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Recommendations for tissue homogenisation and extraction in DNA metabarcoding of Malaise trap samples

View ORCID ProfileVera MA Zizka, View ORCID ProfileMatthias F Geiger, View ORCID ProfileThomas Hörren, View ORCID ProfileAmeli Kirse, Niklas W Noll, View ORCID ProfileLivia Schäffler, Alice M Scherges, View ORCID ProfileMartin Sorg
doi: https://doi.org/10.1101/2022.01.25.477667
Vera MA Zizka
1Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring and Conservation Science, Adenauerallee 160, 53113 Bonn, Germany
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  • For correspondence: v.zizka@leibniz-zfmk.de
Matthias F Geiger
1Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring and Conservation Science, Adenauerallee 160, 53113 Bonn, Germany
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Thomas Hörren
2Entomological Society Krefeld (EVK), Marktstraße 159, 47798 Krefeld, Germany
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Ameli Kirse
1Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring and Conservation Science, Adenauerallee 160, 53113 Bonn, Germany
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Niklas W Noll
1Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring and Conservation Science, Adenauerallee 160, 53113 Bonn, Germany
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Livia Schäffler
1Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring and Conservation Science, Adenauerallee 160, 53113 Bonn, Germany
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Alice M Scherges
1Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring and Conservation Science, Adenauerallee 160, 53113 Bonn, Germany
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Martin Sorg
2Entomological Society Krefeld (EVK), Marktstraße 159, 47798 Krefeld, Germany
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  • ORCID record for Martin Sorg
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Abstract

With increased application of DNA metabarcoding in fast and high-resolution biodiversity assessment, various laboratory protocols have been optimised in recent years and their further evaluation is subject of current research. Homogenisation of bulk samples and subsequent DNA extraction from destructed tissue is one way of starting the metabarcoding process. This essential step in the protocol can either be conducted from wet sample material (e.g. bulk insect samples) soaked in fixative or from completely dried individuals. While the latter method appears to produce more consistent results, it is time consuming and more prone to cross-contamination. We tested both homogenisation approaches with regard to time efficiency and biodiversity assessment of complex arthropod bulk samples, in particular how the amount of processed tissue affects taxon recovery. Both approaches reveal similar taxa compositions and detect a similar total OTU diversity in a single extraction reaction. Increased amounts of tissue used in DNA extraction improved OTU diversity detection and recovered particularly specific low-biomass taxa, making this approach valuable for samples with high biomass and/or diversity. Due to less handling time and lower vulnerability for cross-contamination we recommend the processing of wet material when sample homogenisation is applied.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted January 26, 2022.
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Recommendations for tissue homogenisation and extraction in DNA metabarcoding of Malaise trap samples
Vera MA Zizka, Matthias F Geiger, Thomas Hörren, Ameli Kirse, Niklas W Noll, Livia Schäffler, Alice M Scherges, Martin Sorg
bioRxiv 2022.01.25.477667; doi: https://doi.org/10.1101/2022.01.25.477667
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Recommendations for tissue homogenisation and extraction in DNA metabarcoding of Malaise trap samples
Vera MA Zizka, Matthias F Geiger, Thomas Hörren, Ameli Kirse, Niklas W Noll, Livia Schäffler, Alice M Scherges, Martin Sorg
bioRxiv 2022.01.25.477667; doi: https://doi.org/10.1101/2022.01.25.477667

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