Chemotaxis sensing preference in plant-microbe associations

Future food security will rely on increased crop yields using sustainable agricultural practices to meet the demands for food of the projected world population of 9.7 billion by 2050. The microbiome of the plant rhizosphere (the area around the root is known as the rhizosphere, and the group of microbes in an area is known as a microbiome), which can be compared to its human gut homolog, plays a critical role in plant health, ultimately affecting crop yield. Manipulation of the rhizosphere microbes is a proposed strategy for the achievement of sustainable agricultural practices. However, little is known regarding how most beneficial soil bacteria manage to find their target plants, and how they establish stable associations with the roots of plants once they find them. This gap in knowledge will be addressed by examining how bacteria deploy chemical detecting proteins on their surfaces and by studying how the signals from those sensing proteins enter and move around inside the cell. The work will provide detailed quantitative information about how beneficial soil bacteria precisely find their preferred zones on the root surface, and the results will provide new tools for optimizing design of beneficial plant-bacteria associations. The project will have educational impact by providing research training for undergraduate and graduate students from diverse backgrounds, including those from underrepresented groups in STEM. The project will also engage deaf and hard of hearing students in research and thus enhance participation of this critically underserved and untapped pool of talent.

This project will take advantage of the well-characterized chemotaxis response of the motile soil bacterium, Azospirillum brasilense, as a model because it is a suitable representative of root inhabiting bacteria and it is successfully used to promote the growth of diverse crops in sustainable agricultural practices. The experimental design combines proteomics, genetics and computational modeling to address how motile bacteria set sensing preferences for roots. First, the mechanisms underlying the assembly of distinct chemotaxis receptor arrays which are typical of many beneficial root colonizing bacteria will be established (Objective 1). Next, the dynamic changes in the composition of chemotaxis receptor clusters will be related with changes in bacteria sensing preference and competitiveness in the rhizosphere (Objective 2). Because chemotaxis emerges from a sophisticated signaling pathway, it is difficult to predict population behavior from molecular mechanisms. The experimental data will be integrated with computational modeling to quantitatively describe how motile bacteria set chemotaxis sensing preference with change in their metabolism to precisely accumulate at a specific position in a gradient (Objective 3). Results obtained will uncover the engineering principles for manipulation of and/or the synthetic design of chemotaxis sensing preferences in beneficial soil bacteria. This knowledge is critical to develop future strategies for rhizosphere microbiome optimization for sustainable agriculture.