On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces
Abstract Objective Roller swabbing of surfaces is an effective way to obtain environmental DNA, but the current DNA extraction method for these samples is equipment heavy, time consuming, and increases potential contamination through multiple handling. Here, we used rollers to swab a dog kennel and...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-12-01
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| Series: | BMC Research Notes |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13104-023-06669-5 |
| _version_ | 1827399696609443840 |
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| author | Austin M. Guthrie Paul Nevill Christine E. Cooper Philip W. Bateman Mieke van der Heyde |
| author_facet | Austin M. Guthrie Paul Nevill Christine E. Cooper Philip W. Bateman Mieke van der Heyde |
| author_sort | Austin M. Guthrie |
| collection | DOAJ |
| description | Abstract Objective Roller swabbing of surfaces is an effective way to obtain environmental DNA, but the current DNA extraction method for these samples is equipment heavy, time consuming, and increases potential contamination through multiple handling. Here, we used rollers to swab a dog kennel and compared three DNA extraction approaches (water filtration, roller trimming and direct buffer) using two different platforms (Qiacube, Kingfisher). DNA extraction methods were evaluated based on cost, effort, DNA concentration and PCR result. Results The roller trim method emerged as the optimal method with the best PCR results, DNA concentration and cost efficiency, while the buffer-based methods were the least labour intensive but produced mediocre PCR results and DNA concentrations. Additionally, the Kingfisher magnetic bead extractions generally ranked higher in all categories over the Qiacube column-based DNA extractions. Ultimately, the ideal DNA extraction method for a particular study is influenced by logistical constraints in the field such as the size of the roller, the availability of cold storage, and time constraints on the project. Our results demonstrate the strengths and weaknesses of each approach, allowing for informed decision making by researchers. |
| first_indexed | 2024-03-08T19:49:52Z |
| format | Article |
| id | doaj.art-f9d42fc620664244a0fd5605b7ef841c |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-03-08T19:49:52Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-f9d42fc620664244a0fd5605b7ef841c2023-12-24T12:09:07ZengBMCBMC Research Notes1756-05002023-12-011611610.1186/s13104-023-06669-5On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfacesAustin M. Guthrie0Paul Nevill1Christine E. Cooper2Philip W. Bateman3Mieke van der Heyde4MBioMe - Mine Site Biomonitoring Using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin UniversityMBioMe - Mine Site Biomonitoring Using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin UniversitySchool of Molecular and Life Sciences, Curtin UniversityBehavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin UniversityMBioMe - Mine Site Biomonitoring Using eDNA Research Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin UniversityAbstract Objective Roller swabbing of surfaces is an effective way to obtain environmental DNA, but the current DNA extraction method for these samples is equipment heavy, time consuming, and increases potential contamination through multiple handling. Here, we used rollers to swab a dog kennel and compared three DNA extraction approaches (water filtration, roller trimming and direct buffer) using two different platforms (Qiacube, Kingfisher). DNA extraction methods were evaluated based on cost, effort, DNA concentration and PCR result. Results The roller trim method emerged as the optimal method with the best PCR results, DNA concentration and cost efficiency, while the buffer-based methods were the least labour intensive but produced mediocre PCR results and DNA concentrations. Additionally, the Kingfisher magnetic bead extractions generally ranked higher in all categories over the Qiacube column-based DNA extractions. Ultimately, the ideal DNA extraction method for a particular study is influenced by logistical constraints in the field such as the size of the roller, the availability of cold storage, and time constraints on the project. Our results demonstrate the strengths and weaknesses of each approach, allowing for informed decision making by researchers.https://doi.org/10.1186/s13104-023-06669-5Environmental DNAeDNADNA extraction |
| spellingShingle | Austin M. Guthrie Paul Nevill Christine E. Cooper Philip W. Bateman Mieke van der Heyde On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces BMC Research Notes Environmental DNA eDNA DNA extraction |
| title | On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces |
| title_full | On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces |
| title_fullStr | On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces |
| title_full_unstemmed | On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces |
| title_short | On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces |
| title_sort | on a roll a direct comparison of extraction methods for the recovery of edna from roller swabbing of surfaces |
| topic | Environmental DNA eDNA DNA extraction |
| url | https://doi.org/10.1186/s13104-023-06669-5 |
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