Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale

Nature Biotechnology volume 40, pages 335–344 (2022)Cite this article

Subjects

An Addendum to this article was published on 21 July 2025

Abstract

Many industrial chemicals that are produced from fossil resources could be manufactured more sustainably through fermentation. Here we describe the development of a carbon-negative fermentation route to producing the industrially important chemicals acetone and isopropanol from abundant, low-cost waste gas feedstocks, such as industrial emissions and syngas. Using a combinatorial pathway library approach, we first mined a historical industrial strain collection for superior enzymes that we used to engineer the autotrophic acetogen Clostridium autoethanogenum. Next, we used omics analysis, kinetic modeling and cell-free prototyping to optimize flux. Finally, we scaled-up our optimized strains for continuous production at rates of up to ~3 g/L/h and ~90% selectivity. Life cycle analysis confirmed a negative carbon footprint for the products. Unlike traditional production processes, which result in release of greenhouse gases, our process fixes carbon. These results show that engineered acetogens enable sustainable, high-efficiency, high-selectivity chemicals production. We expect that our approach can be readily adapted to a wide range of commodity chemicals.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Overview of our three-pronged approach for pathway, strain and process optimization.
Fig. 2: Pathway optimization.
Fig. 3: Strain optimization.
Fig. 4: Flux optimization.
Fig. 5: Process optimization and scale-up.
Fig. 6: Life cycle analysis.

Similar content being viewed by others

Data availability

All data presented in this manuscript are available as supplementary data files. Supplementary Tables 1-10 are available on Zenodo: https://doi.org/10.5281/zenodo.5838304. All proteomics raw data are available at the ProteomeXchange Consortium via the MassIVE repository (ftp://massive.ucsd.edu/MSV000085940/) (MassIVE accession: MSV000085940; ProteomeXchange accession: PXD020853). All genome sequences are available through the Joint Genome Institute Integrated Microbial Genomes & Microbiomes system platform or the National Center of Biotechnology Information GenBank under accession numbers provided in Supplementary Table 7. Any additional data may be available from the authors upon reasonable request. Materials are available upon reasonable request and under a material transfer agreement, but strains may require a license.

References

  1. Aguado-Deblas, L. et al. Acetone prospect as an additive to allow the use of castor and sunflower oils as drop-in biofuels in diesel/acetone/vegetable oil triple blends for application in diesel engines. Molecules 25, 2935 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Elfasakhany, A. Performance and emissions analysis on using acetone–gasoline fuel blends in spark-ignition engine. Eng. Sci. Technol. Int. J. 19, 1224–1232 (2016).

    Google Scholar 

  3. Anbarasan, P. et al. Integration of chemical catalysis with extractive fermentation to produce fuels. Nature 491, 235–239 (2012).

    Article  CAS  PubMed  Google Scholar 

  4. Ryan, C. F. et al. Synthesis of aviation fuel from bio-derived isophorone. Sustain. Energy Fuels 4, 1088–1092 (2020).

    Article  CAS  Google Scholar 

  5. Kratzel, A. et al. Inactivation of severe acute respiratory syndrome coronavirus 2 by WHO-recommended hand rub formulations and alcohols. Emerg. Infect. Dis. 26, 1592–1595 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Wernet, G. et al. The ecoinvent database version 3 (part I): overview and methodology. Int. J. Life Cycle Assess. 21, 1218–1230 (2016).

    Article  Google Scholar 

  7. Jones, D. T. & Woods, D. R. Acetone–butanol fermentation revisited. Microbiol. Rev. 50, 484–524 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ismaiel, A. A., Zhu, C. X., Colby, G. D. & Chen, J. S. Purification and characterization of a primary–secondary alcohol dehydrogenase from two strains of Clostridium beijerinckii. J. Bacteriol. 175, 5097–5105 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Hanai, T., Atsumi, S. & Liao, J. C. Engineered synthetic pathway for isopropanol production in Escherichia coli. Appl. Environ. Microbiol. 73, 7814–7818 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. May, A. et al. A modified pathway for the production of acetone in Escherichia coli. Metab. Eng. 15, 218–225 (2013).

