Engineering Biology for Climate & Sustainability
Mitigating Environmental Pollution Goal:
Mitigate pollutants from human-generated waste streams.
More detail about upcycling chemicals and materials can be found in Materials Production & Industrial Processes.
Efficient biodegradation could prove especially useful for breaking down hydrocarbons (e.g., plastics and oils) and removing harmful chemicals from human-generated waste streams, before they reach the larger environment. For water treatment, in particular, biobased systems have been developed to capture fecal coliforms, degrade nutrient runoff from agriculture and aquaculture (e.g., fish waste and feed), and clean up fluorinated compounds. Future advances in biodegradation could enable higher efficiency water purification, reclamation, and even desalination (such as occurs with mangrove trees, see Wang et al., 2020b), where halophilic bacteria could be incorporated into the desalination process to prevent biofouling and reduce chemical use. While some non-model organisms can grow on and process pollutants, more research is needed to identify novel organisms that can handle harsh and polluted environments., In addition to removing pollutants from waste streams, engineering biology can take the process further and upcycle pollutants by converting them into useful products.,
Breakthrough Capabilities & Milestones
Enable the bioremediation of contaminants from municipal wastewater.
Enable scale-up of highly-efficient, engineered microalgae bioremediation of municipal wastewater.*
Environmental conditions (e.g., pH, temperature, flow rate) of wastewater treatment sites.
Potential Solution: Engineer heterotrophic and mixotrophic microalgae robust to a wider range of climatic conditions.,
Develop biological systems to capture waterborne pathogens (e.g., fecal coliforms).
Detecting and destroying specific pathogens and their toxic by-products at scale in wastewater and other municipal water sources.
Potential Solution: Engineer sensing and reporting predatory bacteria against known pathogen classes.
Potential Solution: Engineer organisms to produce coliphage or use other predatory mechanisms to control coliform populations.
Engineer microbes/microbial consortia and enzymes that degrade and/or capture excess pharmaceuticals and endocrine disruptors (e.g., hormones from birth control, pesticide metabolites) in municipal wastewater.**
Metabolic pathways for pharmaceutical degradation are unknown.
Potential Solution: Screen municipal wastewater and other appropriate sources for microbes that degrade drugs of interest, for characterization with -omics and enrichment evolution.
Potential Solution: Identify enzymes upregulated in the presence of pharmaceuticals (transcriptomics) and validate function via heterologous expression and/or knockouts.
Bottleneck/Challenge: Enzymes not expressed natively at sufficiently high levels to clear pharmaceuticals at appreciable rate.
Potential Solution: Upregulate protein expression in native hosts (see for example Ariste & Cabana, 2020).
Engineer microbes that can remove lubricants and fuels from municipal wastewater.
Microbial growth tolerance and efficient absorption of specific hydrophobic waste compounds are unknown.
Potential Solution: Enhance the chemical tolerance of microbes that have native abilities to tolerate and utilize toxic chemicals in wastewater.
Potential Solution: Enhance the production of surfactants that allow for solubilization and access of hydrophobic compounds by microbes.
Potential Solution: Engineer alkane-activation mechanisms (e.g., fumarate) into facultative anaerobic bacteria to maximize processing under poor oxygen conditions.
Engineer biobased filters for inorganic pollutant removal, for example to desalinate water and remove microplastics.
Filters would need to be able to quickly and efficiently trap pollutants/salts while allowing pure water to pass through.
Potential Solution: Design biomolecule or biopolymer based biofilms, perhaps continually replenished with associated (marine) microbes, with sufficient structural integrity and appropriate pore size to trap contaminants.
Potential Solution: Characterize biodegradation of organic contaminants in halophilic microbes.
Potential Solution: Engineer marine microbes that produce surfactants that flocculate or aggregate microplastics.
Engineer microbial conversion of municipal wastewater contaminants into value-added products.
Efficiency of purification and extraction of desired product.
Potential Solution: Engineer consortia capable of distributed metabolism for membrane bioreactors or moving bed biofilm reactors.
Engineer living biofilms to continuously capture broad classes of pollutants in potable water streams.
Stability and maintenance of biofilms exposed to captured pollutants is unknown.
Potential Solution: Develop stable microbial consortia whose members are specialized in the capture of specific pollutants but will persist even when absent.
*Do, C. V. T., Pham, M. H. T., Pham, T. Y. T., Dinh, C. T., Bui, T. U. T., Tran, T. D., & Nguyen, V. T. (2022). Microalgae and bioremediation of domestic wastewater. Current Opinion in Green and Sustainable Chemistry, 34, 100595. https://doi.org/10.1016/j.cogsc.2022.100595
**Gavrilescu, M., Demnerová, K., Aamand, J., Agathos, S., & Fava, F. (2015). Emerging pollutants in the environment: Present and future challenges in biomonitoring, ecological risks and bioremediation. New Biotechnology, 32(1), 147–156. https://doi.org/10.1016/j.nbt.2014.01.001
Enable the bioremediation of pollutants from agriculture and aquaculture.
