EukFunc : A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes

Molecular Ecology Resources, vol. 25, pp. e14118

Abstract

The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes-a prerequisite to better understanding soil systems.

Authors 10

1. Guillaume Lentendu corresponding

   University of Neuchâtel

   Affiliation as printed

   Laboratory of Soil Biodiversity Institute of Biology, University of Neuchâtel Neuchâtel Switzerland

2. David Singer

   CHANGINS - Haute école de viticulture et œnologie

   Affiliation as printed

   Changins College for Viticulture and Enology University of Applied Sciences and Art Western Switzerland Nyon Switzerland

3. Sabine Agatha

   University of Salzburg

   Affiliation as printed

   Department of Environment & Biodiversity Paris Lodron University of Salzburg Salzburg Austria

4. Mohammad Bahram

   Aarhus University · Swedish University of Agricultural Sciences · University of Tartu

   Affiliation as printed

   Department of Agroecology Aarhus University Slagelse Denmark

   Department of Botany Institute of Ecology and Earth Sciences, University of Tartu Tartu Estonia

   Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden

5. S. Emilia Hannula Aachen Department of Environmental Biology Institute of Environmental Sciences (CML)

   Leiden University

   Affiliation as printed

   Department of Environmental Biology Institute of Environmental Sciences (CML), Leiden University, Einsteinweg 2 Leiden the Netherlands

6. Johannes Helder

   Wageningen University & Research

   Affiliation as printed

   Laboratory of Nematology Wageningen University Wageningen the Netherlands

7. Leho Tedersoo

   King Saud University · University of Tartu

   Affiliation as printed

   College of Science, King Saud University Riyadh Saudi Arabia

   Mycology and Microbiology Center University of Tartu Tartu Estonia

8. Walter Traunspurger

   Bielefeld University

   Affiliation as printed

   Animal Ecology Bielefeld University Bielefeld Germany

9. Stefan Geisen

   Wageningen University & Research

   Affiliation as printed

   Laboratory of Nematology Wageningen University Wageningen the Netherlands

10. Enrique Lara

    Consejo Superior de Investigaciones Científicas · Real Jardín Botánico

    Affiliation as printed

    Real Jardín Botánico de Madrid—CSIC Madrid Spain