Rapid detection and continuous monitoring of environmental contaminants.

Engineering Biology for Climate & Sustainability

Mitigation of Environmental Pollution Goal:

Rapid detection and continuous monitoring of environmental contaminants.

Current State-of-the-Art

As we work to mitigate the impacts of climate change and ensure sustainability, the ability to detect and monitor pollution and contaminants in the environment will play a big role in our ability to mitigate and remove them. Currently, environmental contaminants are typically analyzed in lab settings through processes that are costly, labor-intensive, and slow. Compared to lab-based methods for contaminant detection and monitoring, biosensors are more affordable¹ and portable,² and could detect a wide range of contaminants rapidly at the point-of-need.³ For example, microbes have evolved the ability to sense and respond to environmental cues, including nutrients and pollutants.⁴ This sense-and-response ability can be leveraged for detection of pollutants in the environment⁵ and ultimately coupled to remediation. However, using live organisms like E. coli or S. cerevisiae for sensing has practical challenges, such as their stability and “shelf-life,” and raises additional concerns about biocontainment. Cell-free detection approaches, such as in vitro gene expression systems⁶ and nucleic acid-based sensors⁷ that decouple sensing from a host microbe could circumvent some of these issues.⁸^, ⁹ [For a recent review of biosensor technologies for environmental monitoring, see Gavrilaș et al., 2022.¹⁰]

Despite many of the latest advancements, environmental biosensing technologies still need to be more accurate, sensitive, and reliable to enable widespread adoption; moreover, we need to expand the range of analytes detectable. Specific short-term technical challenges include detecting contaminants at or below regulatory limits, providing fast readouts (e.g., < 15 minutes), performing multiplex detection of contaminants in a single device, and enabling automated in situ sample preparation. Further, biosensors are vulnerable to degradation and fouling in the environment, and many biosensors are only intended for single use. To overcome these challenges, more research is needed to improve sensor shelf-life to enable long term monitoring, such as designing more robust biosensing systems and compartmentalizing biosensor components.¹¹ Existing biosensors also primarily rely on fluorescent or colorimetric outputs, which require additional instrumentation for analysis and quantitation. Developing new biosensing and reporting modalities, such as electrochemical readouts, will enable continuous, real time monitoring, by allowing biosensors to be more easily integrated into existing digital sensor networks.

Breakthrough Capabilities & Milestones

Enable the detection and continuous monitoring of pollutants and priority contaminants in the environment using biosensors.

Engineer highly specific, low-cost, and field-deployable biosensors for priority contaminants (e.g., paper-based cell-free systems).

Bottleneck/Challenge: Reliable reporting from point-of-use, cell-free biosensors as to the presence/absence of heavy metal contaminants (e.g., Cd, Hg, Pb) below regulatory (i.e., EPA, WHO) recommended levels.

Potential Solution: Model and redesign the sequences of existing aptamer sensors for higher binding affinity to target heavy metal contaminants.

Bottleneck/Challenge: Biosensor devices and formats need to be designed to report results more quickly (i.e., in less than 15 minutes).

Potential Solution: For detection of biological analytes, enable the biosensor to perform in situ amplification of target genes for faster detection.

Bottleneck/Challenge: Sample preparation and biosensors can be difficult without specialized knowledge and/or prior training.

Potential Solution: Design and build platforms that simplify sample preparations, such as by combining filtration, pre-concentration, and/or solubilization steps, and that involve no chemical hazards and minimal/no power requirements.

Engineer biosensors to be compatible with digital infrastructure.

Bottleneck/Challenge: Electrical responses from electrochemical reporters (e.g., horseradish peroxidase) currently used in biosensing applications are too weak to be detected by commonly available electronic components.

Potential Solution: Engineer or discover electrochemical reporters capable of generating electrical signals that are strong enough to be sensed by commonly available electronic components.

Demonstrate next-generation biosensors with novel detection modalities.

Bottleneck/Challenge: Current biosensors are limited in their range of detection of contaminants listed in EPA National Primary Drinking Water Regulations and WHO guidelines for drinking water.

Potential Solution: Develop high-throughput selection methods to find new contaminant-binding aptamers and proteins.

Potential Solution: Develop computational models using machine learning and artificial intelligence to design new contaminant-binding aptamers or proteins.

Bottleneck/Challenge: Biosensors that are capable of quantitative, multiplex analyses.

Potential Solution: Design biosensing molecules (e.g., proteins, aptamers) that have orthogonal sequences to minimize cross-interference.

Potential Solution: Engineer low-cost, microfluidic sensors with multiple compartments to house biosensors for detecting different analytes.

Bottleneck/Challenge: Point-of-use biosensors to detect highly-toxic pollutants, such as mining byproducts and nuclear waste.

Potential Solution: Engineer robust biosensor molecules that can withstand high toxicity and pH extremes without denaturing.

Bottleneck/Challenge: Biosensors that function and detect priority contaminants in marine environments (nitrates, phosphates, microplastics).

Potential Solution: Design and engineer point-of-use biosensors for deployment in saline (marine) and wastewater applications.

