Show simple item record

dc.contributor.authorJeunen, G.J.
dc.contributor.authorKnapp, M.
dc.contributor.authorSpencer, H.G.
dc.contributor.authorTaylor, H.R.
dc.contributor.authorLamare, M.D.
dc.contributor.authorStat, Michael
dc.contributor.authorBunce, Michael
dc.contributor.authorGemmell, N.J.
dc.date.accessioned2023-03-14T04:43:34Z
dc.date.available2023-03-14T04:43:34Z
dc.date.issued2019
dc.identifier.citationJeunen, G.J. and Knapp, M. and Spencer, H.G. and Taylor, H.R. and Lamare, M.D. and Stat, M. and Bunce, M. et al. 2019. Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecology and Evolution. 9 (3): pp. 1323-1335.
dc.identifier.urihttp://hdl.handle.net/20.500.11937/90909
dc.identifier.doi10.1002/ece3.4843
dc.description.abstract

DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding-based biodiversity studies is gaining popularity as a noninvasive, time-efficient, and cost-effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under-surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA-related 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-level assignment) and universal (broad taxonomic group with genus/family-level assignment) approaches obtained from replicates treated with the optimal and a low-performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose-nitrate membranes and extraction with Qiagen's DNeasy Blood & 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-negative 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-nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit or phenol-chloroform-isoamyl for successful implementation of eDNA multi-marker metabarcoding surveys.

dc.languageEnglish
dc.publisherWILEY
dc.relation.sponsoredbyhttp://purl.org/au-research/grants/arc/LP160101508
dc.relation.sponsoredbyhttp://purl.org/au-research/grants/arc/LP160100839
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectScience & Technology
dc.subjectLife Sciences & Biomedicine
dc.subjectEcology
dc.subjectEvolutionary Biology
dc.subjectEnvironmental Sciences & Ecology
dc.subjectbiodiversity assessment
dc.subjecteDNA
dc.subjectextraction
dc.subjectfiltration
dc.subjectmetabarcoding
dc.subjectEXTRACTION
dc.subjectPCR
dc.subjectQUANTIFICATION
dc.subjectCAPTURE
dc.subjectCONSERVATION
dc.subjectPRIMERS
dc.subjectTOOL
dc.subjectbiodiversity assessment
dc.subjecteDNA
dc.subjectextraction
dc.subjectfiltration
dc.subjectmetabarcoding
dc.titleSpecies-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization
dc.typeJournal Article
dcterms.source.volume9
dcterms.source.number3
dcterms.source.startPage1323
dcterms.source.endPage1335
dcterms.source.issn2045-7758
dcterms.source.titleEcology and Evolution
dc.date.updated2023-03-14T04:43:34Z
curtin.departmentSchool of Molecular and Life Sciences (MLS)
curtin.accessStatusOpen access
curtin.facultyFaculty of Science and Engineering
curtin.contributor.orcidBunce, Michael [0000-0002-0302-4206]
curtin.contributor.researcheridStat, Michael [K-5290-2012]
dcterms.source.eissn2045-7758
curtin.contributor.scopusauthoridStat, Michael [14326104400]
curtin.contributor.scopusauthoridBunce, Michael [55160482300]
curtin.repositoryagreementV3


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record

http://creativecommons.org/licenses/by/4.0/
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/