Engineer soil microbes to sequester and concentrate inorganic contaminants in the soil column (for example, microbially induced calcite precipitation).
The mutual influences of the environment and soil microbes that affect precipitation speed, spatial distribution, and crystal properties have not been sufficiently elucidated.
Potential Solution: Engineer standard microbial hosts (e.g., B. subtilis) to express genetic drivers for inorganic contaminant concentration (e.g., urease enzymes), varying components of the media and study effects on precipitation speed, spatial distribution and crystal properties.
Engineer plants to detect soil contamination through interactions with the rhizosphere and produce a visible output of contamination status.
Requires optimization of plant-rhizosphere communication and reliable plant signal transduction and reporting.
Potential Solution: Engineer microbes to metabolize contaminants into compounds already known to be taken up by plant roots.
Engineer microbes, microbiomes, cell-free systems, or biomaterials designed to target and capture nitrogen, phosphate, and calcium runoff from synthetic fertilizers.
Biosystems need to be optimized to selectively and effectively sequester and concentrate inorganic contaminants.
Potential Solution: Optimize microbes that capture and store excess phosphate.
Potential Solution: Engineer nitrifying bacteria to control nitrogen losses in the soil (reduce oxidation of ammonia, thereby minimizing input fertilizer needs and runoff).
Potential Solution: Engineer microbially induced calcite precipitation for agricultural soils.
Engineer microbes, cell-free systems, or biomaterials that target, capture, and degrade agricultural/aquacultural antibiotics and insecticide contaminants.
Enzymes not expressed natively in soil-associated organisms at sufficiently high levels to clear antibiotics or insecticides at appreciable rate.
Potential Solution: Upregulate protein expression in native hosts.
Enable biological recycling of captured runoff nutrients for new fertilizers.
Highly-mobile phosphorus and nitrogen fertilizer compounds leach quickly through soil.
Potential Solution: Engineer microbes to cycle phosphorus/nitrogen into less-mobile and bioavailable compounds.
Bottleneck/Challenge: Efficiency of employing anaerobic processes in aqueous, aquaculture-related environments.
Potential Solution: Identify and characterize tractable anaerobic organisms that thrive in aquaculture environments.
Engineer macroalgae to bind and degrade toxins in marine environments.
Macroalgae need to be able to selectively recognize toxins for uptake and sequestration or metabolism, without triggering pathways that would result in macroalgal death.
Potential Solution: Surface display of toxin binding proteins that can be adapted and expressed in macroalgae.
Engineer bioremediating microbes, microbiomes, cell-free systems, or biomaterials with programmable lifespans for agricultural and aquacultural environments.
Factors influencing microbial persistence are poorly understood in dynamic environments.
Potential Solution: Employ (meta)genomics, metabolomics, and other tools (especially emerging complementary activity measurements like qSIP, BONCAT, and PMA) to connect microbiome structure to environmental conditions and processes., ,
Bottleneck/Challenge: Factors influencing microbial persistence are poorly understood in dynamic environments.
Potential Solution: Minimal in situ or ex vivo engineering of naturally persistent and ubiquitous subcommunities for defined activities (see Rubin et al., 2022) to take advantage of their natural adaptation to the particular environmental constraints.
Potential Solution: Encapsulated, stabilized cell- and nucleic acid-free engineered enzymes/cofactor systems that can be dispersed into water and soil while maintaining activity for defined periods in variable environments.
For biotechnologies for reducing agricultural runoff (through more effective biofertilizers and more efficient crop uptake of nutrients), please see the Food & Agriculture theme.
Enable the bioremediation of chemical waste from industrial effluent.
Enable in silico prediction of biodegradation pathways for toxic chemical compounds.
Limited availability of databases on chemical toxicity and related biodegradation pathways.
Potential Solution: Use multi-omics technologies to identify and characterize biomolecules and metabolic pathways for toxic chemical biodegradation.
Identify and engineer microbes to biodegrade hazardous chemicals (for example, phenols, endocrine-disrupting chemicals, hydrocarbons, heavy metals).
Bioremediation applications are still primarily limited to a few well-characterized model organisms.
Potential Solution: Identify non-model organisms that can survive and detoxify harmful chemical wastes and develop the tools to engineer them.
Potential Solution: Sequencing and reuse of organisms and genetic systems indigenous (evolving and stable) to environments where these contaminants are released.
Bottleneck/Challenge: Fast-growing microbes favored for bioremediation are often not the most efficient at degrading toxic waste and could create more unwanted microbial biomass.
Potential Solution: Engineer microbes where growth is decoupled from catabolic activity.
Design cell-free systems to degrade toxic waste chemicals generated from chemical production.
Environmental conditions in industrial effluents (e.g., extremely high or low pH) can cause enzymes to denature.
