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  • Publication
    Accès libre
    Higher spatial than seasonal beta diversity of soil protists along elevation gradients
    Biodiversity patterns along elevation gradients have long been studied for plants and animals, but only quite recently for soil microorganisms, especially protists (eukaryotes excluding plants, animals, and fungi). Microorganisms have shorter generation times than macroorganisms, and their abundance, diversity, and community structure are known to vary rapidly in response to abiotic and biotic factors. If microbial diversity varies more seasonally than spatially, a single sampling campaign along an elevation gradient, with contrasted phenologies, could introduce bias into biodiversity studies comparing multiple elevation gradients across different seasons, habitats, regions or latitudes. To address this question, we investigated the relative magnitude of spatial versus temporal diversity (alpha diversity) and community turnover (beta diversity) of soil protist communities along elevation gradients in two distant European mountain ranges. We collected soil samples in forests and grasslands below the treeline along five elevation gradients in two consecutive seasons (spring and summer) in the Spanish Sierra Nevada and the Swiss Alps, covering two distinct biogeographic regions. Using general eukaryotic primers and amplicon sequencing of soil environmental DNA, we decomposed total protist amplicon sequence variants diversity into local alpha- and beta diversity components and identified climatic and edaphic predictors of biodiversity patterns using redundancy analyses. Soil protist communities varied spatially within and among transects but temporal turnover was comparatively low. The best edaphic predictors of community variations were the same in spring and summer, but their explanatory power differed among seasons. The dominant spatial component of beta diversity suggests that patterns of soil protist communities along elevation gradients are more strongly driven by spatial heterogeneity than inter-seasonal turnover. Thus, in temperate climates, our results suggest that sampling only once between the end of spring and late summer across an elevation gradient does not introduce bias due to phenological differences when comparing beta diversity across multiple gradients. Spatio-temporal dynamics of soil protists communities were studied in forests and grasslands below the tree line along five elevation gradients in the Spanish Sierra Nevada and the Swiss Alps during two consecutive seasons (spring and summer). The total diversity of soil protist communities was predominantly shaped by beta-diversity components with spatial heterogeneity rather than temporal turnover as the main driver of soil protist community composition. Community dissimilarity of soil protists did not differ in response to temporal changes between habitats (i.e., forests versus grasslands) The significant edaphic predictors of protist community composition were highly similar in the Swiss Alps and identical in the Spanish Sierra Nevada between both seasons, but their explanatory power varied between spring and summer. Soil protist beta diversity patterns along different elevation gradients remained constant between seasons. This suggests that, in temperate climates, sampling at one time across an elevation gradient will not bias results stemming from phenological contrasts, allowing comparison of beta diversity patterns along such gradients between regions even if sampling is not simultaneous.
  • Publication
    Accès libre
    Soil filtration‐sedimentation improves shelled protist recovery in eukaryotic eDNA surveys
    (2023) ; ;
    Claudine Ah‐Peng
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    Junichi Fujinuma
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    Yasuhiro Kubota
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    Juan Lorite
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    Julio Peñas
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    Shuyin Huang
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    Dominique Strasberg
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    Pascal Vittoz
    ;
    AbstractA 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.
  • Publication
    Accès libre
    Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests
    (2017)
    Mahé, Frédéric
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    de Vargas, Colomban
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    Bass, David
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    Czech, Lucas
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    Stamatakis, Alexandros
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    ; ;
    Mayor, Jordan
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    Bunge, John
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    Sernaker, Sarah
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    Siemensmeyer, Tobias
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    Trautmann, Isabelle
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    Romac, Sarah
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    Berney, Cédric
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    Kozlov, Alexey
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    ;
    Seppey, Christophe V. W
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    Egge, Elianne
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    Wirth, Rainer
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    Trueba, Gabriel
    ;
    Dunthorn, Micah
    High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.