Project description
Digging up root microbes
Promising properties from the root microbiome could replace pesticides and fertilisers and revolutionise modern agriculture. However, soil physicochemical complexity and an extraordinarily complex biotic environment create obstacles that need to be addressed with methods of high spatial and temporal resolution. In combination with synthetic bacterial communities this could enable a mechanistic understanding of bacterial establishment in the rhizosphere. In this context, the EU-funded ROOBABAA project will characterise dynamically evolving, distinct micro-niches for bacterial colonisation of the root. Extensive use of the fluorescent microbial marker strains, monitoring of bacterial metabolism, and tracing of proliferation and taxis will be applied to gain the necessary knowledge enabling the successful use of microbial agents in agriculture.
Objective
Root microbiome research is motivated by the promise of using growth-promoting, disease-suppressive bacteria as transferable, protective agents in agriculture. Yet, such approaches have not realized their potential as pesticide or fertilizer alternatives. Major obstacle are soil physico-chemical complexity and a staggeringly complex biotic environment. Recent establishments of synthetic communities promise to enable mechanistic understanding of bacterial establishment in the rhizosphere. However, current methods crucially lack in spatial and temporal resolution. The root is an assembly of dynamically evolving, distinct micro-niches for bacterial colonization that I propose to characterize by extensive use of fluorescent microbial marker strains, monitoring of bacterial metabolism and tracing of proliferation and taxis. This is complemented by precise manipulations of root development. The fractal, open-growth of roots must result in rapid changes in nutrient composition and cycles of nutrient abundance and restriction, forcing bacteria to oscillate between different survival strategies. These fundamental aspects of micro-niche formation, change and collapse are largely undescribed, yet central to understand success or failure of bacterial colonization. I propose to visualize and dissect these processes by combining cutting-edge tools for visualization, optical and genetic manipulations of both plant and bacteria. Bacterial model systems will be inserted into defined bacterial culture collections and results from mono-associations will be challenged by soil-based gnotobiotic systems and high-resolution community profiling. This project will reveal central, dynamic aspects of bacteria-root interactions within a realistic, time-resolved framework of root development. This knowledge will be crucial for progressing to a mechanistic understanding of root bacteria interaction and the reliable use of bacterial agents in agriculture by predictive design of bacterial niches.
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Funding Scheme
ERC-ADG - Advanced GrantHost institution
1015 LAUSANNE
Switzerland