Towards a better understanding of soil multi-trophic biodiversity through the use of environmental DNA metabarcoding

• Main Author: Calderon Sanou, Irene
• Other Authors: Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Grenoble Alpes 2020-., Wilfried Thuiller
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: HAL CCSD 2022
• Subjects: Biodiversity patterns; Environmental DNA; Metabarcoding; Food web; Patrons de biodiversité; ADN environnemental; Réseaux d'interaction; [SDV.EE]Life Sciences [q-bio]/Ecology; environment; Northern Norway; Subarctic
• Online Access: https://theses.hal.science/tel-03890224; https://theses.hal.science/tel-03890224/document; https://theses.hal.science/tel-03890224/file/CALDERON-SANOU_2022_diffusion.pdf

Although soil organisms represent one-quarter of the whole biodiversity on earth, our current understanding of the main drivers of soil biodiversity along environmental gradients is mostly restricted to a limited set of aboveground macro-organisms. In light of increasing global threats to ecosystems, the inclusion of soil organisms into macroecological studies is crucial to improve predictions of ecological responses of terrestrial ecosystems to global changes and support their conservation. Moreover, multitrophic approaches that account for multiple groups of interacting organisms in the ecosystem allow a more holistic understanding of soil biodiversity and its drivers.In my PhD, I aimed at getting a better understanding of the response of soil multitrophic diversity to rapid environmental changes at regional and local scales, by combining soil environmental DNA metabarcoding data, mathematical and statistical tools derived from network theory, and food web ecology.The thesis is developed in four chapters. First, because most of the analyses were based on eDNA metabarcoding data, I needed to gain a better understanding of the uncertainties associated with the use of eDNA metabarcoding in empirical analyses. In the first chapter, I showed that the use of Shannon diversity led to more reliable results from different ecological analyses. I then proposed a roadmap of crucial curation steps for different types of ecological analyses. Second, using eDNA soil data from subarctic birch forests of Northern Norway, I showed that the effect of severe moth outbreaks has cascaded locally from plant communities to the entire soil food web, creating a shift in the ecosystem state. Next, I studied how soil multitrophic diversity responded to environmental gradients using a large-scale biodiversity observatory in the French Alps (chapters 3 and 4). In the third chapter, I conducted a comparative analysis across major soil trophic groups to assess the drivers of soil diversity in the light of well known ecological hypotheses ...