Mitigate targeted environmental pollutants through biosequestration and biodegradation.

Engineering Biology for Climate & Sustainability

Mitigation of Environmental Pollution Goal:

Mitigate targeted environmental pollutants through biosequestration and biodegradation.

Current State-of-the-Art

Biosequestration leverages biological organisms and biobased systems to recognize, bind, and absorb target contaminants. Examples of biosequestration are primarily seen with carbon, including CO₂, and bacterial and macroalgal binding of heavy metals,¹^, ²^, ³ and there has been demonstrated success of oil spill bioremediation by hydrocarbonoclastic bacteria.⁴^, ⁵ While heavy metals are a significant environmental remediation challenge, so too are other recalcitrant materials, including plastics and per- and polyfluoroalkyl substances (PFAS), which are heavily abundant in waters and soils world-wide. The ability to sequester, and then degrade, these pollutants through biological processes will significantly impact all biospheres.

In general, biosequestration of inorganics tends to be a slow process because the biochemistries involved are inherently toxic to organisms. For example, toxic inorganics can compete with normal metal cofactors for binding in enzymes and damage important biomolecules.⁶ Approaches to circumvent these issues include finding organisms and proteins that are resistant to metal toxicity, engineering cofactor binding competition, enabling organisms to compartmentalize toxins, engineering strong uptake systems, and accelerating enzymatic processes to mineralize inorganics, which can effectively detoxify the pollutant. Alternatively, once inorganic contaminants have been taken up through biosequestration, they could be reduced using conventional chemical processing into solid metal.

In contrast to biosequestration, biodegradation is the breakdown of organic materials by organisms and cellular/cell-free complexes. Importantly, organic contaminants are not necessarily toxic to organisms or disruptive to cells at the molecular level. Detoxification of organic contaminants often occurs via metabolic processes, such as when bacteria or enzymes break down an organic compound into chemicals the cell could use (e.g., acetate). Thus, it is important to engineer metabolic pathways for more efficient breakdown of organic contaminants, in addition to developing organisms and cell-free systems for better binding and recognition of target compounds.

Breakthrough Capabilities & Milestones

Degrade plastic waste through engineered bioprocesses.

Engineer microbes, microbial consortia, or enzymes to efficiently degrade common plastic polymers.

Bottleneck/Challenge: Activity, stability, and reusability of PETase, and other (novel) enzymes to effectively depolymerize polyethylene, polypropylene, and polystyrene.

Potential Solution: Leverage protein engineering to design enzymes for desired traits, such as improved binding and hydrolysis of target polymers.

Potential Solution: Use metagenomic analysis to profile and select for microbial strains with high expression levels of PETase.

Bottleneck/Challenge: Efficiency of microbial production of hydrolytic enzymes, to make biodegradation viable at the industrial scale.

Potential Solution: Engineer microbes and other model organisms to increase the expression of desired hydrolytic enzymes.

Bottleneck/Challenge: Environmental safety of metabolites from degraded plastics.

Potential Solution: Carry-out extensive field trials to identify concerning side products and evolve hydrolytic enzymes to remove such side metabolites.

Enable the integration of degradation enzymes for local, on-demand plastic waste processing.

Bottleneck/Challenge: A wider-range of efficient and thermostable enzymes for plastic polymer degradation are needed (for example, see Lu et al., 2022⁷).

Potential Solution: Further machine learning and deep design for protein engineering.

Potential Solution: Platforms for laboratory evolution of enzymes for plastic degradation.

Develop microbial consortia and enzymatic cocktails for the efficient breakdown of mixed-waste plastics (e.g., multi-layer plastics such as those found in carpets or shoes) and ‘dirty’/used plastics (e.g., takeout containers).

Incorporate engineered invertebrates (e.g., waxworm) into plastic degradation processes.

Bottleneck/Challenge: Incomplete digestion and degradation of plastics in the invertebrate gut could lead to the production of microplastics.

Potential Solution: Use multi-omics techniques and mass spectrometry to investigate and better understand polymer degradation pathways and byproducts in invertebrates that digest plastics.

Potential Solution: Develop secondary degradation processes that use engineered bacteria or fungi to further digest and degrade microplastic byproducts.

Engineer organisms or enzymes to ‘carbon-negatively’ degrade plastics in situ, in different ecological niches (e.g., in soil, on the ocean floor).

Bottleneck/Challenge: Most plastic materials (synthetic polymers) are considered non-biodegradable.

Potential Solution:Engineer organisms or cell-free systems that specifically target labile or bioavailable polymer additives (including colorants, antioxidants, and plasticizers.⁸

Design bioplastics with innate degradation mechanisms (e.g., embedded enzymes).

Engineer microbes and/or develop bioprocesses that recycle plastic hydrolysates into value-added products.

Bottleneck/Challenge: Most bioprocessing product yields and purities from plastic feedstocks are not economically-advantageous.

