Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?
Background High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens id...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2018-06-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/4980.pdf |
| _version_ | 1827612342065561600 |
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| author | Melissa E. Carew Rhys A. Coleman Ary A. Hoffmann |
| author_facet | Melissa E. Carew Rhys A. Coleman Ary A. Hoffmann |
| author_sort | Melissa E. Carew |
| collection | DOAJ |
| description | Background High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries. Methods In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples. Results This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples. Discussion With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation. |
| first_indexed | 2024-03-09T08:21:05Z |
| format | Article |
| id | doaj.art-cad0f571a1144789beec4eadf367cc6a |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:21:05Z |
| publishDate | 2018-06-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-cad0f571a1144789beec4eadf367cc6a2023-12-02T21:50:00ZengPeerJ Inc.PeerJ2167-83592018-06-016e498010.7717/peerj.4980Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?Melissa E. Carew0Rhys A. Coleman1Ary A. Hoffmann2School of BioSciences, The University of Melbourne, Melbourne, Victoria, AustraliaApplied Research, Melbourne Water Corporation, Melbourne, Victoria, AustraliaSchool of BioSciences, The University of Melbourne, Melbourne, Victoria, AustraliaBackground High throughput DNA sequencing of bulk invertebrate samples or metabarcoding is becoming increasingly used to provide profiles of biological communities for environmental monitoring. As metabarcoding becomes more widely applied, new reference DNA barcodes linked to individual specimens identified by taxonomists are needed. This can be achieved through using DNA extraction methods that are not only suitable for metabarcoding but also for building reference DNA barcode libraries. Methods In this study, we test the suitability of a rapid non-destructive DNA extraction method for metabarcoding of freshwater invertebrate samples. Results This method resulted in detection of taxa from many taxonomic groups, comparable to results obtained with two other tissue-based extraction methods. Most taxa could also be successfully used for subsequent individual-based DNA barcoding and taxonomic identification. The method was successfully applied to field-collected invertebrate samples stored for taxonomic studies in 70% ethanol at room temperature, a commonly used storage method for freshwater samples. Discussion With further refinement and testing, non-destructive extraction has the potential to rapidly characterise species biodiversity in invertebrate samples, while preserving specimens for taxonomic investigation.https://peerj.com/articles/4980.pdfDNA barcodingAquaticMetagenomicsInsectMacroinvertebratesBioassessment |
| spellingShingle | Melissa E. Carew Rhys A. Coleman Ary A. Hoffmann Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? PeerJ DNA barcoding Aquatic Metagenomics Insect Macroinvertebrates Bioassessment |
| title | Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? |
| title_full | Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? |
| title_fullStr | Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? |
| title_full_unstemmed | Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? |
| title_short | Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding? |
| title_sort | can non destructive dna extraction of bulk invertebrate samples be used for metabarcoding |
| topic | DNA barcoding Aquatic Metagenomics Insect Macroinvertebrates Bioassessment |
| url | https://peerj.com/articles/4980.pdf |
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