    Article  CAS  PubMed  Google Scholar 

  11. Liang, L. et al. CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli. Metab. Eng. 41, 1–10 (2017).

    Article  CAS  PubMed  Google Scholar 

  12. Soma, Y., Yamaji, T., Matsuda, F. & Hanai, T. Synthetic metabolic bypass for a metabolic toggle switch enhances acetyl-CoA supply for isopropanol production by Escherichia coli. J. Biosci. Bioeng. 123, 625–633 (2017).

    Article  CAS  PubMed  Google Scholar 

  13. Jojima, T., Inui, M. & Yukawa, H. Production of isopropanol by metabolically engineered Escherichia coli. Appl. Microbiol. Biotechnol. 77, 1219–1224 (2008).

    Article  CAS  PubMed  Google Scholar 

  14. Jones, S. W. et al. CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion. Nat. Commun. 7, 12800 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Simpson, S. D. & Köpke, M. Pollution to products: recycling of ‘above ground’ carbon by gas fermentation. Curr. Opin. Biotechnol. 65, 180–189 (2020).

    Article  PubMed  Google Scholar 

  16. Marcellin, E. et al. Low carbon fuels and commodity chemicals from waste gases—systematic approach to understand energy metabolism in a model acetogen. Green Chem. 18, 3020 (2016).

    Article  CAS  Google Scholar 

  17. Kato, J. et al. Metabolic engineering of Moorella thermoacetica for thermophilic bioconversion of gaseous substrates to a volatile chemical. AMB Express 11, 59 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Hoffmeister, S. et al. Acetone production with metabolically engineered strains of Acetobacterium woodii. Metab. Eng. 36, 37–47 (2016).

    Article  CAS  PubMed  Google Scholar 

  19. Banerjee, A., Leang, C., Ueki, T., Nevin, K. P. & Lovley, D. R. A lactose-inducible system for metabolic engineering of Clostridium ljungdahlii. Appl. Environ. Microbiol. 80, 2410–2416 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Garrigues, L., Maignien, L., Lombard, E., Singh, J. & Guillouet, S. E. Isopropanol production from carbon dioxide in Cupriavidus necator in a pressurized bioreactor. N. Biotechnol. 56, 16–20 (2020).

    Article  CAS  PubMed  Google Scholar 

  21. Lee, H. J., Son, J., Sim, S. J. & Woo, H. M. Metabolic rewiring of synthetic pyruvate dehydrogenase bypasses for acetone production in cyanobacteria. Plant Biotechnol. J. 18, 1860–1868 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Torella, J. P. et al. Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system. Proc. Natl Acad. Sci. USA 112, 2337–2342 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Hirokawa, Y., Dempo, Y., Fukusaki, E. & Hanai, T. Metabolic engineering for isopropanol production by an engineered cyanobacterium, Synechococcus elongatus PCC 7942, under photosynthetic conditions. J. Biosci. Bioeng. 123, 39–45 (2016).

    Article  PubMed  Google Scholar 

  24. Zhou, J., Zhang, H., Zhang, Y., Li, Y. & Ma, Y. Designing and creating a modularized synthetic pathway in cyanobacterium Synechocystis enables production of acetone from carbon dioxide. Metab. Eng. 14, 394–400 (2012).

    Article  CAS  PubMed  Google Scholar 

  25. Claassens, N. J., Cotton, C. A. R., Kopljar, D. & Bar-Even, A. Making quantitative sense of electromicrobial production. Nat. Catal. 2, 437–447 (2019).

    Article  CAS  Google Scholar 

  26. Fast, A. G. & Papoutsakis, E. T. Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals. Curr. Opin. Chem. Eng. 1, 380–395 (2012).

    Article  Google Scholar 

  27. Bar-Even, A., Noor, E. & Milo, R. A survey of carbon fixation pathways through a quantitative lens. J. Exp. Bot. 63, 2325–2342 (2012).

    Article  CAS  PubMed  Google Scholar 

  28. Köpke, M. et al. Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc. Natl Acad. Sci. USA 107, 13087–13092 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Fackler, N. et al. Stepping on the gas to a circular economy: accelerating development of carbon-negative chemical production from gas fermentation. Ann. Rev. Chem. Biomol. Eng. 12, 439–470 (2021).

