Enable resource recovery through biomining.

Engineering Biology for Climate & Sustainability

Materials Production & Industrial Processes Goal:

Enable resource recovery through biomining.

For more about enabling engineering biology for the biosequestration of heavy metals, please see Goal: Mitigate targeted environmental pollutants through biosequestion and biodegradation.

Current State-of-the-Art

Current mining processes for heavy metals and the growing abundance of electronic waste opens a path for biology to enable more sustainable and environmentally-friendly capture of resources such as rare earth elements. The recent discovery that numerous environmental strains use rare earth elements as cofactors to alcohol dehydrogenases and naturally bioaccumulate rare earth elements, have opened an emergent area to design bacterial platforms for recovery of these critical metals.¹ Engineered microbes and cell-free systems can, for example, be used to rapidly detect heavy metals in the environment, sequester heavy metal wastes from many different sources, and process or recycle metals through accumulation and mineralization (see Bereza-Malcolm et al., 2015,² Kachieng’a & Unuofin, 2021,³ and Giachino et al., 2021,⁴ respectively). Biomining occurs through the processes of bioleaching, in which the microbes solubilize the metal of interest, and biooxidation, in which a mineral sulfide matrix is oxidized to extract the metal of interest.⁵

The biggest challenges for this technology, particularly for achieving these processes at scale, is toxicity and how little we know about the (metabolic) regulatory processes of bioaccumulation and bioleaching. Many species are able to naturally utilize rare earth elements, but our understanding of where and how these organisms function is quite limited; bioinformatics approaches will be especially helpful in identifying strains able to chelate and bioaccumulate rare earth elements naturally (or are particularly amenable to engineering for such capacity). Approaches have been taken to overcome toxicity by engineering microbes with amplification circuitry to detect hazardous metals in low concentrations from diffuse sources,⁶ use cell-free systems more tolerant to harsh environments,⁷ and by engineering environmental strains for biomining.⁸ Often these materials are found in complex mixtures and sources, and systems will need to be engineered to most efficiently process materials from other contaminants.⁹

Breakthrough Capabilities & Milestones

Mine and extract resources from the natural environment using engineering biology.

Engineer organisms with key traits and tolerances for high-efficiency biomining.

Bottleneck/Challenge: Conventional engineering biology hosts (e.g., E. coli) lack key traits and mechanisms for use in industrial mining applications, such as the ability to tolerate low pH, high temperatures, and high ionic concentrations.

Potential Solution: Identify organisms from relevant environments to serve as new chassis, taking advantage of microbes that naturally chelate rare earth elements in soils.

Potential Solution: Engineer model hosts with lanthanophores.¹⁰

Bottleneck/Challenge: Low transformation and selection efficiency of engineered biomining microbes with desired traits.

Potential Solution: Develop antibiotics that work efficiently in the growth media of the targeted strain.

Potential Solution: Develop nutritional-based selection mechanisms (e.g. new metabolic capability or complemetation of an auxotrophy).

Engineer organisms for biomining low-grade and complex ores.

Bottleneck/Challenge: Low-grade and complex ores contain high concentrations of metal and high levels of metal impurities.

Potential Solution: Increase metal resistance in organisms by engineering and evolving transport proteins and/or metal binding sites.

Potential Solution: Engineer hybrid microbial consortia that contain engineered strains capable of efficient metal bioaccumulation, to reduce metal concentrations for other biomining microbes in the consortium.

Bottleneck/Challenge: Valuable minerals (e.g., rare-earth metals) exist in low concentrations in low-grade and complex ores.

Potential Solution: Identify new lanthanophores in different environmental strains and express heterologously in current bacterial platforms.¹¹

Potential Solution: Identify regulatory mechanisms limiting rare earth transport in methylotrophs to enhance rare earth bioaccumulation and biomineralization to promote these strains as biorecovery platforms.¹²

Potential Solution: Develop engineered strains that express proteins with high affinity for target metals.

Potential Solution: Use protein design and engineering to synthesize enzymes with binding sites that selectively target desired minerals (e.g., rare-earth metals).

Potential Solution: Develop new biosorption technologies, e.g., bacterial phages, to concentrate and separate rare-earth elements (REEs) from non-REEs.

Investigate and characterize bio-respiration as a form of metal extraction, as opposed to bioleaching.

Bottleneck/Challenge: Some metals in their oxidized state form insoluble oxide minerals, which can have value themselves, or help sequester other metals of value.

Potential Solution: Extracellular electron transfer (EET) is a respiratory process that enables bacteria to reduce insoluble substrates; simple pathways (e.g., from Shewanella oneidensis) can be expressed heterologously, but more sophisticated EET pathways (e.g., from Geobacter sulfurreducens) have not yet been reconstructed.

Potential Solution: Identify new, genetically tractable microbes capable of EET that tolerate and/or thrive in extremophile conditions.

Recover mineral and metal resources from waste using engineering biology.

Design and construct biosorption-based, flow-through processes for continuous separation and recovery of valuable minerals from waste streams.

Develop engineered microbial or cell-free systems to recover valuable metals from electronic waste.

Bottleneck/Challenge: Electronic waste contains high levels of toxic metals that reduces or inhibits growth of potential bacterial platforms for recovery.

