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Effects of soil preservation for biodiversity monitoring using environmental DNA
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  • Alessia Guerrieri,
  • Aurélie Bonin,
  • Tamara Münkemüller ,
  • Ludovic Gielly,
  • Wilfried Thuiller,
  • Gentile Francesco Ficetola
Alessia Guerrieri
University of Milan

Corresponding Author:[email protected]

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Aurélie Bonin
University of Milan
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Tamara Münkemüller
Universite Grenoble Alpes
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Ludovic Gielly
Universite Grenoble Alpes
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Wilfried Thuiller
Universite Grenoble Alpes
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Gentile Francesco Ficetola
University of Milan
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Environmental DNA metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa like soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guidelines for best practices so far. Here, we assessed the impact of four methods of soil sample preservation commonly used in metabarcoding studies (preservation at room temperature for 6h, preservation at 4°C for three days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6h at room temperature and preservation for 21 days). For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under optimal conditions (i.e. extraction of eDNA right after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in MOTU richness of bacteria, fungi and eukaryotes across treatments, while the exclusion of rare taxa led to robust results across preservation methods. The differences in community structure among habitats were evident for all treatments, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.
30 Apr 2020Submitted to Molecular Ecology
01 May 2020Submission Checks Completed
01 May 2020Assigned to Editor
22 May 2020Reviewer(s) Assigned
15 Jun 2020Review(s) Completed, Editorial Evaluation Pending
18 Jul 2020Editorial Decision: Revise Minor
10 Sep 2020Review(s) Completed, Editorial Evaluation Pending
10 Sep 20201st Revision Received
23 Sep 2020Editorial Decision: Accept
Jul 2021Published in Molecular Ecology volume 30 issue 13 on pages 3313-3325. 10.1111/mec.15674