{"refrec":{"BRefID":312261,"RR":"<b>Klunder, L.; Duineveld, G.C.A.; Lavaleye, M.S.S.; van der Veer, H.; Palsboll, P.J.; van Bleijswijk, J.D.L.</b> (2019). Diversity of Wadden Sea macrofauna and meiofauna communities highest in DNA from extractions preceded by cell lysis. <i>J. Sea Res. 152</i>: 101764. <a href=\"https://dx.doi.org/10.1016/j.seares.2019.101764\" target=\"_blank\">https://dx.doi.org/10.1016/j.seares.2019.101764</a>","BEntID":304625,"PublicFlag":1,"CheckedFlag":0,"wosflag":1,"vabbflag":0,"RefStringPartII":". <i>J. Sea Res. 152</i>: 101764. <a href=\"https://dx.doi.org/10.1016/j.seares.2019.101764\" target=\"_blank\">https://dx.doi.org/10.1016/j.seares.2019.101764</a>","DocTypID":8,"DocType":"Journal article","MarineFlag":0,"FreshFlag":0,"BrackishFlag":0,"TerrestrialFlag":0,"Authorstring":"Klunder, L.; Duineveld, G.C.A.; Lavaleye, M.S.S.; van der Veer, H.; Palsboll, P.J.; van Bleijswijk, J.D.L.","OrigTitleTranslFlag":0,"Authorstringtrunc":"Klunder, L. <i>et al.</i>","Englishabstract":"Metabarcoding of genetic material in environmental samples has increasingly been employed as a means to assess biodiversity, also of marine benthic communities. Current protocols employed to extract DNA from benthic samples and subsequent bioinformatics pipelines differ considerably. The present study compares three commonly deployed metabarcoding approaches against a morphological approach to assess benthic biodiversity in an intertidal bay in the Dutch Wadden Sea. Environmental DNA was extracted using three different approaches; extraction of extracellular DNA, extraction preceded by cell lysis of a sieved fraction of the sediment, and extraction of DNA directly from small amounts of sediment. DNA extractions after lysis of sieved sediment fractions best recovered the macrofauna diversity whereas direct DNA extraction of small amounts of sediment best recovered the meiofauna diversity. Extractions of extracellular DNA yielded the lowest number of OTUs per sample and hence an incomplete view of benthic biodiversity. An assessment of different bioinformatic pipelines and parameters was conducted using a mock sample with a known species composition. The RDP classifier performed better than BLAST for taxonomic assignment of the samples in this study. Novel metabarcodes obtained from local specimens were added to the SILVA 18S rRNA database to improve taxonomic assignment. This study provides recommendations for a general metabarcoding protocol for marine benthic surveys in the Wadden Sea.","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"Diversity of Wadden Sea macrofauna and meiofauna communities highest in DNA from extractions preceded by cell lysis","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2024-12-10 01:33:17.368041","timezone_type":1,"timezone":"+01:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":"Wadden Sea; Benthic fauna; Metabarcoding; DNA extraction; Bioinformatics","OtherDescriptors":null,"Notes":null,"AnaPub":2019,"MonPub":null,"DateUpdate":"2020-04-01","DateCreate":"2019-07-01","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":"WOS:000486358800003","VABBcode":null,"OpenAcc":1,"DOI":"10.1016/j.seares.2019.101764"},"refs":null,"anarec":{"AnaID":312261,"PubliDate":2019,"Pagination":"101764","XtraPublOfAnaID":null,"ISBN":null,"Volume":"152","Issue":null,"BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":43261,"SerRR":"Journal of Sea Research. Elsevier/Netherlands Institute for Sea Research: Amsterdam; Den Burg.  ISSN 1385-1101; e-ISSN 1873-1414","StandardTitleSer":"Journal of Sea Research","ISSN":"1385-1101","AbbrevSer":"J. Sea Res.","StandardTitleMon":null,"StartPage":null,"Pages":null,"ToPubliDate":null,"BRefBibLvlCode":"S","SerNotes":null},"monrec":null,"serrec":null,"relations":null,"relationsRev":null,"addrec":null,"othpubs":null,"ownerships":null,"authors":[{"AutName":"Klunder","Firstname":"Lise","Initials":"L.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":304625,"AutID":248995,"OrderNr":1,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"COS","InsFSN":"Koninklijk Nederlands Instituut voor Onderzoek der Zee; Coastal Sciences","ORCID":null,"PersID":29809,"InsID":13656},{"AutName":"Duineveld","Firstname":"Gerard","Initials":"G.C.A.","Affiliation":"OCS","Discriminator":null,"CorporateFlag":0,"BEntID":304625,"AutID":238052,"OrderNr":2,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"OCS","InsFSN":"Koninklijk Nederlands Instituut voor Onderzoek der Zee; Ocean Sciences","ORCID":null,"PersID":2924,"InsID":13654},{"AutName":"Lavaleye","Firstname":"Marc","Initials":"M.S.S.