Potential Solution: Increase heavy metal tolerance by genetic engineering or experimental evolution of microbes under appropriate selective pressure conditions.

Bottleneck/Challenge: Elemental composition of electronic waste is highly variable.

Potential Solution: Develop recovery processes at neutral pH that rely on specific metal ligands (siderophore-like molecules) instead of non-specific leaching processes that promote the solubility of toxic metals.

Potential Solution: Develop co-cultures or consortia to synergize recovery.

Integrate biosorption into existing mineral recovery systems to enable sustainable and cost-effective co-extraction.

Bottleneck/Challenge: Differentiation among rare earth elements is chemically challenging.

Potential Solution: Investigate the mechanism that environmental bacterial strains use to differentiate light from heavy lanthanides for integration into current microbial platforms used for recovery.¹³

Potential Solution: Engineer and construct biosorbents for separating different kinds of rare earth elements.

Bottleneck/Challenge: Biosorption and bioleaching may not be significantly economical or sustainable with just the incorporation of a biological processing component.

Potential Solution: Engineer microbes to reuse chemicals (e.g., residual sulfuric or nitric acids) for leaching minerals/metals from waste materials.

Diversify the global rare earth element (REE) supply through engineering biological systems (e.g., bioleaching, biosorption).

Footnotes

Skovran, E., Raghuraman, C., & Martinez-Gomez, N. C. (2019). Lanthanides in Methylotrophy. Current Issues in Molecular Biology, 33, 101–116. https://doi.org/10.21775/cimb.033.101
Bereza-Malcolm, L. T., Mann, G., & Franks, A. E. (2015). Environmental Sensing of Heavy Metals Through Whole Cell Microbial Biosensors: A Synthetic Biology Approach. ACS Synthetic Biology, 4(5), 535–546. https://doi.org/10.1021/sb500286r
Kachieng’a, L. O., & Unuofin, J. O. (2021). The potentials of biofilm reactor as recourse for the recuperation of rare earth metals/elements from wastewater: A review. Environmental Science and Pollution Research, 28(33), 44755–44767. https://doi.org/10.1007/s11356-021-15297-0
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
Gumulya, Y., Boxall, N. J., Khaleque, H. N., Santala, V., Carlson, R. P., & Kaksonen, A. H. (2018). In a Quest for Engineering Acidophiles for Biomining Applications: Challenges and Opportunities. Genes, 9(2), 116. https://doi.org/10.3390/genes9020116
Cai, Y., Zhu, K., Shen, L., Ma, J., Bao, L., Chen, D., Wei, L., Wei, N., Liu, B., Wu, Y., & Chen, S. (2022). Evolved Biosensor with High Sensitivity and Specificity for Measuring Cadmium in Actual Environmental Samples. Environmental Science & Technology, 56(14), 10062–10071. https://doi.org/10.1021/acs.est.2c00627
Beabout, K., Bernhards, C. B., Thakur, M., Turner, K. B., Cole, S. D., Walper, S. A., Chávez, J. L., & Lux, M. W. (2021). Optimization of Heavy Metal Sensors Based on Transcription Factors and Cell-Free Expression Systems. ACS Synthetic Biology, 10(11), 3040–3054. https://doi.org/10.1021/acssynbio.1c00331
Gumulya, Y., Boxall, N. J., Khaleque, H. N., Santala, V., Carlson, R. P., & Kaksonen, A. H. (2018). In a Quest for Engineering Acidophiles for Biomining Applications: Challenges and Opportunities. Genes, 9(2), 116. https://doi.org/10.3390/genes9020116
Han, P., Teo, W. Z., & Yew, W. S. (2022). Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions. Engineering Biology, 6(1), 23–34. https://doi.org/10.1049/enb2.12020
Cotruvo, J. A. (2019). The Chemistry of Lanthanides in Biology: Recent Discoveries, Emerging Principles, and Technological Applications. ACS Central Science, 5(9), 1496–1506. https://doi.org/10.1021/acscentsci.9b00642
Zytnick, A. M., Good, N. M., Barber, C. C., Phi, M. T., Gutenthaler, S. M., Zhang, W., Daumann, L. J., & Martinez-Gomez, N. C. (2022). Identification of a biosynthetic gene cluster encoding a novel lanthanide chelator in Methylorubrum extorquens AM1 (p. 2022.01.19.476857). bioRxiv. https://doi.org/10.1101/2022.01.19.476857
Roszczenko-Jasińska, P., Vu, H. N., Subuyuj, G. A., Crisostomo, R. V., Cai, J., Lien, N. F., Clippard, E. J., Ayala, E. M., Ngo, R. T., Yarza, F., Wingett, J. P., Raghuraman, C., Hoeber, C. A., Martinez-Gomez, N. C., & Skovran, E. (2020). Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1. Scientific Reports, 10(1), 12663. https://doi.org/10.1038/s41598-020-69401-4
Good, N. M., Lee, H. D., Hawker, E. R., Su, M. Z., Gilad, A. A., & Martinez-Gomez, N. C. (2022). Hyperaccumulation of Gadolinium by Methylorubrum extorquens AM1 Reveals Impacts of Lanthanides on Cellular Processes Beyond Methylotrophy. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.820327