Developing Biosensors for Earth System Science

Microbes can be programmed via synthetic biology to report on their behavior, alerting researchers when they have participated in key biogeochemical processes (e.g. denitrification or cell-cell communication) or when their immediate environment has passed a particular physical threshold (e.g. a microbial-scale change in soil water conditions).  This use of synthetic biology has the potential to significantly improve our understanding of microbes’ roles in N, C, and water cycling; however, synthetic microbes have not yet seen wide laboratory use in to study environmental processes because synthetic organisms typically report by fluorescing, making their signals difficult to detect outside the petri dish. We are developing a new suite of biosensors that report instead by releasing easily-detected gases, allowing the real-time, noninvasive monitoring of microbial behavior in soils, sediments, and other complex environmental matrices like marine snow.

We are interested in applying these new microbial tools to a number of problems, ranging from horizontal gene transfer through microbial communication to cryptic element cycling in soils and marine sediments.  Is there a problem you think would be great for a biosensor?  Let us know!  We're always looking for new collaborations.

Current Projects


Shelly designed biosensors with a two-gas reporting system where one gas is constitutively produced to provide information on the number of viable biosensors, and the production of a second gas is coupled to the concentration of AHLs (quorum-sensing molecules used by bacteria) using AHL-dependent transcriptional regulators. She has shown that the ratio of these gases can be used to quantify two AHLs (3-oxo-C6HSL and 3-oxo-C12HSL) in soils under agriculturally-relevant conditions. She also used these biosensors to non-disruptively monitor AHL production by rhizobia in soils and AHL degradation through abiotic or biotic mechanisms.

Ratiometric gas reporting enables in situ AHL quantification in soil, and it provides a simple approach to study how soil conditions affect the bioavailability of AHLs. Together with our previously published results on using gas reporters to track microbial conjugation dynamics in soil, we have demonstrated that the gas reporting method is a generalizable alternative to study microbial gene expression within soil where visual reporters are not compatible. We envision that this easy-to-use gas reporting method will facilitate the development of sophisticated genetic circuits for applications in Earth, environmental, and planetary science.


Many interactions between plants and bacteria depend on communication through extracellular signaling molecules, whose bioavailable concentrations and half-lives can vary with soil conditions. Ilenne aims to understand how the concentrations of these molecules change with biotic and abiotic factors. This work could provide information about the ecological effects of soil amendments and fertilizers, help design strategies for pests control and enhance beneficial microbial processes such as biological nitrogen fixation (BNF).

Ilenne addresses the following challenges in her work:

  1. Analytical tools do not capture time-dependent processes such as production, dilution, and degradation of signals over long incubations.
  2. The high complexity of natural soils makes it difficult to design experiments that allow us to test ecological hypotheses regarding one specific soil parameter at the time.

She has been programming microbes to report on the bioavailability of root exudates and cell-cell signaling molecules using gas reporters as outputs. She  has also helped create a flexible protocol for the production of simplified matrices (artificial soils) with a wide range of physicochemical characteristics that can sustain microbial growth over extended time periods and are compatible with synthetic biology tools. Using these tools, she is exploring microbial niches using soil microorganisms and studying the bioavailability of plant-microbe signaling compounds under different agriculturally relevant conditions and with different soil amendments and. Currently, she is focused on flavonoids, organic acids and AHLs mechanisms of signal loss.


Emm is working to adapt synthetic biology tools for applications in Earth science and soil ecology. Specifically, her research focuses on implementing "biological memory" into gas-reporting biosensors. These memory systems will allow us to track microbial behavior over days-to-months time scales. She is currently developing genetic circuits to track and record horizontal gene transfers in microbial populations.