{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:31:44Z","timestamp":1760146304407,"version":"build-2065373602"},"reference-count":106,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2024,10,26]],"date-time":"2024-10-26T00:00:00Z","timestamp":1729900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Portugal 2020 program, through the project e-Fishing","award":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"]}]},{"name":"Strategic Project granted to MARE\u2014Marine and Environmental Sciences Centre","award":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"]}]},{"name":"Associate Laboratory ARNET","award":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"]}]},{"name":"FCT","award":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"]}]},{"name":"Strategic Funding","award":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"],"award-info":[{"award-number":["MAR20-01-77P3-FEAMP-000006","UIDB\/04292\/2020","UIDP\/04292\/2020","LA\/P\/0069\/2020","2020.07688.BD","UIDB\/04423\/2020","UIDP\/04423\/2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Oceans"],"abstract":"<jats:p>Understanding the ecological dynamics of zooplankton communities is crucial to precisely assessing the health of marine ecosystems and their management. Metabarcoding has contributed to a better understanding of biodiversity in marine environments. However, this methodology still requires protocol optimisation. Here, we used a complementary approach combining molecular and morphological identification methods to identify the zooplankton community inhabiting the Berlengas Archipelago, Portugal. The presence of non-indigenous species was also assessed. The results showed that the metabarcoding approach outperformed the classical morphological identification method, detecting more species with higher resolution. Nevertheless, the classical method was able to identify species that were not detected by the molecular approaches, probably due to a lack of reference data in the databases. The comparison between different molecular approaches showed that COI and bulk DNA gave better results than 18S rRNA and eDNA by detecting higher species diversity. However, complementarities were observed between them. Molecular tools also proved effective in identifying several potential non-indigenous species, identifying, for the first time, several potentially unreported NIS inhabiting the Portuguese marine ecosystems. Overall, our results confirmed the importance of combining both classical and molecular methods to obtain a more refined assessment of the zooplanktonic communities in marine environments.<\/jats:p>","DOI":"10.3390\/oceans5040046","type":"journal-article","created":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T09:51:26Z","timestamp":1730109086000},"page":"805-824","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Advantages of Combining Morphological and Molecular Methods to Characterise Zooplankton Communities: A Case Study of the UNESCO Biosphere Reserve of the Berlengas Archipelago, Portugal"],"prefix":"10.3390","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7995-7304","authenticated-orcid":false,"given":"Marco","family":"Sim\u00f5es","sequence":"first","affiliation":[{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network Associate Laboratory, Polytechnic Institute of Leiria, 2520-630 Peniche, Portugal"},{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9467-3825","authenticated-orcid":false,"given":"S\u00f3nia","family":"Cotrim Marques","sequence":"additional","affiliation":[{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network Associate Laboratory, School of Tourism and Maritime Technology, Polytechnic Institute of Leiria, 2520\u2013614 Peniche, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8558-5786","authenticated-orcid":false,"given":"C\u00e1tia","family":"Costa","sequence":"additional","affiliation":[{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network Associate Laboratory, Polytechnic Institute of Leiria, 2520-630 Peniche, Portugal"},{"name":"Associate Laboratory TERRA, Department of Life Sciences, Centre for Functional Ecology, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal"},{"name":"Centre for Environmental and Marine Studies (CESAM) and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal"}]},{"given":"Maria","family":"da Luz Calado","sequence":"additional","affiliation":[{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network Associate Laboratory, Polytechnic Institute of Leiria, 2520-630 Peniche, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5570-8768","authenticated-orcid":false,"given":"Jorge","family":"Lobo-Arteaga","sequence":"additional","affiliation":[{"name":"IPMA\u2014Portuguese Institute for Sea and Atmosphere I.P., 1495-165 Lisbon, Portugal"},{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network Associate