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As environmental threats increase due to climate change, pollution, and toxin release, there is a critical need for a dynamic system that allows for high-sensitivity detection and rapid reporting of environmental contaminants. Current detection systems have numerous technical and logistical challenges, are expensive, and time-consuming. Bioengineering offers the potential for rapid, cheap, scalable technology. Could we use synthetic biology approaches to design a system that relies on engineered microbes as detection agents? What would this system look like? How close are we to making this theory a reality?

We convened a group of experts on the r/AskScience subreddit to answer your questions about environmental biosensors.

  • Alicia Johnson, Ph.D. – Civic Science Postdoctoral Associate, Baker Institute Center for Health Policy and the Science and Technology Policy Program, Rice University
  • Dorsa Sattari Khavas – Graduate Student, Department of Chemical and Biomolecular Engineering, Rice University
  • Zach LaTurner, Ph.D. – Postdoctoral Associate, Civil and Environmental Engineering Department, Rice University
  • Lauren Stadler, Ph.D. – Associate Professor of Civil and Environmental Engineering, Rice University

Q&A Highlights

 Zach LaTurner –

Usually, we try to pick a microbe that was isolated from the environment of interest since that makes it more likely the microbe naturally has the traits to survive in said environment. Our group also specifically focuses on microbes that are capable of extracellular electron transfer (EET) since this allows them to interface with electronics to quickly report back when they have sensed something. Another consideration is genetic tractability as we need the ability to engineer the organism to incorporate sensing apparatus.

 Zach LaTurner –

The organisms that we are specifically using at Rice currently include (but aren’t limited to): Escherichia coli, which is capable of surviving in many human associated environments, in our case has been engineered to do EET, and has many tools for genetic modification. Geobacter sulfurreducens, which was first isolated from a contaminated ditch, is natively EET capable, and has some tools for genetic modification. Shewenella oneidensis, which was first isolated from a lake, is natively EET capable, and also has some tools for genetic modifications. Some other projects involve Lactiplantibacillus plantarum and Vibrio natriegens.

Lauren Stadler –

Microbes could be engineered to sense and report on their environmental conditions, such as bioavailable nutrients, like nitrogen and phosphorus, or chemical toxins and then report on the levels in the environment by producing an output that could be read out in real-time or after a defined period of time.

Dorsa Sattari Khavas –

pH-sensitive fluorescent proteins such as pHluorin (a GFP variant) change their spectral properties in response to proton concentration and have been widely applied for intracellular pH monitoring. Also, microbes naturally possess acid-responsive transcriptional regulators and promoters (e.g., gadA/gadB and asr in E. coli), which can be directly repurposed as input modules for genetic circuits that respond to changes in extracellular pH.

Zach LaTurner –

pH is a very important environmental parameter for most microbes to sense. Because of that, I would expect there to be many naturally evolved sensors out there that could be repurposed for your application. It might be harder to find one that has the dynamic range relevant to your environment and which is also insensitive to other environmental changes/compounds that could give false positives. You would probably want to look at transcription factors or two component regulatory systems. Unless the internal pH of the cell is also changing, the transcription factor would need a way to sense the environment external to the cell as well. Proteins are generally pH sensitive, so maybe there is a repressor protein, not specifically for pH, that denatures at certain pHs leading to derepression of your genetic circuit.

Alicia Johnson –

There are still a few technical issues to be worked out with making this available for home testing. Things like sensitivity and high specificity to detect low levels, ensuring accuracy and stability of the sensor and overall device, and making it user friendly. There are a few policy reasons too. To truly benefit everyone, these devices should be affordable. Regulation also plays a role as well, what would standardization look like? What happens to that data? How can people follow up on it? These are just a few social/policy questions to consider when sending technologies like water biosensors out into everyday life.

Links related to experts’ work:

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

Real-time bioelectronic sensing of environmental contaminants

Long-duration environmental biosensing by recording analyte detection in DNA using recombinase memory

Information storage across a microbial community using universal RNA barcoding

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