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Soil filtration-sedimentation improves shelled protist recovery in eukaryotic eDNA surveys.
Lentendu, Guillaume; Bruni, Estelle P; Ah-Peng, Claudine; Fujinuma, Junichi; Kubota, Yasuhiro; Lorite, Juan; Peñas, Julio; Huang, Shuyin; Strasberg, Dominique; Vittoz, Pascal; Mitchell, Edward A D.
Afiliación
  • Lentendu G; Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland.
  • Bruni EP; Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland.
  • Ah-Peng C; UMR PVBMT, University of La Réunion, Saint-Pierre, France.
  • Fujinuma J; Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.
  • Kubota Y; Laboratory of Biodiversity and Conservation Biogeography, Faculty of Science, University of the Ryukyus, Nishihara, Japan.
  • Lorite J; Department of Botany, University of Granada, Granada, Spain.
  • Peñas J; Interuniversity Institute for Earth System Research, University of Granada, Granada, Spain.
  • Huang S; Department of Botany, University of Granada, Granada, Spain.
  • Strasberg D; Laboratory of Biodiversity and Conservation Biogeography, Faculty of Science, University of the Ryukyus, Nishihara, Japan.
  • Vittoz P; UMR PVBMT, University of La Réunion, Saint-Pierre, France.
  • Mitchell EAD; Institute of Earth Surface Dynamics, Faculty of Geosciences and Environment, University of Lausanne, Lausanne, Switzerland.
Mol Ecol Resour ; 23(6): 1361-1371, 2023 Aug.
Article en En | MEDLINE | ID: mdl-37157180
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Monitoreo del Ambiente / Eucariontes / ADN Ambiental Límite: Animals Idioma: En Revista: Mol Ecol Resour Año: 2023 Tipo del documento: Article País de afiliación: Suiza Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Monitoreo del Ambiente / Eucariontes / ADN Ambiental Límite: Animals Idioma: En Revista: Mol Ecol Resour Año: 2023 Tipo del documento: Article País de afiliación: Suiza Pais de publicación: Reino Unido