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Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding

Sahraei, Shadi Eshghi and Furneaux, Brendan and Kluting, Kerri and Zakieh, Mustafa and Rydin, Hakan and Hytteborn, Hakan and Rosling, Anna (2022). Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding. Ecology and Evolution. 12 :3 , e8676
[Research article]

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Abstract

Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities 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. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large-scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungsangen 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 investigate 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.

Authors/Creators:Sahraei, Shadi Eshghi and Furneaux, Brendan and Kluting, Kerri and Zakieh, Mustafa and Rydin, Hakan and Hytteborn, Hakan and Rosling, Anna
Title:Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding
Series Name/Journal:Ecology and Evolution
Year of publishing :2022
Volume:12
Number:3
Article number:e8676
Number of Pages:14
Publisher:WILEY
ISSN:2045-7758
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biological Systematics
Keywords:clustering, ITS, rDNA, species hypothesis
URN:NBN:urn:nbn:se:slu:epsilon-p-116850
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-116850
Additional ID:
Type of IDID
DOI10.1002/ece3.8676
Web of Science (WoS)000775192200018
ID Code:27699
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:05 May 2022 08:25
Metadata Last Modified:05 May 2022 08:31

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