Laboratory, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5260-4776","authenticated-orcid":false,"given":"C\u00e1tia","family":"Bartilotti","sequence":"additional","affiliation":[{"name":"IPMA\u2014Portuguese Institute for Sea and Atmosphere I.P., 1495-165 Lisbon, Portugal"},{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network Associate Laboratory, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0883-0610","authenticated-orcid":false,"given":"Maria","family":"Jorge Campos","sequence":"additional","affiliation":[{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network Associate Laboratory, School of Tourism and Maritime Technology, Polytechnic Institute of Leiria, 2520\u2013614 Peniche, Portugal"}]},{"given":"S\u00e9rgio Miguel","family":"Leandro","sequence":"additional","affiliation":[{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network Associate Laboratory, School of Tourism and Maritime Technology, Polytechnic Institute of Leiria, 2520\u2013614 Peniche, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1328-1732","authenticated-orcid":false,"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR\u2014Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1023\/A:1009943402621","article-title":"Zooplankton research: The contribution of limnology to general ecological paradigms","volume":"31","author":"Lampert","year":"1997","journal-title":"Aquat. Ecol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1146\/annurev-marine-120710-100853","article-title":"Plankton and Particle Size and Packaging: From Determining Optical Properties to Driving the Biological Pump","volume":"4","author":"Stemmann","year":"2012","journal-title":"Annu. Rev. Mar. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/icesjms\/fst125","article-title":"Predation control of zooplankton dynamics: A review of observations and models","volume":"71","author":"Daewel","year":"2014","journal-title":"ICES J. Mar. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.hal.2016.12.005","article-title":"Differential interactions between the nematocyst-bearing mixotrophic dinoflagellate Paragymnodinium shiwhaense and common heterotrophic protists and copepods: Killer or prey","volume":"62","author":"Jeong","year":"2017","journal-title":"Harmful Algae"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/j.scitotenv.2018.01.153","article-title":"Plankton dynamics across the freshwater, transitional and marine research sites of the LTER-Italy Network. Patterns, fluctuations, drivers","volume":"627","author":"Morabito","year":"2018","journal-title":"Sci. Total Environ."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"105444","DOI":"10.1016\/j.marenvres.2021.105444","article-title":"Suitability of a dual COI marker for marine zooplankton DNA metabarcoding","volume":"170","author":"Schroeder","year":"2021","journal-title":"Mar. Environ. Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.icesjms.2005.01.002","article-title":"Monitoring pelagic ecosystems using plankton indicators","volume":"62","author":"Beaugrand","year":"2005","journal-title":"ICES J. Mar. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"10120","DOI":"10.1073\/pnas.0913855107","article-title":"Marine biodiversity, ecosystem functioning, and carbon cycles","volume":"107","author":"Beaugrand","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"R679","DOI":"10.1016\/j.cub.2006.08.010","article-title":"Marine ecology: Gelatinous bells may ring change in marine ecosystems","volume":"16","author":"Hay","year":"2006","journal-title":"Curr. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Polyakov, I.V., Alkire, M.B., Bluhm, B.A., Brown, K.A., Carmack, E.C., Chierici, M., Danielson, S.L., Ellingsen, I., Ershova, E.A., and Gardfeldt, K. (2020). Borealization of the Arctic Ocean in Response to Anomalous Advection from Sub-Arctic Seas. Front. Mar. Sci., 7.","DOI":"10.3389\/fmars.2020.00491"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"41","DOI":"10.3354\/meps10694","article-title":"Shift towards the dominance of boreal species in the Arctic: Inter-annual and spatial zooplankton variability in the West Spitsbergen Current","volume":"501","author":"Weydmann","year":"2014","journal-title":"Mar. Ecol. Prog. Ser."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1111\/gcb.13864","article-title":"Warming of Subarctic waters accelerates development of a key marine zooplankton Calanus finmarchicus","volume":"24","author":"Weydmann","year":"2018","journal-title":"Glob. Chang. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00227-021-03887-y","article-title":"Toward a global reference database of COI barcodes for marine zooplankton","volume":"168","author":"Bucklin","year":"2021","journal-title":"Mar. Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"16","DOI":"10.2307\/3225681","article-title":"Zooplankton (Especially Crustaceans and Rotifers) As Indicators of Water-Quality","volume":"97","author":"Gannon","year":"1978","journal-title":"Trans. Am. Microsc. Soc."