{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T15:46:24Z","timestamp":1791992784763,"version":"4.4.0"},"reference-count":41,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2019,1,15]],"date-time":"2019-01-15T00:00:00Z","timestamp":1547510400000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,1,15]],"date-time":"2019-01-15T00:00:00Z","timestamp":1547510400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["LP160100839"],"award-info":[{"award-number":["LP160100839"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["LP160101508"],"award-info":[{"award-number":["LP160101508"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008247","name":"University of Otago","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008247","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Ecology and Evolution"],"published-print":{"date-parts":[[2019,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding\u2010based biodiversity studies is gaining popularity as a noninvasive, time\u2010efficient, and cost\u2010effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under\u2010surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA\u2010related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species\u2010level assignment) and universal (broad taxonomic group with genus\/family\u2010level assignment) approaches obtained from replicates treated with the optimal and a low\u2010performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose\u2010nitrate membranes and extraction with Qiagen's DNeasy Blood &amp; Tissue Kit outperformed other combinations of capture and extraction methods, showing a ninefold improvement in DNA yield over the poorest performing methods. Use of optimized protocols resulted in a significant increase in OTU and species richness for targeted metabarcoding assays. However, changing protocols made little difference to the OTU and taxon richness obtained using universal metabarcoding assays. Our results demonstrate an increased risk of false\u2010negative species detection for targeted eDNA approaches when protocols with poor DNA isolation efficacy are employed. Appropriate optimization is therefore essential for eDNA monitoring to remain a powerful, efficient, and relatively cheap method for biodiversity assessments. For seawater, we advocate filtration through cellulose\u2010nitrate membranes and extraction with Qiagen's DNeasy Blood &amp; Tissue Kit or phenol\u2010chloroform\u2010isoamyl for successful implementation of eDNA multi\u2010marker metabarcoding surveys.<\/jats:p>","DOI":"10.1002\/ece3.4843","type":"journal-article","created":{"date-parts":[[2019,1,15]],"date-time":"2019-01-15T05:41:26Z","timestamp":1547530886000},"page":"1323-1335","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":101,"title":["Species\u2010level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization"],"prefix":"10.1002","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7458-3550","authenticated-orcid":false,"given":"Gert\u2010Jan","family":"Jeunen","sequence":"first","affiliation":[{"name":"Department of Anatomy University of Otago Dunedin New Zealand"},{"name":"Department of Zoology University of Otago Dunedin New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Knapp","sequence":"additional","affiliation":[{"name":"Department of Anatomy University of Otago Dunedin New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hamish G.","family":"Spencer","sequence":"additional","affiliation":[{"name":"Department of Zoology University of Otago Dunedin New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7951-0772","authenticated-orcid":false,"given":"Helen R.","family":"Taylor","sequence":"additional","affiliation":[{"name":"Department of Anatomy University of Otago Dunedin New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miles D.","family":"Lamare","sequence":"additional","affiliation":[{"name":"Department of Marine Science University of Otago Dunedin New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Stat","sequence":"additional","affiliation":[{"name":"Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences Curtin University Perth Western Australia Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0302-4206","authenticated-orcid":false,"given":"Michael","family":"Bunce","sequence":"additional","affiliation":[{"name":"Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences Curtin University Perth Western Australia Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0671-3637","authenticated-orcid":false,"given":"Neil J.","family":"Gemmell","sequence":"additional","affiliation":[{"name":"Department of Anatomy University of Otago Dunedin New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,1,15]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2014.06.009"},{"key":"e_1_2_10_3_1","volume-title":"Collins guide to the sea fishes of New Zealand\/by Tony Ayling; with 48 colour plates by Geoffrey J. Cox and 475 line drawings by the author","author":"Ayling T.","year":"1987"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1832"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.3123"},{"key":"e_1_2_10_6_1","volume-title":"New Zealand coastal marine invertebrates","author":"Cook S. C.","year":"2010"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000831"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2014.11.018"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2664.2012.02171.x"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.2041-1014.2012.00642.x"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmars.2017.00314"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq461"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12421"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12138"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2014.11.040"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0179251"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0121655"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts199"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2015.09.021"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2014.11.020"},{"issue":"34","key":"e_1_2_10_21_1","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","volume":"10","author":"Leray M.","year":"2013","journal-title":"Frontiers in Zoology"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0124671"},{"key":"e_1_2_10_23_1","doi-asserted-by":"crossref","unstructured":"Oberacker P. Stepper P. Bond D. M. H\u00f6hn S. Focken J. Schelle L. \u2026Jurkowski T. P.(2018).Bio\u2010On\u2010Magnetic\u2010Beads (BOMB): Open platform for high\u2010throughput nucleic acid extraction and manipulation. bioRxiv. Available athttp:\/\/biorxiv.org\/content\/early\/2018\/09\/12\/414516.abstract.","DOI":"10.1101\/414516"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/0167-7012(87)90025-X"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0073935"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13481"},{"issue":"3","key":"e_1_2_10_27_1","first-page":"358","article-title":"PCR: How to kill unwanted DNA","volume":"12","author":"Prince A. M.","year":"1992","journal-title":"BioTechniques"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12281"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2009.01.021"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.208"},{"key":"e_1_2_10_31_1","doi-asserted-by":"publisher","DOI":"10.1111\/2041-210X.12683"},{"key":"e_1_2_10_32_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-12501-5"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0041732"},{"key":"e_1_2_10_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2014.11.019"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0114329"},{"key":"e_1_2_10_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2014.11.017"},{"key":"e_1_2_10_37_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12460"},{"key":"e_1_2_10_38_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.40.3.1128.2002"},{"key":"e_1_2_10_39_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.marpolbul.2009.09.007"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep40368"},{"key":"e_1_2_10_41_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2115"},{"key":"e_1_2_10_42_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt593"}],"container-title":["Ecology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fece3.4843","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/ece3.4843","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/ece3.4843","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/am-pdf\/10.1002%2Fece3.4843","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/ece3.4843","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/ece3.4843","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,6]],"date-time":"2023-09-06T21:52:41Z","timestamp":1694037161000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/ece3.4843"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,15]]},"references-count":41,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2019,2]]}},"alternative-id":["10.1002\/ece3.4843"],"URL":"https:\/\/doi.org\/10.1002\/ece3.4843","archive":["Portico"],"relation":{},"ISSN":["2045-7758","2045-7758"],"issn-type":[{"value":"2045-7758","type":"print"},{"value":"2045-7758","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,1,15]]},"assertion":[{"value":"2018-08-31","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-11-25","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-01-15","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}