Fighting freshwater oil spills
We have all heard about devastating marine oil spills, which put ecosystems as well as humans under great threat. This is a great danger for marine live and biodiversity [1]. However, people often overlook that oil spills appear in freshwater habitats like rivers, too. Here they are usually from less great extent, resulting in less public awareness and less scientific research. But in fact, oil spills happen more often in freshwater than in the sea and impose potentially a greater threat to human health [2, 3]. Furthermore, oil spill cleanup is more challenging in rivers [4].
This is because oil in rivers will be less likely to form a continuous film on the surface. Instead, water flux facilitates formation of oil in water emulsions [5]. In addition, freshwater has a lower density than sea water, promoting oil sinking into the water. This means, oil will be more likely to form microscopic micelles, which get distributed throughout the entire water body [2, 6]. This makes conventional cleanup complicated [3] and alternatives like under-water vacuum cleaning are ineffective [4].
This is because oil in rivers will be less likely to form a continuous film on the surface. Instead, water flux facilitates formation of oil in water emulsions [5]. In addition, freshwater has a lower density than sea water, promoting oil sinking into the water. This means, oil will be more likely to form microscopic micelles, which get distributed throughout the entire water body [2, 6]. This makes conventional cleanup complicated [3] and alternatives like under-water vacuum cleaning are ineffective [4].
Oil is made up of numerous compounds, many of which threaten ecosystems. Polycyclic aromatic hydrocarbons (PAHs) are dangerous components of crude as well as refined oil [7]. Large quantities of PAHs can be released into the environment by accidental spillage during transport, extraction or refinery of crude petroleum [8]. As they are xenobiotics, they cannot be biodegraded easily and hence show great persistence in the environment. They are known to be toxic, carcinogenic and mutagenic [7] and thereby contribute to an oil spill related ecosystem collapse [8].
Our approach: synBio against PAHs
We believe that synthetic biology with the ability to produce highly specific enzymes which attack PAH molecules offers a great chance here for a new cleanup method. This is why we engineered bacteria able to break down multiple PAHs. To ensure efficient biodegradation and inhibit biocontamination of GMOs, our bacteria will be immobilized inside a device, which can be installed at critical target sites in rivers. Water, oil and native bacteria will just flow through it, but our engineered strain on the inside will biodegrade toxic PAH molecules, efficiently and cost-effectively cleaning rivers.
Design
The US environmental protection agency lists 16 PAHs as priority pollutants, which show great toxicity and can be commonly found in water bodies [8, 9]. Further research revealed that from these 16 PAHs especially naphthalene, phenanthrene and pyrene pollute rivers in high amounts [10]. Therefore we decided to tackle biodegradation of those PAHs.
Researching about possible chassis, we came across the very promising strain Pseudomonas vancouverensis DSM8368. [11] It shows great stress resistance, making it resilient to live in polluted waters [12]. In addition, its hydrophobic surface facilitates binding and subsequent degradation of PAHs [13]. P. vancouverensis can already completely metabolize naphthalene and phenanthrene but lacks the ability to degrade pyrene [14]. That’s where synBio can help. We introduced five enzymes/enzyme complexes into our chassis enabling it to cleave one pyrene ring and thereby channeling pyrene into its native phenanthrene degradation pathway. In this way it shall be able to metabolize pyrene completely to TCA-intermediates (see our engineering page).
Our drylab team discussed and simulated different designs for our device to ensure optimal contact between polluted water and engineered bacteria (see our model page). To validate our biocontainment strategy, we tested different immobilization strategies on our chassis. In addition, we characterized crucial pyrene degradation enzymes, gaining more insight information in the pathway’s functionality in order to improve it further. Check out our results page for more information.
Our drylab team discussed and simulated different designs for our device to ensure optimal contact between polluted water and engineered bacteria (see our model page). To validate our biocontainment strategy, we tested different immobilization strategies on our chassis. In addition, we characterized crucial pyrene degradation enzymes, gaining more insight information in the pathway’s functionality in order to improve it further. Check out our results page for more information.
