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SoilLife Report Summary

Project ID: 320499
Funded under: FP7-IDEAS-ERC
Country: Switzerland

Final Report Summary - SOILLIFE (The Hidden Frontier: Quantitative Exploration of Physical and Ecological Origins of Microbial Diversity in Soil)

Stand-alone description of the project and its outcomes
The primary objective of the ERC ‘SoilLife’ project was to develop quantitative tools and framework to disentangle physical and ecological origins of microbial diversity in soil. In addressing this complex question, the project has developed an individual-based and spatially-resolved modeling platform that integrates soil pore structure, micro-hydrological conditions, nutrient diffusion, and microbial motility dispersion and interactions. The various forms of the computational platform enabled the systematic testing of hypotheses and long standing questions of relevance to contemporary soil microbial ecology. Additionally, the project has developed new physical and biological experimental models for studying the impacts of hydration status and dynamics, and nutrients availability and composition on microbial growth patterns, self-organization and trophic interactions.
The research project has achieved the following objectives: We have transformed the modeling framework that was originally developed for idealized hydrated surface roughness networks. The complex structure of soil aggregates has been abstracted to a three-dimensional (3-D) angular pore network model that allows direct comparison with percolation theory and previous 2-D models. The 3-D network model has permitted the study of the mechanisms governing microbial dispersal (microbes are represented as individual, motile agents) in porous media depending on hydration conditions. The new model has also enabled the study of emerging spatial arrangements of multispecies microbial communities in soil aggregates based on environmental conditions, and has revealed how incompatible metabolic processes (aerobic and anaerobic respiration) can nevertheless coexist in aerated soil due to pore architecture, chemical gradients and water distribution. Finally, the 3-D model has been successfully upscaled to account for microbial activity at the scale of the soil profile. Another extension of the modeling framework has consisted in the development of a scalable patchy surface model. This extension has permitted the modeling of microbial life in soil at larger spatial and temporal scales. The model uses discrete hexagonal patches, each with defined roughness and water-retention properties, which reduces the computation burden needed for simulations and allows us to upscale predictions. This new model has been successfully used to simulate changes in microbial diversity due to variation in hydration conditions (desert microbial community experiencing a rainfall event), and is in agreement with available field data. Furthermore, the model has been used to explain microbial carbon and nitrogen cycling in biological soil crusts that dominate arid regions. We have developed new mechanistic individual-based models of microbial consortia on rough surfaces, and we have shown how trophic interactions between microbes shape the spatial self-organization of consortia. In parallel, we have developed experimental models of microbial consortia and communities in the laboratory based on well-characterized microbial species. We have designed and constructed experimental (micro-)habitats, such as a ceramic porous surfaces and artificial pore networks, that can be used to observe and measure microbial growth and distribution. These experimental systems have enabled fine control over the environmental conditions (nutrients, hydration level) and direct quantification of microbial organization. The output of experiments in controlled systems were in agreement with numerical simulations and showed how motile bacterial populations spatially organize in response to chemical counter-gradients and pore structure, revealing basic principles that help understand microbial organization in natural habitats.

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