    Article  Google Scholar 

  30. Jin, S. et al. Synthetic biology on acetogenic bacteria for highly efficient conversion of C1 gases to biochemicals. Int. J. Mol. Sci. 21, 7639 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Takors, R. et al. Using gas mixtures of CO, CO2 and H2 as microbial substrates: the do’s and don’ts of successful technology transfer from laboratory to production scale. Microb. Biotechnol. 11, 606–625 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Jones, D. T. Applied acetone–butonal fermentation. In: Clostridia: Biotechnology and Medical Applications (eds Dürre, P. & Bahl, H.) 125–168 (Wiley, 2001).

  33. Jones, D. T. & Keis, S. Origins and relationships of industrial solvent-producing clostridial strains. FEMS Microbiol. Rev. 17, 223–232 (1995).

    Article  CAS  Google Scholar 

  34. Karim, A. S. et al. In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design. Nat. Chem. Biol. 16, 912–919 (2020).

    Article  CAS  PubMed  Google Scholar 

  35. Krüger, A. et al. Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways. Metab. Eng. 62, 95–105 (2020).

    Article  PubMed  Google Scholar 

  36. Heap, J. T., Pennington, O. J., Cartman, S. T. & Minton, N. P. A modular system for Clostridium shuttle plasmids. J. Microbiol. Methods 78, 79–85 (2009).

    Article  CAS  PubMed  Google Scholar 

  37. Maddock, D. J., Patrick, W. M. & Gerth, M. L. Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Eng. Des. Sel. 28, 251–258 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Köpke, M. et al. Reconstruction of an acetogenic 2,3-butanediol pathway involving a novel NADPH-dependent primary–secondary alcohol dehydrogenase. Appl. Environ. Microbiol. 80, 3394–3403 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Valgepea, K. et al. H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum. Biotechnol. Biofuels 11, 55 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  40. de Souza Pinto Lemgruber, R. et al. Systems-level engineering and characterisation of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB). Metab. Eng. 53, 14–23 (2019).

    Article  PubMed  Google Scholar 

  41. Maia, P., Rocha, I. & Rocha, M. Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction. In: GECCO 2017: Proceedings of the Genetic and Evolutionary Computation Conference Companion 1661–1668 (Association for Computing Machinery, 2017).

  42. Zitzler, E., Laumanns, M. & Thiele, L. SPEA2: improving the Strength Pareto Evolutionary Algorithm. In: Proceedings of the Fifth Conference on Evolutionary Methods for Design 95–100 (Association for Computing Machinery, 2001).

  43. Takanashi, M. & Saito, T. Characterization of two 3-hydroxybutyrate dehydrogenases in poly(3-hydroxybutyrate)-degradable bacterium, Ralstonia pickettii T1. J. Biosci. Bioeng. 101, 501–507 (2006).

    Article  CAS  PubMed  Google Scholar 

  44. Segawa, M., Wen, C., Orita, I., Nakamura, S. & Fukui, T. Two NADH-dependent (S)-3-hydroxyacyl-CoA dehydrogenases from polyhydroxyalkanoate-producing Ralstonia eutropha. J. Biosci. Bioeng. 127, 294–300 (2019).

    Article  CAS  PubMed  Google Scholar 

  45. Tan, Y., Liu, Z.-Y., Liu, Z. & Li, F.-L. Characterization of an acetoin reductase/2,3-butanediol dehydrogenase from Clostridium ljungdahlii DSM 13528. Enzyme Microb. Technol. 79–80, 1–7 (2015).

    Article  PubMed  Google Scholar 

  46. Kim, J., Chang, J. H., Kim, E. J. & Kim, K. J. Crystal structure of (R)-3-hydroxybutyryl-CoA dehydrogenase PhaB from Ralstonia eutropha. Biochem. Biophys. Res. Commun. 443, 783–788 (2014).