References
[1] A. Jernelöv, "The threats from oil spills: now, then, and in the future," Ambio, vol. 39, 5-6, pp. 353–366, 2010, doi: 10.1007/s13280-010-0085-5.
[2] D. Kvočka, D. Žagar, and P. Banovec, "A Review of River Oil Spill Modeling," Water, vol. 13, no. 12, p. 1620, 2021, doi: 10.3390/w13121620.
[3] AMERICAN PETROLEUM INSTITUTE, "Options for Minimizing Environmental Impacts of Freshwater Spill Response," vol. 1994. [Online]. Available: https://response.restoration.noaa.gov/sites/default/files/shoreline_countermeasures_freshwater.pdf
[4] US Office of Response and Restauration, Oil spills in rivers. [Online]. Available: https://response.restoration.noaa.gov/oil-and-chemical-spills/oil-spills/resources/oil-spills-rivers.html (accessed: Sep. 24 2024).
[5] Oil in Freshwater: Chemistry, Biology, Countermeasure Technology, p. 15: Elsevier, 1987.
[6] B. J. Baca and C. D. Getter, "FRESHWATER OIL SPILL CONSIDERATIONS: PROTECTION AND CLEANUP," International Oil Spill Conference Proceedings, vol. 1985, no. 1, pp. 385–390, 1985, doi: 10.7901/2169-3358-1985-1-385.
[7] A. T. Lawal, "Polycyclic aromatic hydrocarbons. A review," Cogent Environmental Science, vol. 3, no. 1, p. 1339841, 2017, doi: 10.1080/23311843.2017.1339841#d1e147.
[8] Dr. Marc Brandt, Doreen Einhenkel-Arle, Polycyclic Aromatic Hydrocarbons. [Online]. Available: https://www.umweltbundesamt.de/sites/default/files/medien/376/publikationen/polycyclic_aromatic_hydrocarbons_web.pdf (accessed: Sep. 24 2024).
[9] Umweltprobenbank des Bundes, EPA-List. [Online]. Available: https://www.umweltprobenbank.de/en/documents/13446 (accessed: Sep. 25 2024).
[10] Peter Heininger, Reinhard Schild, Karin de Beer, Carles Planas, Patrick Roose, and Ole Sortkjaer, Ermittlung der gewässerseitigen Einträge von Polyzyklischen Aromatischen Kohlenwasserstoffen (PAKs) in die Nordsee auf der Basis einer harmonisierten Methodik (internationales Pilotprojekt). [Online]. Available: https://www.umweltbundesamt.de/sites/default/files/medien/publikation/long/2182.pdf (accessed: Sep. 25 2024).
[11] W. W. Mohn, A. E. Wilson, P. Bicho, and E. R. Moore, "Physiological and phylogenetic diversity of bacteria growing on resin acids," Systematic and applied microbiology, vol. 22, no. 1, pp. 68–78, 1999, doi: 10.1016/S0723-2020(99)80029-0.
[12] D. C. Volke, P. Calero, and P. I. Nikel, "Pseudomonas putida," Trends in microbiology, vol. 28, no. 6, pp. 512–513, 2020, doi: 10.1016/j.tim.2020.02.015.
[13] G. Hwang, Y.-M. Ban, C.-H. Lee, C.-H. Chung, and I.-S. Ahn, "Adhesion of Pseudomonas putida NCIB 9816-4 to a naphthalene-contaminated soil," Colloids and surfaces. B, Biointerfaces, vol. 62, no. 1, pp. 91–96, 2008, doi: 10.1016/j.colsurfb.2007.09.014.
[14] Y. Yang, R. F. Chen, and M. P. Shiaris, "Metabolism of naphthalene, fluorene, and phenanthrene: preliminary characterization of a cloned gene cluster from Pseudomonas putida NCIB 9816," Journal of bacteriology, vol. 176, no. 8, pp. 2158–2164, 1994, doi: 10.1128/jb.176.8.2158-2164.1994.
