Scholarship code CU5.291

Soil and plant-associated microbial communities for resilience to climate changes

  • Reference person
  • Host University/Institute
    Fondazione Edmund Mach
  • Internship
  • Research Keywords
    Plant microbiome
    Soil microbiome
  • Reference ERCs
  • Reference SDGs
    GOAL 2: Zero Hunger
    GOAL 13: Climate Action
    GOAL 15: Life on Land


Every plant tissue is colonized by a complex microbial community that contributes to plant fitness in a variety of ways, including nutrient uptake, resilience to environmental stress and resistance to pathogens colonization. For this reason, arbuscular mycorrhizal fungi (AMF) and plant growth promoting bacteria (PGPB) are considered either as “biofertilizers” or “bioprotectors”. Microbial communities associated with fruits influence their quality and the process of ripening with an impact on post-harvest conservation. The assembly of plant-associated microbial communities is a tightly regulated process that is determined by complex interactions between the microorganisms, their host and the environment. Soil is the major reservoir of plant colonizing organisms that are actively recruited by the host through a variety of mechanisms, but other sources of colonization, including insect vectors, also contribute to shaping plant microbiota. A holistic approach considering the effect of microorganisms on different plant organs and their interactions with the environment would be helpful for developing strategies for crop improvement based on plant-associated microbiota. In this framework, using crop wild relatives (CWRs) and their microbiota offers a wide range of new possibilities.Metagenomics is the technique of choice to characterize complex microbial communities. By targeting conserved marker genes (16S for bacteria,ITS for fungi) it is now possible to characterize the taxonomic profile of complex microbial communities. Direct sequencing of the complete genomic repertoire of the community can provide a full account of its metabolic potential, and, in addition, increase taxonomic resolution to subspecies-level for disentangling in greater detail the structure of the microbiome. Fondazione Edmund Mach hosts some of the largest plant collections in Europe, including more than 3500 grape, 1000 apple, and 400 berries varieties. We will use both targeted and untargeted metagenomic sequencing to characterize the microbial communities that colonize host plants and the possible sources of microbial colonization. This approach will allow to gain a comprehensive picture with strain level resolution of the plant-associated microbiome and of its metabolic potential. Specifically, we will concentrate on soil, root associated microbiota, endophytic compartments and fruit microbiota using blueberry plants (Vaccinium spp.) as model organisms. A selection of wild plants from the Italian Alps will be collected and analyzed as well. The structure and composition of the plant-associated microbiome in different accessions grown under similar environmental conditions will be analyzed, in order to highlight the extent by which the genetics of the host shapes the composition of the microbial communities. Data on phenotypic characteristics of the plant, productivity and fruit metabolic features will be collected and correlated with composition of the microbial communities to identify microbial species associated with resilience against environmental stress, productivity, fruit quality and post-harvest conservation. These data will be complemented by a meta-analysis of publicly available plant and soil-associated metagenome data, to build a comprehensive genomic catalog of soil and plant associated microorganisms that will pave the way for further studies to understand the assembly, evolution, and biogeography of microbial communities in cultivated and wild perennial plants.

Suggested skills:

The successful candidate is expected to have good knowledge of basic microbiology and microbial genomics. In addition, the ideal candidate has good knowledge of major bioinformatic tools and methods, including familiarity with the Unix operating system, genome assembly and annotation tools. Prior experience with metagenomics is desirable. Working knowledge of one high level programming language such as python and/or of the R statistical programming language is a plus.

Research team and environment

The Research and Innovation Centre (CRI) of the Fondazione Edmund Mach pursues scientific research, develops biotechnologies, and promotes innovation for agriculture, bioeconomy, ecology, biodiversity, the environment and food. The Centre focuses on basic and applied research on: (i) strategic supply chains of the Trentino agrosystem; (ii) forest and alpine ecology; (iii) biodiversity evolution and conservation; (iv) effects of climate change on natural and agro ecosystems; (v) bioeconomy, (vi) agrobiotecnology. The multidisciplinary functionality of the Center is guaranteed by the matrix organization and the transversal integration of the 21 Units and 21 Technological facilities on 4 thematic areas, namely Agrosystems and Bioeconomy, Biodiversity, Ecology and Environment, Food and Nutrition and Computational Biology. The Centre has 21 cutting-edge technological platforms operated by highly qualified personnel, including a Plant Phenotyping platform, a Sequencing and Genotyping platform and a Metabolomic platform. The Centre hosts three major germoplasm banks, namely:Grapevine germplasm collection that includes species of the genus Vitis, cultivars of V. Vinifera subsp. Sativa, V.V. Subsp. Sylvestris and interspecific hybrids;Apple germplasm collection that includes species of the Malus genus, cultivar of M. X domestica, M. Sylvestris, M. Sieversii, M. Orientalis and interspecific hybrids;Berries germplasm collection that comprises species of the Vaccinium genus, such as V. Corymbosum, V. Angustifolium, V. Virgatum, V. Myrtillus, V. Vitis ideae, V. Macrocarpon and hybrids, Rubus, Fragaria x ananassa, Ribes and other minor crops.