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":304625,"AutID":248010,"OrderNr":3,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"OCS","InsFSN":"Koninklijk Nederlands Instituut voor Onderzoek der Zee; Ocean Sciences","ORCID":null,"PersID":26369,"InsID":13654},{"AutName":"van der Veer","Firstname":"Henk","Initials":"H.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":304625,"AutID":272106,"OrderNr":4,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"COS","InsFSN":"Koninklijk Nederlands Instituut voor Onderzoek der Zee; Coastal Sciences","ORCID":null,"PersID":5044,"InsID":13656},{"AutName":"Palsboll","Firstname":"Per","Initials":"P.J.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":304625,"AutID":238774,"OrderNr":5,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"van Bleijswijk","Firstname":"Judith","Initials":"J.D.L.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":304625,"AutID":242816,"OrderNr":6,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"MMB","InsFSN":"Koninklijk Nederlands Instituut voor Onderzoek der Zee; Marine Microbiology and Biogeochemistry","ORCID":"0000-0002-4748-8168","PersID":11075,"InsID":13655}],"mapdetails":null,"datasets":null,"monographs":null,"monparts":null,"serparts":null,"BEntOpen":304625,"BEntPrivate":null,"availability":[{"BInstID":330843,"LibID":2779,"BRefID":312261,"EmbargoDate":"01/04/2020","FullEmbargoDate":{"date":"2020-04-01 00:00:00.000000","timezone_type":3,"timezone":"Europe/Brussels"},"PhysMedID":16,"hasOCRd":1,"ShelfLocCode":"330843","RFID":null,"PaidValue":null,"Medium":"Server","Description":null,"Acronym":null,"Library":"NIOZ","DutchTerm":null,"URL":null,"ClassifID":260,"Classification":"NIOZ Open Repository","ReqLink":null,"ClassifTypID":1,"URLLocation":"https://www.vliz.be/imisdocs/publications/","SubDir":1,"InternalReq":null,"LoggedInReq":null,"Disclaimer":"Disclaimer_NIOZ","DutchDisclaimer":null,"FileFormat":".pdf","FileDescr":"pdf","InsPub":1,"InsID":397,"FileFormID":6,"LendableFlag":null,"PublicFlag":1,"orderLib":"NIOZ","Notes":null,"AccConID":null,"AccessConstraint":null,"LicURL":null},{"BInstID":330842,"LibID":2779,"BRefID":312261,"EmbargoDate":null,"FullEmbargoDate":null,"PhysMedID":16,"hasOCRd":null,"ShelfLocCode":"330842","RFID":null,"PaidValue":null,"Medium":"Server","Description":null,"Acronym":null,"Library":"NIOZ","DutchTerm":null,"URL":null,"ClassifID":261,"Classification":"NIOZ files","ReqLink":1,"ClassifTypID":3,"URLLocation":"https://www.vliz.be/imisdocs/publications/","SubDir":1,"InternalReq":1,"LoggedInReq":null,"Disclaimer":null,"DutchDisclaimer":null,"FileFormat":".pdf","FileDescr":"pdf","InsPub":1,"InsID":397,"FileFormID":6,"LendableFlag":null,"PublicFlag":1,"orderLib":"NIOZ","Notes":null,"AccConID":null,"AccessConstraint":null,"LicURL":null}],"litstyles":null,"thespers":null,"arch2discl":805,"SERpubls":[{"PublName":"Elsevier","City":"Amsterdam; Den Burg"},{"PublName":"Netherlands Institute for Sea Research","City":"Amsterdam; Den Burg"}],"MONpubls":null,"pictures":[],"thestermsPath":null,"thestermsASFA":null,"taxtermsASFA":null,"geotermsASFA":null,"collections":null,"conf":null,"proj":null,"Physdatasets":null,"spcols":{"805":{"SpName":"Koninklijk Nederlands Instituut voor Onderzoek der Zee","SpColID":805,"ParSpColID":null,"TopParID":null,"ShortName":"NIOZ","URLLocation":"https://www.vliz.be/imis/nioz/imis.php?refid=","LibID":2779,"OpenRepoFlag":1,"SpTypID":1,"TopParIDNotWebsite":null,"SpColPath":"NIOZ"}},"doi":null,"publs":null,"serparttypes":null,"monauthors":null,"MParts":null,"SParts":null,"hLibs":null,"langs":[{"BEntID":304625,"AbstractFlag":0,"LangID":15,"LangCode":"en","Lang":"English","DutchTerm":"Engels","LangCodeExtended":"eng"},{"BEntID":304625,"AbstractFlag":1,"LangID":15,"LangCode":"en","Lang":"English","DutchTerm":"Engels","LangCodeExtended":"eng"}],"urls":[{"URL":"https://dx.doi.org/10.1016/j.seares.2019.101764","externalID":"10.1016/j.seares.2019.101764","URLTypeCode":"DOI","URLID":77155,"URLTypID":13,"URLType":"DOI","URLPrefix":"http://dx.doi.org/"}],"thesterms":null,"taxterms":null,"geoterms":null,"othterms":null,"asfacodes":null,"asfa2codes":null,"thestermsFRIS":null,"taxtermsFRIS":null,"geotermsFRIS":null,"othtermsFRIS":null,"resmessage":"","complete":1,"sessions":{"newSesName":"Leonne.van.der.Weegen@nioz.nl","newSesDate":{"date":"2019-07-01 09:59:23.777000","timezone_type":3,"timezone":"Europe/Brussels"},"updSesName":"T'Jampens, Roeland, R.","updSesDate":{"date":"2020-04-01 01:39:53.730000","timezone_type":3,"timezone":"Europe/Brussels"}}}