    Article  CAS  PubMed  Google Scholar 

  47. Boynton, Z. L., Bennet, G. N. & Rudolph, F. B. Cloning, sequencing, and expression of clustered genes encoding beta-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 178, 3015–3024 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Vick, J. E. et al. Escherichia coli enoyl-acyl carrier protein reductase (FabI) supports efficient operation of a functional reversal of the β-oxidation cycle. Appl. Environ. Microbiol. 81, 1406–1416 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  49. Liew, F. et al. Metabolic engineering of Clostridium autoethanogenum for selective alcohol production. Metab. Eng. 40, 104–114 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Mahamkali, V. et al. Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum. Proc. Natl Acad. Sci. USA 117, 13168–13175 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Greene, J., Daniell, J., Köpke, M., Broadbelt, L. & Tyo, K. E. J. Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production. Biochem. Eng. J. 148, 46–56 (2019).

    Article  CAS  Google Scholar 

  52. Wehrs, M. et al. Engineering robust production microbes for large-scale cultivation. Trends Microbiol. 27, 524–537 (2019).

    Article  CAS  PubMed  Google Scholar 

  53. Hoff, B. et al. Unlocking nature’s biosynthetic power—metabolic engineering for the fermentative production of chemicals. Angew. Chem. Int. Ed. Engl. 60, 2258–2278 (2021).

    Article  CAS  PubMed  Google Scholar 

  54. Nielsen, J. & Keasling, J. D. Engineering cellular metabolism. Cell 164, 1185–1197 (2016).

    Article  CAS  PubMed  Google Scholar 

  55. Crater, J. S. & Lievense, J. C. Scale-up of industrial microbial processes. FEMS Microbiol. Lett. 365, 138 (2018).

    Article  Google Scholar 

  56. Bertsch, J. & Müller, V. Bioenergetic constraints for conversion of syngas to biofuels in acetogenic bacteria. Biotechnol. Bioeng. 8, 210 (2015).

    Google Scholar 

  57. Schuchmann, K. & Müller, V. Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria. Nat. Rev. Microbiol. 12, 809–821 (2014).

    Article  CAS  PubMed  Google Scholar 

  58. Erb, T. J. Back to the future: why we need enzymology to build a synthetic metabolism of the future. Beilstein J. Org. Chem. 15, 551–557 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Diether, M., Nikolaev, Y., Allain, F. H. & Sauer, U. Systematic mapping of protein-metabolite interactions in central metabolism of Escherichia coli. Mol. Syst. Biol. 15, e9008 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Kim, H. M., Chae, T. U., Choi, S. Y., Kim, W. J. & Lee, S. Y. Engineering of an oleaginous bacterium for the production of fatty acids and fuels. Nat. Chem. Biol. 15, 721–729 (2019).

    Article  CAS  PubMed  Google Scholar 

  61. Amin, S. A., Chavez, E., Porokhin, V., Nair, N. U. & Hassoun, S. Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data. Microb. Cell Fact. 18, 109 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  62. Vögeli, B. et al. Archaeal acetoacetyl-CoA thiolase/HMG-CoA synthase complex channels the intermediate via a fused CoA-binding site. Proc. Natl Acad. Sci. USA 115, 3380–3385 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  63. Chen, I. M. A. et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res. 49, D751–D763 (2021).

    Article  CAS  PubMed  Google Scholar 

  64. Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).

    Article  CAS  PubMed  Google Scholar 

  65. Nguyen, L., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, 256–259 (2019).

    Article  Google Scholar 

  68. Fero, M. J., Craft, J. K., Trang, V. & Hillson, N. J. Combinatorial-hierarchical DNA library design using the TeselaGen DESIGN Module with j5. Methods Mol. Biol. 2205, 19–47 (2020).

    Article  CAS  PubMed  Google Scholar 

  69. Liew, F. M. et al. Gas fermentation—a flexible platform for commercial scale production of low-carbon-fuels and chemicals from waste and renewable feedstocks. Front. Microbiol. 7, 694 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  70. Valgepea, K. et al. Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum. Metab. Eng. 41, 202–211 (2017).

