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...
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Gespeichert in:

Autor*in:	Austin M. Guthrie [verfasserIn] Paul Nevill [verfasserIn] Christine E. Cooper [verfasserIn] Philip W. Bateman [verfasserIn] Mieke van der Heyde [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	Environmental DNA eDNA DNA extraction

Übergeordnetes Werk:	In: BMC Research Notes - BMC, 2008, 16(2023), 1, Seite 6
Übergeordnetes Werk:	volume:16 ; year:2023 ; number:1 ; pages:6

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s13104-023-06669-5

Katalog-ID:	DOAJ098736965

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520			\|a 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.
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Guthrie</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2023</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a">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. 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callnumber-first	Q - Science
author	Austin M. Guthrie
spellingShingle	Austin M. Guthrie misc QH301-705.5 misc Q1-390 misc Environmental DNA misc eDNA misc DNA extraction misc Medicine misc R misc Biology (General) misc Science (General) On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces
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topic_title	QH301-705.5 Q1-390 On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces Environmental DNA eDNA DNA extraction
topic	misc QH301-705.5 misc Q1-390 misc Environmental DNA misc eDNA misc DNA extraction misc Medicine misc R misc Biology (General) misc Science (General)
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title	On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces
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title_full	On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces
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title_sort	on a roll: a direct comparison of extraction methods for the recovery of edna from roller swabbing of surfaces
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title_auth	On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces
url	https://doi.org/10.1186/s13104-023-06669-5 https://doaj.org/article/f9d42fc620664244a0fd5605b7ef841c https://doaj.org/toc/1756-0500
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On a roll: a direct comparison of extraction methods for the recovery of eDNA from roller swabbing of surfaces

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