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.3844\/ajassp.2009.1815.1819","article-title":"A Review: Potentiality of Zooplankton as Bioindicator","volume":"6","author":"Ferdous","year":"2009","journal-title":"Am. J. Appl. Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.watres.2018.03.003","article-title":"Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive","volume":"138","author":"Hering","year":"2018","journal-title":"Water Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"108587","DOI":"10.1016\/j.ecolind.2022.108587","article-title":"A systematic study of zooplankton-based indices of marine ecological change and water quality: Application to the European marine strategy framework Directive (MSFD)","volume":"135","author":"Ndah","year":"2022","journal-title":"Ecol. Indic."},{"key":"ref_18","first-page":"215","article-title":"1\u2014Introduction","volume":"11","author":"Lenz","year":"2000","journal-title":"ICES Zooplankton Methodol. Man."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1016\/j.dsr2.2010.09.018","article-title":"Deep-sea sampling on CMarZ cruises in the Atlantic Ocean\u2014An Introduction","volume":"57","author":"Wiebe","year":"2010","journal-title":"Deep Sea Res. Part II Top. Stud. Oceanogr."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Bucklin, A., Batta-Lona, P.G., Questel, J.M., Wiebe, P.H., Richardson, D.E., Copley, N.J., and O\u2019Brien, T.D. (2022). COI Metabarcoding of Zooplankton Species Diversity for Time-Series Monitoring of the NW Atlantic Continental Shelf. Front. Mar. Sci., 9.","DOI":"10.3389\/fmars.2022.867893"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Matos, A., Ledoux, J.-B., Dom\u00ednguez P\u00e9rez, D., Almeida, D., and Antunes, A. (2020). Omics Advances in the Study of Zooplankton, CRC Press.","DOI":"10.1201\/9781351021821-15"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2234","DOI":"10.1016\/j.dsr2.2010.09.025","article-title":"A \u201cRosetta Stone\u201d for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean)","volume":"57","author":"Bucklin","year":"2010","journal-title":"Deep Sea Res. Part II Top. Stud. Oceanogr."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/lom3.10237","article-title":"Evaluation of marine zooplankton community structure through environmental DNA metabarcoding","volume":"16","author":"Djurhuus","year":"2018","journal-title":"Limnol. Oceanogr. Methods"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1093\/plankt\/fbw023","article-title":"Metabarcoding of marine zooplankton: Prospects, progress and pitfalls","volume":"38","author":"Bucklin","year":"2016","journal-title":"J. Plankton Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1002\/lom3.10240","article-title":"Can morphology reliably distinguish between the copepods Calanus finmarchicus and C-glacialis, or is DNA the only way?","volume":"16","author":"Choquet","year":"2018","journal-title":"Limnol. Oceanogr. Methods"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1023\/A:1003933603879","article-title":"Molecular genetic analyses of species boundaries in the sea","volume":"420","author":"Knowlton","year":"2000","journal-title":"Hydrobiologia"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1080\/17451000.2016.1268261","article-title":"The perils of online biogeographic databases: A case study with the \u2018monospecific\u2019 genus Aegina (Cnidaria, Hydrozoa, Narcomedusae)","volume":"13","author":"Lindsay","year":"2017","journal-title":"Mar. Biol. Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1086\/BBLv227n2p161","article-title":"High-Throughput Sequencing Characterizes Intertidal Meiofaunal Communities in Northern Gulf of Mexico (Dauphin Island and Mobile Bay, Alabama)","volume":"227","author":"Brannock","year":"2014","journal-title":"Biol. Bull."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1146\/annurev-marine-120308-080950","article-title":"DNA Barcoding of Marine Metazoa","volume":"3","author":"Bucklin","year":"2011","journal-title":"Annu. Rev. Mar. Sci."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1834","DOI":"10.1111\/j.1365-294X.2012.05550.x","article-title":"Bioinformatic challenges for DNA metabarcoding of plants and animals","volume":"21","author":"Coissac","year":"2012","journal-title":"Mol. Ecol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2045","DOI":"10.1111\/j.1365-294X.2012.05470.x","article-title":"Towards next-generation biodiversity assessment using DNA metabarcoding","volume":"21","author":"Taberlet","year":"2012","journal-title":"Mol. Ecol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Carroll, E.L., Gallego, R., Sewell, M.A., Zeldis, J., Ranjard, L., Ross, H.A., Tooman, L.K., O\u2019Rorke, R., Newcomb, R.D., and Constantine, R. (2019). Multi-locus DNA metabarcoding of zooplankton communities and scat reveal trophic interactions of a generalist predator. Sci. Rep., 9.","DOI":"10.1038\/s41598-018-36478-x"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1111\/mec.16251","article-title":"Environmental conditions drive zooplankton community structure in the epipelagic oceanic water of the southern Gulf of Mexico: A molecular approach","volume":"31","author":"Cicala","year":"2022","journal-title":"Mol. Ecol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1002\/ece3.2667","article-title":"Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies","volume":"7","author":"Clarke","year":"2017","journal-title":"Ecol. