Scholarship code CU5.296

Identify and preserve the unique microbial terroir in a changing alpine environment

  • Reference person
    Rota Stabelli
  • Host University/Institute
    University of Trento
  • Internship
  • Research Keywords
    Microbial biodiversity
    Metagenomic analyses
    Climate change
  • Reference ERCs
    LS8_6 P
    LS8_2 B
  • Reference SDGs
    GOAL 12: Responsible Consumption and Production
    GOAL 13: Climate Action
    GOAL 15: Life on Land


The uniqueness of the Alpine territory and of its agricultural products depends on various abiotic and biotic factors: one of these factors is the microbial community (bacteria, protozoans and fungi) that resides on soil. Commonly used metagenomic techniques such as (amplicon based) metabarcoding can reveal the overall microbial diversity of an ecosystem, but it fails to identify microbial strains or species that are unique to a given environment or area. The indentification and phylogentic profiling of these microorganisms is key to define the uniqueness of specific mountain terroirs, and a first step in planning their conservation in a scenario of continuous climate change.It is now possible to discriminate otherwise indistinguishable microbial varieties using shotgun metagenomic techniques by coupling metagenome-assembled genomes with evolutionary studies. This project aims at applying advanced metagenomic and phylogentic tecniques to characterize the local microbial uniqueness of the Alpine territory. Material of study will be environmental soil samples for which shotgun genome samples is present in databases. Bioinformatic pipelines will be developed to metagenomically assemble genomes from these samples with particular emphasis on the understudied fungal biodiversity. Assembled genomes will be compared with available reference genomes to identify unique local variants using phylogenetic method, and their diversification will be infer the timing of. Molecular clock techniques. These analyses shall reveal unique microbial strains/species that characterize certain regional areas or conditions. A special case of study will be the microbial communities sampled on an Alpine altitudinal gradient to understand the diversity associated with different temperatures. An other case study will be the identification of unique fermenting yeasts associated with spontaneous fermentation in selected Alpine wines. Both studies will be used to forecast the risk of loosing unique terroirs because of global warming and industrialization processes. The project has both long-term biodiversity and economic goals. Definition of unique terroirs is an added value to Alpine agriculture because it helps defining identity, cultural rootedness, and irreproducibility. Knowledge of the actual diversity and uniqueness of soil microorganism is a key step to plan future conservation management in a scenario of continuous climate change.

Suggested skills:

Knowledge of phylogenetic methods including molecular clock and DNA Barcoding Data processing and pipelines using self-made scripts in Python and Bash.Good evolutionary and ecological backgroundKnowledge of soil organisms in particular fungi and bacteria.Principles of morphological identification

Research team and environment

The Molecular Evolution and Phylogenomics lab at University of Trento.The lab is specializes in reconstructing the evolutionary and ecological history of all types of organisms in particular those of agricultural and biomedical importance. We infer phylogenies using model driven inferences, we reconstruct pattern of molecular evolution using phylogenomics, and estimate divergences using molecular clock techniques. Different types of organisms and data are used ranging from barcoding to whole genomes, from metabarcoding to shotgun metagenomics. We collaborate with various colleagues worldwide to study insects, plants, fungi, bacteria and viruses of economical, conservation, biomedical, and environmental interest. The lab has access to state of the art biomolecular, microscopy and computational facilities (two clusters).