Mechanisms of Soil Restructuring by Bacterial Aggregates: towards a more efficient and resilient Agriculture

Soil bacteria are of critical importance to soil health.

Soil pore-size distribution over multiple length scales, which facilitates nutrient transport, depends on the presence of soil aggregates, cohesive organo-mineral assemblies formed by bacterial activity. Aggregates support plant health and increase soil stability.

Although restoring aggregate structure in degraded soil can yield great benefits for extreme-weather resilience and agricultural productivity, we lack any mechanistic understanding of how aggregates are formed by bacteria.

This knowledge gap hampers the deployment of promising bio-augmentation strategies for soil restoration, such as inoculation of soil with aggregate-promoting bacteria.

The objective of AgriGate is to narrow this gap by elucidating the biophysical mechanisms of bacterial aggregate-formation.

I will focus on the reciprocal mechanical interactions between bacteria and soil grains, using interdisciplinary methods over multiple spatial scales.

I will first develop a novel microfluidic chip granting real-time optical access to bacterial dynamics inside a three-dimensional bed of model soil grains.

AgriGate’s hypotheses are that (1) there exists an optimal grain size and inoculant richness for bacteria-led aggregation, and (2) that bacterial extracellular polymeric substances (EPS) are necessary for aggregation. I will test these hypotheses by varying grain size, inoculant richness, and bacterial EPS-production in the chip.

Microfluidic experiments will be combined with experiments in bacteria-loaded soil columns observed by X-ray tomography, to extend results to the macroscopic scale and link microscale structure to macroscale function.

The search for optimal aggregation conditions will be formalized mechanistically and extended by a numerical model of bacterial colony growth in a cohesive granular medium.

Together, AgriGate’s new tools and results will provide a strong basis for fundamental and applied studies on soil bio-augmentation.