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Stefanni, S., Stankovic, D., Borme, D., de Olazabal, A., Juretic, T., Pallavicini, A., and Tirelli, V. (2018). Multi-marker metabarcoding approach to study mesozooplankton at basin scale. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-30157-7"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1901","DOI":"10.1111\/eva.12694","article-title":"Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities","volume":"11","author":"Zhang","year":"2018","journal-title":"Evol. Appl."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1111\/1755-0998.13201","article-title":"Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes","volume":"20","author":"Giebner","year":"2020","journal-title":"Mol. Ecol. Resour."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"e4705","DOI":"10.7717\/peerj.4705","article-title":"DNA metabarcoding of littoral hard-bottom communities: High diversity and database gaps revealed by two molecular markers","volume":"6","author":"Wangensteen","year":"2018","journal-title":"PeerJ"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e11057","DOI":"10.7717\/peerj.11057","article-title":"DNA metabarcoding of zooplankton communities: Species diversity and seasonal variation revealed by 18S rRNA and COI","volume":"9","author":"Zhao","year":"2021","journal-title":"PeerJ"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Lindeque, P.K., Parry, H.E., Harmer, R.A., Somerfield, P.J., and Atkinson, A. (2013). Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0081327"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Lobo, J., Shokralla, S., Costa, M.H., Hajibabaei, M., and Costa, F.O. (2017). DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-15823-6"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Yang, J.H., Zhang, X.W., Xie, Y.W., Song, C., Zhang, Y., Yu, H.X., and Burton, G.A. (2017). Zooplankton Community Profiling in a Eutrophic Freshwater Ecosystem-Lake Tai Basin by DNA Metabarcoding. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-01808-y"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Garcia-Vazquez, E., Georges, O., Fernandez, S., and Ardura, A. (2021). eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-86731-z"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"105230","DOI":"10.1016\/j.envint.2019.105230","article-title":"eDNA metabarcoding in zooplankton improves the ecological status assessment of aquatic ecosystems","volume":"134","author":"Yang","year":"2020","journal-title":"Environ. Int."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Davy, C.M., Kidd, A.G., and Wilson, C.C. (2015). Development and Validation of Environmental DNA (eDNA) Markers for Detection of Freshwater Turtles. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0130965"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2252","DOI":"10.1002\/ece3.1497","article-title":"Toward accurate molecular identification of species in complex environmental samples: Testing the performance of sequence filtering and clustering methods","volume":"5","author":"Flynn","year":"2015","journal-title":"Ecol. Evol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.jembe.2016.12.002","article-title":"Comparison of morphological and next generation DNA sequencing methods for assessing zooplankton assemblages","volume":"487","author":"Harvey","year":"2017","journal-title":"J. Exp. Mar. Biol. Ecol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e2444","DOI":"10.7717\/peerj.2444","article-title":"Genetic signatures of ecological diversity along an urbanization gradient","volume":"4","author":"Kelly","year":"2016","journal-title":"PeerJ"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"4214","DOI":"10.1002\/ece3.2186","article-title":"Estimating species richness using environmental DNA","volume":"6","author":"Olds","year":"2016","journal-title":"Ecol. Evol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1146\/annurev.energy.31.020105.100235","article-title":"Global marine biodiversity trends","volume":"31","author":"Sala","year":"2006","journal-title":"Annu. Rev. Environ. Resour."