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.
Highlights
Microbes are exquisite miniature sensors, able to sense, integrate, and respond dynamically to a wide range of environmental conditions
We describe how emerging synthetic biology tools have the potential to improve the performance of traditional biosensors and expand their application to study challenging questions in the Earth and environmental sciences, including the role that cell-cell communication plays in coordinating cellular behavior in native environments, the effects of physical and chemical heterogeneity on microbial behaviors and growth, and capturing fleeting reactions like the cryptic cycling of nutrients that underlie microbial syntrophies
We focus on two examples where biosensors can be used to study the influence of environmental conditions on microbial interactions via: (1) cell-to-cell signaling mediated by diffusible chemical signals, and (2) horizontal gene transfer of conjugative plasmids
Summary
Microbes are exquisite miniature sensors, able to sense, integrate, and respond dynamically to a wide range of environmental conditions. Biosensors pair well with more holistic –omics approaches (Figure 1), which provide a systems-level view of the organisms, biomacromolecules, and metabolites in a sample This -omics information can be used to reconstruct the potential of a sampled environment to perform an ecological process, for example by detecting the presence of genes that underlie the production of greenhouse gases. We describe how emerging synthetic biology tools have the potential to improve the performance of traditional biosensors and expand their application to study challenging questions in the Earth and environmental sciences, including the role that cell-cell communication plays in coordinating cellular behavior in native environments, the effects of physical and chemical heterogeneity on microbial behaviors and growth, and capturing fleeting reactions like the cryptic cycling of nutrients that underlie microbial syntrophies. While a few early tools were employed within environmental samples (DeAngelis et al, 2005, 2007), these tools have not been widely accessible to the Earth and environmental science communities
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