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Soil eukaryote community shift but not composition is consistently recovered by different OTU inference methods applied to long read metabarcoding data
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  • Shadi Eshghi Sahraei,
  • Brendan Furneaux,
  • Kerri Kluting,
  • Mustafa Zahieh,
  • Håkan Rydin,
  • Håkan Hytteborn,
  • Anna Rosling
Shadi Eshghi Sahraei
Uppsala Universitet

Corresponding Author:[email protected]

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Brendan Furneaux
Uppsala Universitet
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Kerri Kluting
Uppsala Universitet
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Mustafa Zahieh
Uppsala Universitet
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Håkan Rydin
Uppsala Universitet
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Håkan Hytteborn
Uppsala Universitet
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Anna Rosling
Uppsala Universitet
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Abstract

Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communites of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing and evaluated the performance of three different methods for generation of operational taxonomic units (OTUs). The field site at Kungsängen Nature Reserve has drawn frequent visitors since Linnaeus’s time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic-dry part that has a species rich grass-dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigare how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30-40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.
26 Oct 2021Submitted to Molecular Ecology Resources
15 Nov 2021Submission Checks Completed
15 Nov 2021Assigned to Editor
16 Nov 2021Reviewer(s) Assigned
14 Dec 2021Review(s) Completed, Editorial Evaluation Pending