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1780","DOI":"10.1111\/ddi.13167","article-title":"Trends in the detection of aquatic non-indigenous species across global marine, estuarine and freshwater ecosystems: A 50-year perspective","volume":"26","author":"Bailey","year":"2020","journal-title":"Divers. Distrib."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"113947","DOI":"10.1016\/j.marpolbul.2022.113947","article-title":"First evaluation of ballast water management systems on operational ships for minimizing introductions of nonindigenous zooplankton","volume":"182","author":"Bailey","year":"2022","journal-title":"Mar. Pollut. Bull."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Ardura, A., Borrell, Y.J., Fernandez, S., Arenales, M.G., Martinez, J.L., and Garcia-Vazquez, E. (2020). Nuisance Algae in Ballast Water Facing International Conventions. Insights DNA Metabarcoding Ships Arriving Bay Biscay. Water, 12.","DOI":"10.3390\/w12082168"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.marenvres.2015.09.013","article-title":"eDNA and specific primers for early detection of invasive species\u2014A case study on the bivalve Rangia cuneata, currently spreading in Europe","volume":"112","author":"Ardura","year":"2015","journal-title":"Mar. Environ. Res."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Borrell, Y.J., Miralles, L., Do Huu, H., Mohammed-Geba, K., and Garcia-Vazquez, E. (2017). DNA in a bottle-Rapid metabarcoding survey for early alerts of invasive species in ports. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0183347"},{"key":"ref_56","unstructured":"QGIS (2024). QGIS Geographic Information System. Open Source Geospatial Foundation Project, QGIS Development Team. Version: 3.28.3."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/1742-9994-10-34","article-title":"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. Frontiers in Zoology","volume":"10","author":"Leray","year":"2013","journal-title":"Front Zool"},{"key":"ref_58","first-page":"294","article-title":"DNA primers for amplification of mitochondrial Cytochrome C oxidase subunit I from diverse metazoan invertebrates","volume":"3","author":"Folmer","year":"1994","journal-title":"Mol. Mar. Biol. Biotechnol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Pitz, K.J., Guo, J.C., Johnson, S.B., Campbell, T.L., Zhang, H.B., Vrijenhoek, R.C., Chavez, F.P., and Geller, J. (2020). Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0235159"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"6136","DOI":"10.1111\/mec.14286","article-title":"Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre","volume":"26","author":"Sommer","year":"2017","journal-title":"Mol Ecol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Estaki, M., Jiang, L., Bokulich, N.A., McDonald, D., Gonz\u00e1lez, A., Kosciolek, T., Martino, C., Zhu, Q., Birmingham, A., and V\u00e1zquez-Baeza, Y. (2020). QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data. Curr. Protoc. Bioinform., 70.","DOI":"10.1002\/cpbi.100"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e53535","DOI":"10.3897\/mbmg.4.53535","article-title":"BOLDigger \u2013 a Python package to identify and organise sequences with the Barcode of Life Data systems","volume":"4","author":"Buchner","year":"2020","journal-title":"Metabarcoding Metagenomics"},{"key":"ref_64","unstructured":"Baker, C.B. (2024, September 01). A utility to generate input files for taxonomy assignment in QIIME from the NCBI database. Available online: https:\/\/github.com\/bakerccm\/entrez_qiime."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Robeson, M.S., O\u2019Rourke, D.R., Kaehler, B.D., Ziemski, M., Dillon, M.R., Foster, J.T., and Bokulich, N.A. (2021). RESCRIPt: Reproducible sequence taxonomy reference database management for the masses. PLoS Comput. Biol., 17.","DOI":"10.1371\/journal.pcbi.1009581"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"706907","DOI":"10.3389\/fgene.2021.706907","article-title":"ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram","volume":"12","author":"Gao","year":"2021","journal-title":"Front. Genet."},{"key":"ref_67","unstructured":"(2024, September 01). vegan: Community Ecology Package. Available online: https:\/\/cran.r-project.org\/web\/packages\/vegan\/vegan.pdf."},{"key":"ref_68","unstructured":"Kerns, G.J., and Chang, G.A. (2024, September 01). RcmdrPlugin.IPSUR: An IPSUR Plugin for the R Commander. Available online: https:\/\/ipsur.r-forge.r-project.org\/rcmdrplugin\/installation.php."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"3566","DOI":"10.1890\/08-1823.1","article-title":"Associations between species and groups of sites: Indices and statistical inference","volume":"90","author":"Legendre","year":"2009","journal-title":"Ecology"},{"key":"ref_70","unstructured":"AquaNIS (2024, September 01). Information system on Aquatic Non-Indigenous and Cryptogenic Species. Available online: http:\/\/www.corpi.ku.lt\/databases\/index.php\/aquanis\/."