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dc.contributor.authorLear, Gavinen_NZ
dc.contributor.authorDickie, Ianen_NZ
dc.contributor.authorBanks, Jonathan C.en_NZ
dc.contributor.authorBoyer, Stephaneen_NZ
dc.contributor.authorBuckley, Hannah L.en_NZ
dc.contributor.authorBuckley, Thomas R.en_NZ
dc.contributor.authorCruickshank, Roben_NZ
dc.contributor.authorDopheide, Andrewen_NZ
dc.contributor.authorHandley, Kim M.en_NZ
dc.contributor.authorHermans, Syrieen_NZ
dc.contributor.authorKamke, Janineen_NZ
dc.contributor.authorLee, Charles Kai-Wuen_NZ
dc.contributor.authorMacDiarmid, Robinen_NZ
dc.contributor.authorMorales, Sergio E.en_NZ
dc.contributor.authorOrlovich, David A.en_NZ
dc.contributor.authorSmissen, Roben_NZ
dc.contributor.authorWood, Jamieen_NZ
dc.contributor.authorHoldaway, Roberten_NZ
dc.date.accessioned2018-03-15T22:39:57Z
dc.date.available2018-01-01en_NZ
dc.date.available2018-03-15T22:39:57Z
dc.date.issued2018en_NZ
dc.identifier.citationLear, G., Dickie, I., Banks, J., Boyer, S., Buckley, H. L., Buckley, T. R., … Holdaway, R. (2018). Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. New Zealand Journal of Ecology, 42(1), 10–50A. https://doi.org/10.20417/nzjecol.42.9en
dc.identifier.issn0110-6465en_NZ
dc.identifier.urihttps://hdl.handle.net/10289/11732
dc.description.abstractAdvances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.
dc.format.mimetypeapplication/pdf
dc.language.isoenen_NZ
dc.publisherNew Zealand Ecological Societyen_NZ
dc.rights© 2018 New Zealand Ecological Society. Used with permission.
dc.subjectScience & Technologyen_NZ
dc.subjectLife Sciences & Biomedicineen_NZ
dc.subjectEcologyen_NZ
dc.subjectEnvironmental Sciences & Ecologyen_NZ
dc.subjectbiological heritageen_NZ
dc.subjectbiodiversity monitoringen_NZ
dc.subjectcommunity profilingen_NZ
dc.subjectDNA primersen_NZ
dc.subjectDNA sequencingen_NZ
dc.subjecteDNAen_NZ
dc.subjectenvironmental DNAen_NZ
dc.subjectIlluminaen_NZ
dc.subjectmetabarcodingen_NZ
dc.subjectmetagenomicsen_NZ
dc.subjectmolecular ecologyen_NZ
dc.subjectPOLYMERASE-CHAIN-REACTIONen_NZ
dc.subjectARBUSCULAR MYCORRHIZAL FUNGIen_NZ
dc.subjectEUKARYOTIC MICROBIAL COMMUNITIESen_NZ
dc.subjectRIBOSOMAL-RNA SEQUENCESen_NZ
dc.subjectDOUBLE-STRANDED-RNAen_NZ
dc.subjectGREAT CRESTED NEWTen_NZ
dc.subjectCYTOCHROME-B GENEen_NZ
dc.subjectOXIDASE SUBUNIT-Ien_NZ
dc.subjectBACTERIAL COMMUNITYen_NZ
dc.subjectNEW-ZEALANDen_NZ
dc.titleMethods for the extraction, storage, amplification and sequencing of DNA from environmental samplesen_NZ
dc.typeJournal Article
dc.identifier.doi10.20417/nzjecol.42.9en_NZ
dc.relation.isPartOfNew Zealand Journal of Ecologyen_NZ
pubs.begin-page10
pubs.elements-id219906
pubs.end-page50A
pubs.issue1en_NZ
pubs.publication-statusPublisheden_NZ
pubs.volume42en_NZ
dc.identifier.eissn1177-7788en_NZ


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