    Article  CAS  PubMed  Google Scholar 

  71. Ebrahim, A., Lerman, J. A., Palsson, B. O. & Hyduke, D. R. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst. Biol. 7, 74 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  72. Gonçalves, E., Pereira, R., Rocha, I. & Rocha, M. Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression. J. Comput. Biol. 19, 102–114 (2012).

    Article  PubMed  Google Scholar 

  73. Kwon, Y. C. & Jewett, M. C. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci. Rep. 5, 8663 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Jewett, M. C. & Swartz, J. R. Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis. Biotechnol. Bioeng. 86, 19–26 (2004).

    Article  CAS  PubMed  Google Scholar 

  75. Jewett, M. C., Calhoun, K. A., Voloshin, A., Wuu, J. J. & Swartz, J. R. An integrated cell-free metabolic platform for protein production and synthetic biology. Mol. Syst. Biol. 4, 220 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  76. Karim, A. S., Rasor, B. J. & Jewett, M. C. Enhancing control of cell-free metabolism through pH modulation. Synth. Biol. 5, ysz027 (2020).

    Article  CAS  Google Scholar 

  77. Batth, T. S. et al. Protein aggregation capture on microparticles enables multipurpose proteomics sample preparation. Mol. Cell. Proteomics 18, 1027–1035 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Walker, C., Ryu, S., Giannone, R. J., Garcia, S. & Trinh, C. T. Understanding and eliminating the detrimental effect of thiamine deficiency on the oleaginous yeast Yarrowia lipolytica. Appl. Environ. Microbiol 86, e02299–19 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Taverner, T. et al. DanteR: an extensible R-based tool for quantitative analysis of -omics data. Bioinformatics 28, 2404–2406 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank members of LanzaTech’s Synthetic Biology, Strain Development, Process Integration, Analytics, Engineering Design & Development, AI & Modeling, Computational Biology and Freedom Pines teams for their support and conversations about this work, in particular A. Juminaga, A. Quattlebaum, A. Shah, J. Winkler, J. Cogan, L. Fantroy, M. Maas, M. Martin, N. Gayner, N. Fackler, R. C. Tappel, S. Nagaraju, S. Chong, V. Reynoso, W. P. Mitchell and W. Allen, and R. Kalvakaalva for his work on the Addendum, which provides additional information on the life-cycle analysis. We would also like to thank the Joint Genome Institute DNA synthesis team for their support and conversations on this work, in particular J.-F. Chen, M. Harmon-Smith, R. Evans and Y. Yoshikuni. Funding: Acetone strain and process development, genome-scale modeling, LCA work and initial pilot runs were supported by the U.S. Department of Energy Bioenergy Technologies Office under contract nos. DE-EE0007566 and CRADA/NFE-16-06364 between LanzaTech and the Oak Ridge National Laboratory (F.L., R.N., T.A., C.C., R.O.J., L.W., J.S., P.C., S.D.T., Z.R., A.G., L.T., N.L.E., J.C.B., J.D., R.C., T.J.T., R.J.G., R.L.H., S.D.S., S.D.B., C.L. and M.K.). Cell-free prototyping work was funded by the U.S. Department of Energy Office of Science, Biological and Environmental Research Division, Genomic Science Program, under contract nos. DE-SC0018249 and FWP ERKP903 (F.L., B.J.R., R.O.J., N.L.E., T.J.T., R.J.G., R.L.H., A.S.K., S.D.S., S.D.B., M.C.J. and M.K.). This manuscript was co-authored by UT-Battelle under contract no. DE-AC05-00OR22725 with the U.S. Department of Energy (T.J.T., N.L.E., R.J.G. and R.L.H.). DNA synthesis for the gene libraries was supported by the Joint Genome Institute Community Science Program under award no. CSP-503280; https://doi.org/10.46936/10.25585/60001121 (M.C.J. and M.K.). The work conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under contract no. DE-AC02-05CH11231. B.J.R. is supported by a National Defense Science and Engineering Graduate Fellowship (award ND-CEN-017-095). We also thank the following investors in LanzaTech’s technology: BASF, CICC Growth Capital Fund I, CITIC Capital, Indian Oil Company, K1W1, Khosla Ventures, the Malaysian Life Sciences Capital Fund, L. P., Mitsui, the New Zealand Superannuation Fund, Novo Holdings A/S, Petronas Technology Ventures, Primetals, Qiming Venture Partners, Softbank China and Suncor.