Enable the deployment of biosensors for field applications and long-term environmental monitoring.

Bottleneck/Challenge: Biofouling and environmental degradation severely limit the capacity for biosensors to be used in environmental monitoring applications.

Potential Solution: Develop anti-fouling biomaterials to encapsulate and protect biosensors.

Potential Solution: Evolve biosensors for long-term functional robustness under complex conditions (pH, temperature, fouling agent fluctuations).

Bottleneck/Challenge: Strong biocontainment strategies for biosensors.

Potential Solution: Develop encapsulation materials that selectively allows the entering and exiting of certain molecules (e.g., analytes and other molecules are allowed to enter the flow cell, but biosensing components are prohibited from leaving).

Bottleneck/Challenge: Limited number of biosensors that work at application-relevant sensitivity and dynamic range.

Potential Solution: Develop transcription factors that can be induced by virtually any small molecule.

Potential Solution: Develop novel workflows that accelerate the design of key sensor response characteristics (e.g., half-maximal induction concentration (K_1/2), at appropriate dynamic range, among others).

Engineer autonomous, self-regulating biosensors that can detect and remediate pollutants.

Bottleneck/Challenge: Enabling long-term passive monitoring in open systems requires consideration of biosafety and biocontainment.

Potential Solution: Develop stable engineered microbial consortia that can respond to and remove any detected pollutants within a limited time-line (e.g., using memory circuits to detect a threshold number of response events that triggers consortia death and release of enzymatic remediators).

Potential Solution: Enrich naturally-occuring communities from polluted environments, using -omics tools to characterize them and engineering/enhance their activity.

Footnotes

Khanmohammadi, A., Jalili Ghazizadeh, A., Hashemi, P., Afkhami, A., Arduini, F., & Bagheri, H. (2020). An overview to electrochemical biosensors and sensors for the detection of environmental contaminants. Journal of the Iranian Chemical Society, 17(10), 2429–2447. https://doi.org/10.1007/s13738-020-01940-z
Bilal, M., & Iqbal, H. M. N. (2019). Microbial-derived biosensors for monitoring environmental contaminants: Recent advances and future outlook. Process Safety and Environmental Protection, 124, 8–17. https://doi.org/10.1016/j.psep.2019.01.032
Zhang, K., Zhang, H., Cao, H., Jiang, Y., Mao, K., & Yang, Z. (2021). Rolling Circle Amplification as an Efficient Analytical Tool for Rapid Detection of Contaminants in Aqueous Environments. Biosensors, 11(10), 352. https://doi.org/10.3390/bios11100352
Gupta, A., Gupta, R., & Singh, R. L. (2016). Microbes and Environment. Principles and Applications of Environmental Biotechnology for a Sustainable Future, 43–84. https://doi.org/10.1007/978-981-10-1866-4_3
Inda, M. E., & Lu, T. K. (2020). Microbes as Biosensors. Annual Review of Microbiology, 74(1), 337–359. https://doi.org/10.1146/annurev-micro-022620-081059
Karig, D. K. (2017). Cell-free synthetic biology for environmental sensing and remediation. Current Opinion in Biotechnology, 45, 69–75. https://doi.org/10.1016/j.copbio.2017.01.010
Wang, Z., Yu, R., Zeng, H., Wang, X., Luo, S., Li, W., Luo, X., & Yang, T. (2019). Nucleic acid-based ratiometric electrochemiluminescent, electrochemical and photoelectrochemical biosensors: A review. Microchimica Acta, 186(7), 405. https://doi.org/10.1007/s00604-019-3514-6
Jung, J. K., Alam, K. K., Verosloff, M. S., Capdevila, D. A., Desmau, M., Clauer, P. R., Lee, J. W., Nguyen, P. Q., Pastén, P. A., Matiasek, S. J., Gaillard, J.-F., Giedroc, D. P., Collins, J. J., & Lucks, J. B. (2020). Cell-free biosensors for rapid detection of water contaminants. Nature Biotechnology, 38(12), 1451–1459. https://doi.org/10.1038/s41587-020-0571-7
Silverman, A. D., Karim, A. S., & Jewett, M. C. (2020). Cell-free gene expression: An expanded repertoire of applications. Nature Reviews Genetics, 21(3), 151–170. https://doi.org/10.1038/s41576-019-0186-3
Gavrilaș, S., Ursachi, C. Ștefan, Perța-Crișan, S., & Munteanu, F.-D. (2022). Recent Trends in Biosensors for Environmental Quality Monitoring. Sensors, 22(4), 1513.https://doi.org/10.3390/s22041513
Li, L., Zhang, R., Tian, X., Li, T., Pu, B., Ma, C., Ba, F., Xiong, C., Shi, Y., Li, J., Keasling, J., Zhang, J., & Liu, Y. (2022). Configurable Compartmentation Enables In Vitro Reconstitution of Sustained Synthetic Biology Systems (p. 2022.03.19.484972). bioRxiv. https://doi.org/10.1101/2022.03.19.484972

Last updated: September 19, 2022 Back