},{"key":"ref_71","unstructured":"WoRMS EB (2024, September 01). World Register of Marine Species. Available online: https:\/\/www.marinespecies.org\/."},{"key":"ref_72","unstructured":"Razouls, C.D.N., Kouwenberg, J., and de Bov\u00e9e, F. (2024, January 20). Biodiversity of Marine Planktonic Copepods (Morphology, Geographical Distribution and Biological Data). Available online: http:\/\/copepodes.obs-banyuls.fr\/en."},{"key":"ref_73","unstructured":"RStudio Team (2020). RStudio: Integrated Development for R, RStudio, PBC. Available online: http:\/\/www.rstudio.com\/."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"S96","DOI":"10.1098\/rsbl.2003.0025","article-title":"Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species","volume":"270","author":"Hebert","year":"2003","journal-title":"Proc. R. Soc. B-Biol. Sci."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.dsr2.2009.08.005","article-title":"DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition","volume":"57","author":"Bucklin","year":"2010","journal-title":"Deep Sea Res. Part II Top. Stud. Oceanogr."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1111\/1755-0998.12138","article-title":"Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys","volume":"13","author":"Geller","year":"2013","journal-title":"Mol. Ecol. Resour."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/scientificamerican1008-82","article-title":"Barcode of life","volume":"299","author":"Stoeckle","year":"2008","journal-title":"Sci. Am."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.tree.2011.11.010","article-title":"Sequencing our way towards understanding global eukaryotic biodiversity","volume":"27","author":"Bik","year":"2012","journal-title":"Trends Ecol. Evol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1111\/mec.15587","article-title":"Capturing open ocean biodiversity: Comparing environmental DNA metabarcoding to the continuous plankton recorder","volume":"30","author":"Suter","year":"2021","journal-title":"Mol. Ecol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1002\/ece3.4742","article-title":"Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding","volume":"9","author":"Sawaya","year":"2019","journal-title":"Ecol. Evol."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Ershova, E.A., Descoteaux, R., Wangensteen, O.S., Iken, K., Hoperoft, R.R., Smoot, C., Grebmeier, J.M., and Bluhm, B.A. (2019). Diversity and Distribution of Meroplanktonic Larvae in the Pacific Arctic and Connectivity with Adult Benthic Invertebrate Communities. Front. Mar. Sci., 6.","DOI":"10.3389\/fmars.2019.00490"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1093\/sysbio\/syaa026","article-title":"Repositories for Taxonomic Data: Where We Are and What is Missing","volume":"69","author":"Miralles","year":"2020","journal-title":"Syst. Biol."},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Blanco-Bercial, L., Cornils, A., Copley, N., and Bucklin, A. (2014). DNA barcoding of marine copepods: Assessment of analytical approaches to species identification. PLoS Curr., 6.","DOI":"10.1371\/currents.tol.cdf8b74881f87e3b01d56b43791626d2"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"31","DOI":"10.3354\/meps12373","article-title":"18S V9 metabarcoding correctly depicts plankton estuarine community drivers","volume":"584","author":"Abad","year":"2017","journal-title":"Mar. Ecol. Prog. Ser."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1002\/ece3.1986","article-title":"18S rRNA V9 metabarcoding for diet characterization: A critical evaluation with two sympatric zooplanktivorous fish species","volume":"6","author":"Albaina","year":"2016","journal-title":"Ecol. Evol."},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Andruszkiewicz, E.A., Sassoubre, L.M., and Boehm, A.B. (2017). Persistence of marine fish environmental DNA and the influence of sunlight. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0185043"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1111\/mec.13481","article-title":"Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA","volume":"25","author":"Port","year":"2016","journal-title":"Mol. Ecol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1111\/j.1365-294X.2009.04520.x","article-title":"Species discovery in marine planktonic invertebrates through global molecular screening","volume":"19","author":"Goetze","year":"2010","journal-title":"Mol. Ecol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/s002270050446","article-title":"Simple molecular method to distinguish the identity of Calanus species (Copepoda: Calanoida) at any developmental stage","volume":"133","author":"Lindeque","year":"1999","journal-title":"Mar. Biol."},{"key":"ref_90","first-page":"39","article-title":"DNA barcoding of pelagic cnidarians: Current status and future prospects","volume":"62","author":"Lindsay","year":"2015","journal-title":"Bull. Plankton Soc. Jpn."