K. S., Corstorphine, E. A. & Hebert, P. D. N. Exploring Canadian echinoderm diversity through DNA Barcodes. PLoS ONE 11(11), e0166118 (2016).
Carr, C. M., Hardy, S. M., Brown, T. M., Macdonald, T. A. & Hebert, P. D. N. A Tri-Oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes. PLoS ONE 6(7), e22232 (2011).
Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).
Katoh, K., Misawa, K., Kuma, K. I. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based 585 on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
Christodoulou, M. et al. GenBank. https://identifiers.org/ncbi/bioproject:PRJNA1236822.
Christodoulou, M. et al. Dataset: DS-GEANS1. GEANS Reference. dx. https://doi.org/10.5883/DS-GEANS1 Library.
Rimet, F. et al. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life. Metabarcoding Metagenom. 5, e58056, 17–33 (2021).
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol. 38, 3022–3027 (2021).