Soil microbes are increasingly recognized as key components of terrestrial ecosystems, and accordingly many soil metagenomics papers were published in recent years, but surprisingly none of them assessed the environmental niche of microorganisms nor attempted to use niche quantifications to predict the spatial distributions of OTUs but also of their assemblages (community predictions), now and in the future. Few also quantified biotic interactions within and among groups. Protists were also very rarely studied, and robust comparative analyses of >2 microbial groups and macroorganisms along the same environmental gradients are still missing. One identified reason for these gaps is that large soil datasets robustly sampled, together with macroorganisms data, along wide environmental gradients are still needed to address these questions.


Here, we propose to answer these questions by using a large biodiversity dataset, including soil metagenomics data but also plants and insects data, sampled from a previous project in the Swiss Western Alps but not yet used for the proposed analyses. More specifically, we intend to:

  1. further unravel and compare the ecology and biogeography of Bacteria, Fungi and Protista, among them and with plants and insects
  2. build models and future predictions of soil microbe distributions
  3. identify possible biotic interactions among them, and with plants
  4. integrate significant biotic interactions into models and predictions of microbial communities and plants, under present and future conditions (global changes).

Advanced methods developed in the group in previous SNF and European projects will allow addressing all the proposed dimensions: quantifying abiotic responses and environmental niches, quantifying biotic interactions, modelling OTU/species and their assemblages, and deriving spatially-explicit global change projections. The use of sequence count abundance for microbial taxonomic units (OTUs) will require adapting some tools, but solutions exist for all analytical approaches that were already partially implemented in the group.


The project will ultimately provide answers to key questions like:

  • How do fine scale biogeographic patterns of microbes compare among groups and with macroorganisms?
  • How do niches of microbes compare to those of macroorganisms?
  • Do patterns of biotic interactions differ among microbial groups?
  • How do they interact with plants?
  • Can we predict the distribution of microbial OTU and assemblages?
  • How will global change affect these distributions in the future, and can it affect conservation decisions?
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