Potential Solution: New pathways and enzymatic cascades are needed to produce valuable products from plastic hydrolysates.⁹

For more on engineering biology to recycle/up-cycle plastic waste, please see Goal: Enable sustainable production of plastics and chemicals. | Breakthrough Capability: Produce commodity chemicals by upcycling waste streams via bioprocessing.

Enable the biodegradation of per- and polyfluoroalkyl substances (PFAS) in water and soil.¹⁰

Demonstrate the efficient biodegradation of PFAS, perfluorooctanoic acid (PFOA), and perfluorooctanesulfonic acid (PFOS) in managed settings (e.g., water treatment plants, bioreactors).

Bottleneck/Challenge: Compared to alternative degradation methods, biodegradation of PFAS is more cost-effective, but still time consuming (takes days to fully degrade).

Potential Solution: Fully map the degradation pathways and enzymes of PFAS and PFOS degrading microbes (e.g., Pseudomonas) to enable biodegradation of PFAS in less than 24 hours.

Bottleneck/Challenge: The presence of other chemicals may decrease the rate at which microbes degrade PFAS.

Potential Solution: Develop high-throughput methods to test degradation efficiency of perfluorinated compounds in the presence of other common waste stream pollutants, to identify characteristics that allow microbes or complexes to function at high degradation efficiencies.

Operationalize enzymes and microbes to degrade PFAS contaminants in dilute waste streams (concentration less than 200 ng/L*), such as municipal water sources.

Bottleneck/Challenge: Most PFOS and PFOA compounds are considered terminally degraded due to the high strength of their carbon—fluorine bonds.

Potential Solution: Engineer dehalogenation and defluorination pathways into the metabolic pathways of model organisms.¹¹

Demonstrate biodegradation of PFAS, PFOA, and PFOS in semi-managed and unmanaged settings (e.g., farmland, coastal areas and marine environments).

Bottleneck/Challenge: Biodegradation of PFAS at low concentrations (<200 ng/L).

Potential Solution: Engineer metabolic pathways in native (anaerobic) microbes that exclusively require the relatively high oxidation states of perfluorinated chemicals.¹²

Bottleneck/Challenge: Biodegradation of complex mixtures of PFAS contaminants that co-exist in soil or water matrices.

Potential Solution: Engineer bacterial consortia or plant-microbe-fungi symbiotic systems to enable the extraction of multiple PFAS contaminants.

*Liu, J., & Mejia Avendaño, S. (2013). Microbial degradation of polyfluoroalkyl chemicals in the environment: A review. Environment International, 61, 98–114. https://doi.org/10.1016/j.envint.2013.08.022

Enable the biosequestration of heavy metals in the environment and at scale.

Identify and engineer microbes tolerant to biosequestration of heavy metals from the environment.

Bottleneck/Challenge: Toxicity tolerance and heavy metal uptake varies between bacterial strain and the type of metal.

Potential Solution: Leverage metagenomics to characterize organisms and enzymes that have adapted to heavily polluted environments to identify useful biological parts for toxin removal and remediation.

Potential Solution: Engineer microbes to take up and sequester multiple types of heavy metal simultaneously, such as through broad-spectrum metal chelating proteins or biomolecules with high affinity and capacity.

Potential Solution: As an alternative to whole organisms, develop protein-based materials for binding and recovering heavy metals, particularly from waste streams.

Engineer microbial pathways to efficiently express selective metal binding proteins and biomolecules.

Enable cost-effective, industrial production of metal binding proteins or biomolecules at scale.

Engineer plants to improve their capacity for heavy metal uptake and accumulation.

Bottleneck/Challenge: Phytoremediation can be a particularly slow and/or laborious process.

Potential Solution: Engineer plants for faster growth and increased biomass.

Potential Solution: Inoculate plant root and/or rhizobia with filamentous fungi and microbes engineered to increase heavy metal uptake.

Potential Solution: Investigate the effects of overexpressing certain metal chelating ligands on the overall growth and metal toxicity tolerance of the plant.

Bottleneck/Challenge: Heavy metal accumulation causes oxidative stress in plants.

Potential Solution: Characterize oxidative stress response in hyperaccumulators, to identify effective antioxidant enzymes, pathways, and DNA repair mechanisms.

Potential Solution: Based on a fuller understanding of oxidative stress in plants, engineer specific genes, enzymes, and pathways to increase antioxidant activities in phytoremediation plants.

Develop microbes to selectively mineralize or mobilize metals in the environment.

Bottleneck/Challenge: Metal selectivity and tolerance is significantly variable across microbial species, thus microbes or consortia would need to be tailored for the environment.¹³

Potential Solution: Engineer consortia with multiple mechanisms of soil detoxification to be broadly applied.

Bottleneck/Challenge: Not all contaminated soils are suitable for bioremediation, due to poor natural conditions, including lack of oxygen and extreme temperature.¹⁴

Potential Solution: Employ indigenous microbial strains, wherever possible, that have shown hardiness to local conditions.

