Using Volatile Gas Production As an Output for Genetic Circuits to Report on Programmed Microbial Behaviors in a Soil

Microbes drive processes in the Earth system far exceeding their physical scale, mediating significant fluxes in biogeochemical cycles. Microbial behavior also affects soil development, water quality, and crop yields. The tools of synthetic biology have the potential to significantly improve our understanding of the roles that microbes play in these processes, as well as the effects that heterogeneous environmental materials have on microbial behaviors. However, synthetic biology has not yet seen wide use within environmental materials (soils, sediments, and biomass) because synthetically programmed microbes are hard to deploy into these materials, the vast majority of which are not transparent and are heterogeneous. Traditional visual reporting strategies used to read out circuit status are challenging to use in Earth materials because environmental matrices display high absorbance and auto-fluorescence at wavelengths of light used for traditional visual reporters like GFP. These technical limitations have made it challenging to use programmed microbes to study how variation in soil environmental parameters (moisture, nutrient status, mineralogy, structure, and temperature) affect real-time biological behaviors. To help synthetic biology make the petri-dish-to-soil transition, we are using enzymes that produce small volatile gases as gene expression reporters in soils. We will present data showing that this approach can be used to report on microbial gene expression dynamics in bulk soils at and below the water holding capacity. We will also describe the signal-to-noise for this reporting strategy within a Typic Hapludalf soil from Kellogg Biological Station that consists of a mixture of sand, silt, and clay. Furthermore, we will describe our studies using gas reporting to monitor two dynamic soil microbial processes within this soil, horizontal gene transfer and quorum sensing, and our efforts to benchmark the signal from a volatile gas against standard reporting approaches. Unlike previously described reporters of gene expression, these gas reporters should be useful for studies of microbial processes within soil samples at a range of scales, including sealed vessels widely used by soil scientists to monitor the dynamics of greenhouse gas production.