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.1Skovran, E., Raghuraman, C., & Martinez-Gomez, N. C. (2019). Lanthanides in Methylotrophy. Current Issues in Molecular Biology, 33, 101–116. View Publication. 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., 2015,2Bereza-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. View Publication. Kachieng’a & Unuofin, 2021,3Kachieng’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. View Publication. and Giachino et al., 2021,4Giachino, 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. View Publication. 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.5Gumulya, 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. View Publication.

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,6Cai, 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. View Publication. use cell-free systems more tolerant to harsh environments,7Beabout, 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. View Publication. and by engineering environmental strains for biomining.8Gumulya, 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. View Publication. 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.9Han, 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. View Publication.

Breakthrough Capabilities & Milestones

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

Recover mineral and metal resources from waste using engineering biology.

Footnotes

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
Last updated: September 19, 2022 Back