Microbial diversity in forest soils

Post-doctoral researcher : Yannick Colin
University : Université de Pau
Contract period : 20 months

Research topic Microbial diversity in forest soils

Research team and supervising scientitsts
Research team : UMR 1136 Tree/Micro-organism Interactions (IAM) Ecogenomic team
Supervisor : Stéphane Uroz


Context and state of the art Nutrient availability is a fundamental parameter of biogeochemical cycles and regulates both soil fertility and the functioning of an ecosystem. Among terrestrial ecosystems, forests grown on nutrient-poor soils (historically rich soils are dedicated to agricultural crops) in our temperate regions are among the least human-modified ecosystems, compared to agricultural soils, and which are increasingly being exploited for their wood as a resource. A result of this exploitation is accentuated soil depletion, as nutrients accumulated in tree biomass cannot be recycled. However, these features do not prevent forests from growing. In this context, we might well wonder where precisely the necessary nutrients are coming from.

Aside from contributions related to atmospheric deposition and nutrients recycled in dead roots and leaves, soil minerals are the major source of nutrient cations available for the functioning of the ecosystem. The release of nutrients from these minerals (weathering processes) therefore becomes a process critical to the proper functioning of the ecosystem. But how does this mineral weathering operate? What are the relative contributions of abiotic and biotic reactions in this weathering process? What environmental conditions (pH, nutrient cations, microbial habitat availability) impact the structure and function of microbial communities involved in biogeochemical cycles?

The current challenge is to determine: 1) the actors and their interactions, 2) their contributions to the process of mineral alteration and to soil fertility, 3) to identify the molecular mechanisms involved in the process of mineral weathering, and 4) to identify what drives the structuring of these microbial communities.

Objectives and specific questions to be addressed This postdoctoral project will aim to address questions 1) and 4) by way of conducting a detailed study of the distribution and diversity of bacterial communities in different reaction interfaces of forest soils. The objectives are to determine what environmental conditions (pH, poor environment, root zone, fuel type, type of mineral) influence taxonomic diversity and functional communities. The analysis of fungal communities will be also performed on certain habitats. This project is supported by the ANR JC ‘Bactoweather’ and the LabEx ARBRE project ‘INABACT’.

Relevant scientific and socio-economic issues From a scientific perspective, the key issues are determining how environmental conditions (physico-chemical soil characteristics, certain microbial habitats, etc.) influence the taxonomic and functional structure of bacterial communities. The socio-economic issues are to identify potential groups of taxonomic markers characterizing the state of the soil and environmental conditions. These bioindicators will allow for 1), a better understanding of the distribution of bacterial communities and 2), the adjustment of soil management practices.

Methodological approaches and expected resultes This project will be carried out in close collaboration with a PhD student. The doctoral student will learn about the diversity of bacterial communities through a cultivable approach and the postdoctoral researcher will gain insight about the diversity of total communities using environmental genomics approaches (monogenic metagenomics targeting bacterial and fungal communities from DNA chips). This project should further our understanding of microbial communities in the forest at the site located in Montiers-sur-Saulx should help us to identify potential links that exist between nutrient cation availability and the structure of bacterial communities.