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Soil filtration-sedimentation improves shelled protist discovery in eukaryotic eDNA surveys
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  • Guillaume Lentendu,
  • Estelle P. Bruni,
  • Claudine Ah-Peng,
  • Junichi Fujinuma,
  • Yasuhiro Kubota,
  • Juan Lorite,
  • Julio Peñas,
  • Shuyin Huang,
  • Dominique Strasberg,
  • Pascal Vittoz,
  • Edward A. D. Mitchell
Guillaume Lentendu
University of Neuchâtel Institute of Biology

Corresponding Author:[email protected]

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Estelle P. Bruni
University of Neuchâtel Institute of Biology
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Claudine Ah-Peng
Université de la Réunion
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Junichi Fujinuma
University of Tartu Institute of Ecology and Earth Sciences
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Yasuhiro Kubota
University of the Ryukyus
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Juan Lorite
University of Granada
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Julio Peñas
University of Granada
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Shuyin Huang
University of the Ryukyus
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Dominique Strasberg
Université de la Réunion
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Pascal Vittoz
University of Lausanne Faculty of Geosciences and Environment
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Edward A. D. Mitchell
University of Neuchâtel Institute of Biology
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Abstract

A large part of the soil protist diversity is missed in metabarcoding studies based on 0.25 g of soil environmental DNA (eDNA) and universal primers due to ca. 80 % co-amplification of non-target plants, animals and fungi. To overcome this problem, enrichment of the substrate used for eDNA extraction is an easyly implemented option but its effect has not yet been tested. In this study, we evaluated the effect of a 150 µm mesh size filtration and sedimentation method to improve the recovery of protist eDNA, while reducing the co-extraction of plant, animal and fungal eDNA, using a set of contrasted forest and alpine soils from La Réunion, Japan, Spain and Switzerland. Biodiversity of the whole eukaryotic community was estimated with V4 18S rRNA metabarcoding and classical amplicon sequence variant calling. A 2-3-fold enrichment in shelled protists (Euglyphida, Arcellinida and Chrysophyceae) was observed at the sample level with the proposed method, with, at the same time, a 2-fold depletion of Fungi and a 3-fold depletion of Embryophyceae. Protist alpha diversity was slightly lower in filtered samples due to reduced coverage in Variosea and Sarcomonadea, but significant differences were observed in only one region. Beta diversity was mostly impacted by region and habitat, and explained the same variance in bulk soil and filtered samples. The increase resolution in the soil protist diversity provided by the filtration-sedimentation method is a strong argument to include it in the standard preparation of any future soil for protist eDNA metabarcoding studies.
20 Dec 2022Submitted to Molecular Ecology Resources
04 Jan 2023Submission Checks Completed
04 Jan 2023Assigned to Editor
04 Jan 2023Review(s) Completed, Editorial Evaluation Pending
06 Jan 2023Reviewer(s) Assigned
27 Feb 2023Editorial Decision: Revise Minor
31 Mar 20231st Revision Received
04 Apr 2023Submission Checks Completed
04 Apr 2023Assigned to Editor
04 Apr 2023Review(s) Completed, Editorial Evaluation Pending
05 Apr 2023Reviewer(s) Assigned
26 Apr 2023Editorial Decision: Accept