Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences

Abstract

The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.

Artificial soils reveal individual factor controls on microbial processes

“…In soil, cell-cell communication is mediated by diverse signaling molecules with varied chemistries (DeAngelis, 2016; Schmidt et al, 2019). Signal chemistry and soil properties are thought to modulate signal bioavailability over space and time (Del Valle et al, 2020). Biosensors are ideal for studying how signal bioavailability varies in soils as biosensors report on microbial perception at the micron scale (van der Meer, 2010; Del Valle et al, 2020).…”

“…7b). Additionally, gas biosensors could be coded to report on the bioavailability of other environmental parameters, such as different signaling molecules, intermediates in biogeochemical cycles, metal ions critical to the biocatalysis underlying these cycles, and osmolytes critical to survival in harsh environmental conditions (Del Valle et al, 2020).…”

Programming living sensors for environment, health and biomanufacturing

“…1 ). Expression of any desired genes is referred as ‘reporter’ encoding detectable (Lopreside et al., 2019 ; Del Valle et al., 2021 ) or functional outputs (Hwang et al., 2014 ; Din et al., 2016 ; Chowdhury et al., 2019 ) (Fig. 1 ).…”

Real-time environmental monitoring of contaminants using living electronic sensors

“…Recent strides in biosensing enable the detection of contaminants via different modalities. Synthetic biology has yielded field-deployable biosensors that monitor chemical contaminants ( 5 ), reporting them as visual signals ( 6 , 7 ). Alternatively, bioelectronic sensors have been developed using bacteria that couple chemical sensing to the production of electrical current through a process called extracellular electron transfer (EET) ( 8 – 12 ).…”