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Using Synthetic Biology to fight Environmental Pollution: New insights into an old problem


Guest post by Anastasia P. Athanasakoglou

‘’Pollution is not a new phenomenon – and nor is action to counter it… There is, however, now a need – and an opportunity – to dramatically step up our ambition.’’

Towards a pollution-free planet: Report of the Executive Director of the United Nations Environment Programme to the 3rd session of the United Nations Environment Assembly


Synthetic Biology (SYNBIO) is a well-established scientific field that offers solutions to a span of societal problems. One specific area where SYNBIO applications seems to hold great promise, even though research is still limited, is combating environmental pollution. With more than 2 million tons of human waste disposed in water bodies every day (UN WWAP 2003), a broad range of harmful substances ends up in the environment, contaminating terrestrial and aquatic ecosystems. Persistent microplastics, pharmaceuticals, personal care products and other hazardous contaminants from industrial and agricultural activities are accumulating more and more on a global scale, reaching critical levels of toxicity. The consequences from the presence of such contaminants in the environment can be particularly severe for all living organisms. In many cases, the health risks from exposure to specific substances are yet to be evaluated, igniting concerns even more.

The use of living microorganisms for detoxification of polluted water or soil sites is not a new practice. Bioremediation, as it is called, is a process that exploits metabolic activities of naturally occurring microbial strains or communities for degradation of harmful pollutants. Even though bioremediation has been proven effective, it is usually limited to specific classes of contaminants. It is consequently tempting to think that expansion of specific metabolic activities through the application of SYNBIO methodologies could widen the range of pollutants that can be degraded and simultaneously improve the efficiency and rate of decontamination.

Read more: Making the World Go Round: Building a Circular Bioeconomy with Synthetic Biology

In their publication ‘‘Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology’’, P. Dvorak, P. Nikel, J. Damborsky and V. de Lorenzo provide a comprehensive overview of how the SYNBIO workflow can be applied to engineer biodegradation pathways in bacterial strains. As a first step, it is essential to choose the contaminant(s) of interest and determine all possible catabolic pathways and their corresponding constituents (metabolites & enzymes). For this purpose, a variety of databases and pathway prediction tools have already been developed and are available for use. Similar tools can assist on the prediction of toxicity of degradation by-products that are undesirable both for the engineered microbes, but also for the final purification process. Once this is set, an appropriate microbial host that will be used as a chassis for engineering the degradation pathway should be selected. The choice is based on different criteria including growth rates, physiological responses to stress conditions and ability to provide specific enzyme cofactors. According to the well-known Design-Build-Test-Analyze cycle of SYNBIO, the following steps of the process require a continuous cycle of expression of the pathway building blocks to the heterologous host, followed by evaluation of the degradation process and optimization of the pathway performance. What is usually applied in these steps is a combination of computational tools to identify rate-limiting reactions and experimental tools to target and improve the activity of bottleneck enzymes. Illustrating examples of how these concepts can be applied have been recently demonstrated with the efficient degradation of the recalcitrant compounds 1,3-dichloroprop-1-ene and 1,2,3-trichloropropane by engineered Pseudomonas putida strains.

The SYNBIO approach to fight environmental pollution seems appealing. Engineered microbes can be particularly effective for bioremediation and can have a great impact in resistant compounds that natural strains cannot eliminate, or have not yet evolved to eliminate. Along that aspect, directed evolution can significantly assist efforts, in those cases where native enzymes are performing insufficiently. The potential for effective decontamination is further increased when considering developments in engineering synthetic microbial consortia, rather than individual strains, for the same purpose. By distributing the metabolic burden into multiple strains, the process can be optimized and undesirable effects, such as toxicity can be minimized. Other possibilities include engineering strains for biomonitoring and more recent advances propose simultaneous pollutant decontamination and synthesis of useful compounds from the waste products. The latter creates opportunities for development of economically viable solutions in environmental biotechnology.

Even though these opportunities are exciting, research in the field in still in its infancy. The limitations to be addressed are still many and the challenges are focused mainly on the stability of the engineered systems, the influence of exogenous biotic and abiotic conditions and the applicability of the proposed methods in the context of large-scale systems.

The major limitation, however, seems to revolve around ethical implications raised from SYNBIO applications in environmental issues. Concerns include, but are not limited to, undesirable spread of engineered organisms in nature and escape of recombinant DNA through horizontal gene transfer to natural populations. While environmental SYNBIO practitioners are already working on addressing these concerns by developing genetic firewalls that prevent any of the unwished scenarios (non-natural DNA bases and/or amino-acids that are limited to the genetic engineered microorganisms, genetic circuits that limit the survival of recombinant DNA to the engineered host or are only triggered by specific stimuli, cell-free SYNBIO approaches), what is still missing is a collective effort to educate and familiarize the general population with biotechnological solutions to societal issues of increasing concern. Only then, SYNBIO practices that aim to fight pollution can really start laying the first stones to provide global solutions to this global threat.


Anastasia Athanasakoglou is a postdoctoral researcher at the Swiss Federal Institute of Aquatic Science and Technology. She completed her PhD in biochemistry of marine natural products at the University of Copenhagen, where she also worked on Synthetic Biology approaches to establish production of secondary metabolites in heterologous hosts. Currently, she is working on investigating and characterizing metabolic pathways in complex microbial communities responsible for degradation of environmental pollutants. Find her on Twitter and Researchgate.

More on the topic:

‘’Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology’’, P. Dvorak, P. Nikel, J. Damborsky and V. de Lorenzo, Biotechnol. Adv. 2017, 35(7):845-866, doi: 10.1016/j.biotechadv.2017

‘’Bioremediation at a global scale: from the test tube to planet Earth’’, V. de Lorenzo, P. Marlière, R. Solé, Microb. Biotechnol. 2016, 9(5):618-25, doi: 10.1111/1751-7915.12399

‘’Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms’’, M. Schmidt and V. de Lorenzo, Curr. Opin. Biotechnol. 2016, 38:90-6, doi: 10.1016/j.copbio.2016.01.006

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