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1093\/jhered\/esy026","article-title":"Molecular Insights Into the Ctenophore Genus Beroe in Europe: New Species, Spreading Invaders","volume":"109","author":"Johansson","year":"2018","journal-title":"J. Hered."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Bowman, R.E. (2000). Food of Northwest Atlantic Fishes and Two Common Species of Squid, NOAA Technical Memorandum NMFS-NE-155.","DOI":"10.5962\/bhl.title.4024"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"39","DOI":"10.2174\/1874450801004010039","article-title":"A qualitative assessment of sponge-feeding organisms from the Mexican Pacific coast","volume":"4","author":"CJ","year":"2010","journal-title":"Open Mar. Biol. J."},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Lorders, F.L., Miranda, R.J., Nunes, J., and Barros, F. (2018). Spongivory by Fishes on Southwestern Atlantic Coral Reefs: No Evidence of Top-Down Control on Sponge Assemblages. Front. Mar. Sci., 5.","DOI":"10.3389\/fmars.2018.00256"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"R146","DOI":"10.1016\/j.cub.2015.12.024","article-title":"Tunicates","volume":"26","author":"Holland","year":"2016","journal-title":"Curr. Biol."},{"key":"ref_96","unstructured":"Sadro, S. (2008). Porifera: The Sponges, Available online: https:\/\/api.semanticscholar.org\/CorpusID:5650532."},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Cornwell, L.E., Fileman, E.S., Bruun, J.T., Hirst, A.G., Tarran, G.A., Findlay, H.S., Lewis, C., Smyth, T.J., McEvoy, A.J., and Atkinson, A. (2020). Resilience of the Copepod Oithona similis to Climatic Variability: Egg Production, Mortality, and Vertical Habitat Partitioning. Front. Mar. Sci., 7.","DOI":"10.3389\/fmars.2020.00029"},{"key":"ref_98","doi-asserted-by":"crossref","unstructured":"Hure, M., Batistic, M., and Garic, R. (2022). Copepod Diel Vertical Distribution in the Open Southern Adriatic Sea (NE Mediterranean) under Two Different Environmental Conditions. Water, 14.","DOI":"10.3390\/w14121901"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1093\/icesjms\/fsz021","article-title":"Time-series metabarcoding analysis of zooplankton diversity of the NW Atlantic continental shelf","volume":"76","author":"Bucklin","year":"2019","journal-title":"ICES J. Mar. Sci."},{"key":"ref_100","doi-asserted-by":"crossref","unstructured":"Kelly, R.P., Closek, C.J., O\u2019Donnell, J.L., Kralj, J.E., Shelton, A.O., and Samhouri, J.F. (2017). Genetic and Manual Survey Methods Yield Different and Complementary Views of an Ecosystem. Front. Mar. Sci., 3.","DOI":"10.3389\/fmars.2016.00283"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1093\/icesjms\/fsu020","article-title":"Richness-abundance relationships for zooplankton in ballast water: Temperate versus Arctic comparisons","volume":"71","author":"Chan","year":"2014","journal-title":"ICES J. Mar. Sci."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1126\/science.261.5117.78","article-title":"Ecological Roulette: The Global Transport of Nonindigenous Marine Organisms","volume":"261","author":"Cariton","year":"1993","journal-title":"Science"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1038\/s41893-019-0245-y","article-title":"Global forecasts of shipping traffic and biological invasions to 2050","volume":"2","author":"Sardain","year":"2019","journal-title":"Nat. Sustain."},{"key":"ref_104","doi-asserted-by":"crossref","unstructured":"von Ammon, U., Wood, S.A., Laroche, O., Zaiko, A., Tait, L., Lavery, S., Inglis, G.J., and Pochon, X. (2018). Combining morpho-taxonomy and metabarcoding enhances the detection of non-indigenous marine pests in biofouling communities. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-34541-1"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1742-9994-11-19","article-title":"Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida)","volume":"11","author":"Cornils","year":"2014","journal-title":"Front. Zool."},{"key":"ref_106","first-page":"5","article-title":"Le Zooplancton du plateau continental d\u2019El-Kala (M\u00e9diterran\u00e9e sud-occidentale): Composition et abondance en mai 1996","volume":"24","author":"Ounissi","year":"1999","journal-title":"J. Rech. Oc\u00e9anogr."}],"container-title":["Oceans"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2673-1924\/5\/4\/46\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:21:14Z","timestamp":1760113274000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2673-1924\/5\/4\/46"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,26]]},"references-count":106,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["oceans5040046"],"URL":"https:\/\/doi.org\/10.3390\/oceans5040046","relation":{},"ISSN":["2673-1924"],"issn-type":[{"type":"electronic","value":"2673-1924"}],"subject":[],"published":{"date-parts":[[2024,10,26]]}}}