Cities of old are often described as fetid places, but if you could walk down the streets of an ancient Roman metropolis, you might be surprised at its cleanliness. Ancient Romans stood out, among many other things, for their aqueduct construction and water management. Their towns were mostly free from bad odors generated by wastewater, but how did they manage it?

Romans directed their wastewater to wells or tanks outside the city, where it was treated by microbial activity. They didn’t know it, but they were pioneering the use of bioremediation: harnessing living organisms to consume and break down environmental pollutants.

Although bioremediation has been widely used throughout history, this term became known in 1975 with a report entitled Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products, by R.L. Raymond and coworkers.[1]  However, the process was popularized in the 1980s as a technology for cleaning oil-contaminated coastlines, especially after the Exxon Valdez oil spill in 1989.[2]

Nowadays, we are facing a great environmental crisis. The rapid deterioration of ecosystems, the increasing global temperatures, the loss of biodiversity, and widespread pollution are just some of the alarming signs of it.

On this last point, bioremediation using synthetic microorganisms to degrade contaminants and restore ecosystems emerges as a hope. Microorganisms tailored through synthetic biology can adapt to different types of pollution and operate in various environments. Leveraging their ability to degrade toxic compounds, they are a promising solution to mitigate the negative impacts of human activity on the environment.

Heavy metals, a good starting point

Heavy metals build up in ecosystems due to industrial, technological, agricultural, and mining activities, as well as the indiscriminate use of chemical fertilizers containing these compounds. One cleanup method involves identifying the essential elements for genetic reprogramming, particularly in major metal-oxidizing bacteria like Acidithiobacillus spp.

This genus stands out for its crucial role in bioleaching and bioremediation, due to its extreme environmental adaptability and unique metabolic characteristics. However, the lack of an ideal reporter gene has hindered the understanding of gene expression and regulatory mechanisms in these chemoautotrophic bacteria.

In a recent study[3], firefly luciferase gene was used as a reporter in Acidithiobacillus caldus, creating a luciferase reporter system (Luc) to assess the transcriptional strength of various gene promoters. This system was employed to analyze the regulatory effect of the ferric uptake regulator (Fur) on the feoP gene expression in Acidithiobacillus caldus.

Understanding this mechanism allows for the optimization of bioremediation processes by understanding and enhancing gene expression related to metal uptake and metabolism. This knowledge is useful to select or engineer more efficient bacterial strains, developing precise control strategies, and enabling real-time monitoring of bioremediation activities, ultimately leading to more effective, cost-efficient, and sustainable environmental remediation efforts.

Improving existing biological tools

Another way to mitigate the effects of toxic metals through bioremediation is using biofilms. In this case, they are not only limited to heavy metals but have a multitude of uses, such as addressing the effects of hydrocarbons and pesticides.

Synthetic biology offers great potential for controlling biofilms by improving and expanding existing biological tools, introducing new functions into the system, and exploring new approaches to genetic regulation. With synthetic biology, we can produce biomaterials for beneficial biofilm applications and model biofilms with precise temporal and spatial structures.

Because they can regenerate, we can use biofilms for various purposes. For example, a selective mercury detoxification system was established in which a mercury detector (MerR promoter) was constitutively expressed in E. coli. Subsequently, free mercury was dynamically captured through a synthesized nanofiber called curli.[4]

Studies like these exemplify how bioengineered biofilms can be used for the selective recovery of heavy metals from wastewater and solid waste. However, now it’s time to test these synthetic biofilms on a larger scale to evaluate their performance.[5]

Plastic, the eternal enemy

Synthetic biology also plays a significant role in the microbial decontamination of plastics. PET (Polyethylene terephthalate) has been the most studied plastic by researchers in bioremediation for the past 20 years — it’s widely considered non-biodegradable due to its high crystallinity and the aromatic nature of its molecules.

A recent study reported a promising and eco-friendly solution for the biological decomposition of PET waste in a saltwater environment, using a eukaryotic microalga instead of a bacterium as a model system. The results showed that, through synthetic biology, the diatom P. tricornutum can become a valuable chassis for the biological degradation of PET, especially for bioremediation approaches in PET-polluted seawater.[6]

While these methods pose a significant step forward in tackling the environmental crisis, it’s important to bear in mind that introducing a microorganism into an ecosystem carries certain risks. These include potential competition with native species, unintended gene transfer, or negative interactions with beneficial organisms, among others. Such impacts can influence ecosystem biodiversity and disrupt ecological balance.

To mitigate them, rigorous risk assessment protocols need to be implemented, as well as continuous monitoring, biosecurity measures, and appropriate containment strategies. While advancements in bioremediation and synthetic biology offer promising solutions to environmental challenges, it’s crucial to approach them with caution and thorough consideration of potential risks.

By acknowledging these risks and adopting proactive measures, we can responsibly harness the transformative potential of these technologies, ensuring sustainable progress. In a few years, who knows, we might have a catalogue of tailored bacterial janitors on call for environmental cleanup duty!


  1. Carol Litchfield (2005) “Thirty Years & Counting: Bioremediation in Its Prime? “ BioScience, Volume 55, Issue 3, March 2005, Pages 273–279,[0273:TYACBI]2.0.CO;2 
  2. James R. Bragg, Roger C. Prince, E. James Harner & Ronald M. Atlas (1994) “Effectiveness of bioremediation for the Exxon Valdez oil spill.” Nature 368, 413–418.
  3. Xianke Chen, Xiujie Liu, Yuhui Gao…  & Linxu Chen (2020) “Application of Firefly Luciferase (Luc) as a Reporter Gene for the Chemoautotrophic and Acidophilic Acidithiobacillus spp.” Curr Microbiol 77, 3724–3730.
  4. Pei Kun R. Tay, Peter Q. Nguyen, & Neel S. Joshi (2017) “A Synthetic Circuit for Mercury Bioremediation Using Self-Assembling Functional Amyloids” ACS Synthetic Biology 6, 10, 1841–185
  5. Zhong Li, Xinyu Wang, Jie Wang…& Fuhui Wang (2022) ”Bacterial biofilms as platforms engineered for diverse applications” Biotechnology Advances, Volume 57
  6. Daniel Moog, Johanna Schmitt, Jana Senger… & Uwe G Maier (2019) “Using a marine microalga as a chassis for polyethylene terephthalate (PET) degradation” Microb Cell Fact.