Computational Colloids: Engineered Bacteria As Computational Agents in the Design and Manufacture of New Materials and Structures

We report on a novel project to integrate a civil engineering application with Synthetic Biology through the development of a mechanical sensing bacteria system. The project integrates a team of molecular biologists, civil engineers and an architect.  The aim of the project is to create a bio-based system to strengthen soils in response to mechanical forces. In this system, synthetic bacteria would act as a biological grout enabling, for example, self-constructing foundations. Aside from the geotechnical applications such a technology would push well beyond the current state of the art and challenge a new generation of engineering designers to think at multiple scales from molecular to the built environment and to anticipate civil engineering with living organisms. 

Microbial activity is important to many geotechnical process and bacteria can be responsible for cementing soils. Bacteria, such as Sporosarcina pasteurii and Bacillus megaterium produce ammonia which, in turn, causes calcium carbonate to precipitate. Microorganisms also have a significant impact on the fertility of soils in the upper layers.  Until recently it was thought that bacteria activity decreases substantially with depth. However, bacteria  are  known  to  move  freely  through  many  types  of soils, and they can also  attach to soil particles to form biofilm. This buildup of biofilms can, in turn, change the geotechnical characteristics of soils.

The growth, survivability, adaptation and associated genetic response of bacteria to pressure have been studied in relation to low-pressure environments (sub-0.1 MPa), and ocean bacteria in high-pressure environments (from 10 MPa to over 100 MPa). However, little work has been done at moderate pressures associated with, for example, pore pressures in geotechnical processes (between 0.1 and 10 MPa).

In our project, we have initially studied differential gene expression in response to moderate pressure using Escherichia coli K-12 as model organism. Selected gene promoters are being cloned upstream of  reporter genes to test sensitivity to pressure (at 0.1 to 1 MPa) and engineer a mechanical sensing bacteria. In parallel experiments are being carried out to test that the promoters’ response was pressure-stress specific and not related to other biological stresses. We are also developing a method to build a prototype system using hydrogels as a proxy for soil volumes and to visualize the response of the bacteria to pore pressure changes in three dimensions. In addition, we developed a computational model to link geotechnical modelling with gene expression data which integrates a finite element model of soils under load with diffusion models to calculate effective stress and pore pressure. The resulting visualisations give us an indication of how our proposed system may perform and support the process of model driven design.