Potential Solution: Improve protein stability to enable enzymatic degradation of chemical waste under extreme conditions.
Bottleneck/Challenge: Lack of biocatalysts for specific toxic waste chemicals.
Potential Solution: Enzyme design and directed evolution to generate a range of required biocatalysts that can operate under specific environmental conditions.
Incorporate engineered microbial or cell-free systems into chemical production processes to degrade toxic waste chemicals in situ.
Microbial chassis are growth-sensitive to chemical waste components.
Potential Solution: Engineer microbes and enzymes with high tolerance to chemical waste.
Bottleneck/Challenge: Lack of suitable biocatalysts and microbial chasses for degradation of toxic byproducts.
Potential Solution: Identify microbes and enzymes that can degrade secondary toxic byproducts produced from biodegradation.
Bottleneck/Challenge: Engineered microbes highly-robust to toxic environments raise concerns for biocontainment breach.
Potential Solution: Develop tools to engineer microbes to be contained in the designated environment.
Enable valorization of breakdown products and waste, such as via directly-coupled bioenergy generation or high-value product synthesis from engineered remediation organisms.
High level of impurities and concentration of toxins in waste streams.
Potential Solution: Selection and engineering of host strains tolerant to complex and toxic environments, such as halophiles, or strains engineered with high-lipase expression.
- Li, X., Yang, C., Zeng, G., Wu, S., Lin, Y., Zhou, Q., Lou, W., Du, C., Nie, L., & Zhong, Y. (2020). Nutrient removal from swine wastewater with growing microalgae at various zinc concentrations. Algal Research, 46, 101804. https://doi.org/10.1016/j.algal.2020.101804
- Coppola, D., Lauritano, C., Palma Esposito, F., Riccio, G., Rizzo, C., & de Pascale, D. (2021). Fish Waste: From Problem to Valuable Resource. Marine Drugs, 19(2), 116. https://doi.org/10.3390/md19020116
- Ferrando, L., & Matamoros, V. (2020). Attenuation of nitrates, antibiotics and pesticides from groundwater using immobilised microalgae-based systems. Science of The Total Environment, 703, 134740. https://doi.org/10.1016/j.scitotenv.2019.134740
- Moreira, I. S., Amorim, C. L., Murphy, C. D., & Castro, P. M. L. (2018). Strategies for Biodegradation of Fluorinated Compounds. In R. Prasad & E. Aranda (Eds.), Approaches in Bioremediation: The New Era of Environmental Microbiology and Nanobiotechnology (pp. 239–280). Springer International Publishing. https://doi.org/10.1007/978-3-030-02369-0_11
- Wang, Y., Lee, J., Werber, J. R., & Elimelech, M. (2020b). Capillary-driven desalination in a synthetic mangrove. Science Advances, 6(8), eaax5253. https://doi.org/10.1126/sciadv.aax5253
- Sysoev, M., Grötzinger, S. W., Renn, D., Eppinger, J., Rueping, M., & Karan, R. (2021). Bioprospecting of Novel Extremozymes From Prokaryotes—The Advent of Culture-Independent Methods. Frontiers in Microbiology, 12, 196. https://doi.org/10.3389/fmicb.2021.630013
- Yun, S. H., Choi, C.-W., Lee, S.-Y., Park, E. C., & Kim, S. I. (2016). A Proteomics Approach for the Identification of Novel Proteins in Extremophiles. In P. H. Rampelotto (Ed.), Biotechnology of Extremophiles: Advances and Challenges (pp. 303–319). Springer International Publishing. https://doi.org/10.1007/978-3-319-13521-2_10
- Cornwall. (2021). Could plastic-eating microbes take a bite out of the recycling problem? Science. https://www.science.org/content/article/could-plastic-eating-microbes-take-bite-out-recycling-problem
- Lad, B. C., Coleman, S. M., & Alper, H. S. (2022). Microbial valorization of underutilized and nonconventional waste streams. Journal of Industrial Microbiology and Biotechnology, 49(2), kuab056. https://doi.org/10.1093/jimb/kuab056
- Aggarwal, C., Singh, D., Soni, H., & Pal, A. (2021). Heterotrophic Cultivation of Microalgae in Wastewater. In A. Kumar, A. Pal, S. S. Kachhwaha, & P. K. Jain (Eds.), Recent Advances in Mechanical Engineering (pp. 493–506). Springer Nature. https://doi.org/10.1007/978-981-15-9678-0_43
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- Ariste, A. F., & Cabana, H. (2020). Challenges in Applying Cross-Linked Laccase Aggregates in Bioremediation of Emerging Contaminants from Municipal Wastewater. In D. Schlosser (Ed.), Laccases in Bioremediation and Waste Valorisation (pp. 147–171). Springer International Publishing. https://doi.org/10.1007/978-3-030-47906-0_6
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Last updated: September 19, 2022