[2] D. Kvočka, D. Žagar, and P. Banovec, "A Review of River Oil Spill Modeling," Water, vol. 13, no. 12, p. 1620, 2021, doi: 10.3390/w13121620.
[3] AMERICAN PETROLEUM INSTITUTE, "Options for Minimizing Environmental Impacts of Freshwater Spill Response," vol. 1994. [Online]. Available: https://response.restoration.noaa.gov/sites/default/files/shoreline_countermeasures_freshwater.pdf
[4] US Office of Response and Restauration, Oil spills in rivers. [Online]. Available: https://response.restoration.noaa.gov/oil-and-chemical-spills/oil-spills/resources/oil-spills-rivers.html (accessed: Sep. 24 2024).
[5] Oil in Freshwater: Chemistry, Biology, Countermeasure Technology, p. 15: Elsevier, 1987.
[6] B. J. Baca and C. D. Getter, "FRESHWATER OIL SPILL CONSIDERATIONS: PROTECTION AND CLEANUP," International Oil Spill Conference Proceedings, vol. 1985, no. 1, pp. 385–390, 1985, doi: 10.7901/2169-3358-1985-1-385.
[7] A. T. Lawal, "Polycyclic aromatic hydrocarbons. A review," Cogent Environmental Science, vol. 3, no. 1, p. 1339841, 2017, doi: 10.1080/23311843.2017.1339841#d1e147.
[8] Dr. Marc Brandt, Doreen Einhenkel-Arle, Polycyclic Aromatic Hydrocarbons. [Online]. Available: https://www.umweltbundesamt.de/sites/default/files/medien/376/publikationen/polycyclic_aromatic_hydrocarbons_web.pdf (accessed: Sep. 24 2024).
[9] Umweltprobenbank des Bundes, EPA-List. [Online]. Available: https://www.umweltprobenbank.de/en/documents/13446 (accessed: Sep. 25 2024).
[10] Peter Heininger, Reinhard Schild, Karin de Beer, Carles Planas, Patrick Roose, and Ole Sortkjaer, Ermittlung der gewässerseitigen Einträge von Polyzyklischen Aromatischen Kohlenwasserstoffen (PAKs) in die Nordsee auf der Basis einer harmonisierten Methodik (internationales Pilotprojekt). [Online]. Available: https://www.umweltbundesamt.de/sites/default/files/medien/publikation/long/2182.pdf (accessed: Sep. 25 2024).
[11] W. W. Mohn, A. E. Wilson, P. Bicho, and E. R. Moore, "Physiological and phylogenetic diversity of bacteria growing on resin acids," Systematic and applied microbiology, vol. 22, no. 1, pp. 68–78, 1999, doi: 10.1016/S0723-2020(99)80029-0.
[12] D. C. Volke, P. Calero, and P. I. Nikel, "Pseudomonas putida," Trends in microbiology, vol. 28, no. 6, pp. 512–513, 2020, doi: 10.1016/j.tim.2020.02.015.
[13] G. Hwang, Y.-M. Ban, C.-H. Lee, C.-H. Chung, and I.-S. Ahn, "Adhesion of Pseudomonas putida NCIB 9816-4 to a naphthalene-contaminated soil," Colloids and surfaces. B, Biointerfaces, vol. 62, no. 1, pp. 91–96, 2008, doi: 10.1016/j.colsurfb.2007.09.014.
[14] Y. Yang, R. F. Chen, and M. P. Shiaris, "Metabolism of naphthalene, fluorene, and phenanthrene: preliminary characterization of a cloned gene cluster from Pseudomonas putida NCIB 9816," Journal of bacteriology, vol. 176, no. 8, pp. 2158–2164, 1994, doi: 10.1128/jb.176.8.2158-2164.1994.