Potential Solution: Consider engineering of extremophiles and anaerobic species for metal uptake.

For more about enabling engineering biology for uptake and processing of metals, please see Goal: Enable resource recovery through biomining.

Footnotes

Giachino, A., Focarelli, F., Marles-Wright, J., & Waldron, K. J. (2021). Synthetic biology approaches to copper remediation: Bioleaching, accumulation and recycling. FEMS Microbiology Ecology, 97(2), fiaa249. https://doi.org/10.1093/femsec/fiaa249
Ankit, Bordoloi, N., Tiwari, J., Kumar, S., Korstad, J., & Bauddh, K. (2020). Efficiency of Algae for Heavy Metal Removal, Bioenergy Production, and Carbon Sequestration. In R. N. Bharagava (Ed.), Emerging Eco-friendly Green Technologies for Wastewater Treatment (pp. 77–101). Springer. https://doi.org/10.1007/978-981-15-1390-9_4
Mazur, L. P., Cechinel, M. A. P., de Souza, S. M. A. G. U., Boaventura, R. A. R., & Vilar, V. J. P. (2018). Brown marine macroalgae as natural cation exchangers for toxic metal removal from industrial wastewaters: A review. Journal of Environmental Management, 223, 215–253. https://doi.org/10.1016/j.jenvman.2018.05.086
Adeleye, A. O., Nkereuwem, M. E., Omokhudu, G. I., Amoo, A. O., Shiaka, G. P., & Yerima, M. B. (2018). Effect of microorganisms in the bioremediation of spent engine oil and petroleum related environmental pollution. Journal of Applied Sciences and Environmental Management, 22(2), 157–167. https://doi.org/10.4314/jasem.v22i2.1
Ron, E. Z., & Rosenberg, E. (2014). Enhanced bioremediation of oil spills in the sea. Current Opinion in Biotechnology, 27, 191–194. https://doi.org/10.1016/j.copbio.2014.02.004
Dudev, T., & Lim, C. (2014). Competition among Metal Ions for Protein Binding Sites: Determinants of Metal Ion Selectivity in Proteins. Chemical Reviews, 114(1), 538–556. https://doi.org/10.1021/cr4004665
Lu, H., Diaz, D. J., Czarnecki, N. J., Zhu, C., Kim, W., Shroff, R., Acosta, D. J., Alexander, B. R., Cole, H. O., Zhang, Y., Lynd, N. A., Ellington, A. D., & Alper, H. S. (2022). Machine learning-aided engineering of hydrolases for PET depolymerization. Nature, 604(7907), 662–667. https://doi.org/10.1038/s41586-022-04599-z
Sheridan, E. A., Fonvielle, J. A., Cottingham, S., Zhang, Y., Dittmar, T., Aldridge, D. C., & Tanentzap, A. J. (2022). Plastic pollution fosters more microbial growth in lakes than natural organic matter. Nature Communications, 13(1), 4175. https://doi.org/10.1038/s41467-022-31691-9
Kim, H. T., Kim, J. K., Cha, H. G., Kang, M. J., Lee, H. S., Khang, T. U., Yun, E. J., Lee, D.-H., Song, B. K., Park, S. J., Joo, J. C., & Kim, K. H. (2019). Biological Valorization of Poly(ethylene terephthalate) Monomers for Upcycling Waste PET. ACS Sustainable Chemistry & Engineering, 7(24), 19396–19406. https://doi.org/10.1021/acssuschemeng.9b03908
Shahsavari, E., Rouch, D., Khudur, L. S., Thomas, D., Aburto-Medina, A., & Ball, A. S. (2021). Challenges and Current Status of the Biological Treatment of PFAS-Contaminated Soils. Frontiers in Bioengineering and Biotechnology, 8. https://doi.org/10.3389/fbioe.2020.602040
Seong, H. J., Kwon, S. W., Seo, D.-C., Kim, J.-H., & Jang, Y.-S. (2019). Enzymatic defluorination of fluorinated compounds. Applied Biological Chemistry, 62(1), 62. https://doi.org/10.1186/s13765-019-0469-6
Kim, M. H., Wang, N., & Chu, K. H. (2014). 6:2 Fluorotelomer alcohol (6:2 FTOH) biodegradation by multiple microbial species under different physiological conditions. Applied Microbiology and Biotechnology, 98(4), 1831–1840. https://doi.org/10.1007/s00253-013-5131-3
González Henao, S., & Ghneim-Herrera, T. (2021). Heavy Metals in Soils and the Remediation Potential of Bacteria Associated With the Plant Microbiome. Frontiers in Environmental Science, 9. https://doi.org/10.3389/fenvs.2021.604216
Kapahi, M., & Sachdeva, S. (2019). Bioremediation Options for Heavy Metal Pollution. Journal of Health & Pollution, 9(24), 191203. https://doi.org/10.5696/2156-9614-9.24.191203

Last updated: September 19, 2022 Back