Soil filtration-sedimentation improves shelled protist recovery in eukaryotic eDNA surveys.
Détails
Télécharger: Lentendu etal 2023_Soil filtration improves protist.pdf (1214.32 [Ko])
Etat: Public
Version: Final published version
Licence: CC BY-NC 4.0
Etat: Public
Version: Final published version
Licence: CC BY-NC 4.0
ID Serval
serval:BIB_D00C2F484700
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Soil filtration-sedimentation improves shelled protist recovery in eukaryotic eDNA surveys.
Périodique
Molecular ecology resources
ISSN
1755-0998 (Electronic)
ISSN-L
1755-098X
Statut éditorial
Publié
Date de publication
08/2023
Peer-reviewed
Oui
Volume
23
Numéro
6
Pages
1361-1371
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: ppublish
Publication Status: ppublish
Résumé
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 easily 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. Total eukaryotic diversity was estimated by V4 18S rRNA metabarcoding and classical amplicon sequence variant calling. A 2- to 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 varied mostly between regions and habitats, which explained the same proportion of variance in bulk soil and filtered samples. The increased resolution in soil protist diversity estimates provided by the filtration-sedimentation method is a strong argument in favour of including it in the standard protocol for soil protist eDNA metabarcoding studies.
Mots-clé
Animals, Eukaryota/genetics, DNA, Environmental, Soil, Ecosystem, Plants/genetics, Biodiversity, DNA Barcoding, Taxonomic/methods, Chrysophyceae, environmental DNA, filtration, protists, soil, testate amoebae
Pubmed
Web of science
Open Access
Oui
Création de la notice
15/05/2023 14:04
Dernière modification de la notice
21/08/2024 6:24