Author information

Author notes

  1. These authors contributed equally: Fungmin Eric Liew, Robert Nogle, Tanus Abdalla.

Authors and Affiliations

  1. LanzaTech Inc., Skokie, IL, USA

    Fungmin Eric Liew, Robert Nogle, Tanus Abdalla, Christina Canter, Rasmus O. Jensen, Lan Wang, Jonathan Strutz, Sashini De Tissera, Alexander P. Mueller, Zhenhua Ruan, Allan Gao, Loan Tran, Jason C. Bromley, James Daniell, Robert Conrado, Séan D. Simpson, Steven D. Brown, Ching Leang & Michael Köpke

  2. Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA

    Blake J. Rasor, Ashty S. Karim & Michael C. Jewett

  3. Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA

    Blake J. Rasor, Ashty S. Karim & Michael C. Jewett

  4. Center for Synthetic Biology, Northwestern University, Evanston, IL, USA

    Blake J. Rasor, Ashty S. Karim & Michael C. Jewett

  5. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA

    Payal Chirania, Nancy L. Engle, Timothy J. Tschaplinski, Richard J. Giannone & Robert L. Hettich

  6. Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA

    Payal Chirania

  7. Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA

    Michael C. Jewett

  8. Simpson Querrey Institute, Northwestern University, Chicago, IL, USA

    Michael C. Jewett

Authors
  1. Fungmin Eric Liew
    View author publications

    Search author on:PubMed Google Scholar

  2. Robert Nogle
    View author publications

    Search author on:PubMed Google Scholar

  3. Tanus Abdalla
    View author publications

    Search author on:PubMed Google Scholar

  4. Blake J. Rasor
    View author publications

    Search author on:PubMed Google Scholar

  5. Christina Canter
    View author publications

    Search author on:PubMed Google Scholar

  6. Rasmus O. Jensen
    View author publications

    Search author on:PubMed Google Scholar

  7. Lan Wang
    View author publications

    Search author on:PubMed Google Scholar

  8. Jonathan Strutz
    View author publications

    Search author on:PubMed Google Scholar

  9. Payal Chirania
    View author publications

    Search author on:PubMed Google Scholar

  10. Sashini De Tissera
    View author publications

    Search author on:PubMed Google Scholar

  11. Alexander P. Mueller
    View author publications

    Search author on:PubMed Google Scholar

  12. Zhenhua Ruan
    View author publications

    Search author on:PubMed Google Scholar

  13. Allan Gao
    View author publications

    Search author on:PubMed Google Scholar

  14. Loan Tran
    View author publications

    Search author on:PubMed Google Scholar

  15. Nancy L. Engle
    View author publications

    Search author on:PubMed Google Scholar

  16. Jason C. Bromley
    View author publications

    Search author on:PubMed Google Scholar

  17. James Daniell
    View author publications

    Search author on:PubMed Google Scholar

  18. Robert Conrado
    View author publications

    Search author on:PubMed Google Scholar

  19. Timothy J. Tschaplinski
    View author publications

    Search author on:PubMed Google Scholar

  20. Richard J. Giannone
    View author publications

    Search author on:PubMed Google Scholar

  21. Robert L. Hettich
    View author publications

    Search author on:PubMed Google Scholar

  22. Ashty S. Karim
    View author publications

    Search author on:PubMed Google Scholar

  23. Séan D. Simpson
    View author publications

    Search author on:PubMed Google Scholar

  24. Steven D. Brown
    View author publications

    Search author on:PubMed Google Scholar

  25. Ching Leang
    View author publications

    Search author on:PubMed Google Scholar

  26. Michael C. Jewett
    View author publications

    Search author on:PubMed Google Scholar

  27. Michael Köpke
    View author publications

    Search author on:PubMed Google Scholar

Contributions

T.J.T., A.S.K., S.D.S., S.D.B., C.L., M.C.J. and M.K. designed the study. R.O.J. and F.L. performed the sequence mining. F.L. developed the combinatorial library framework. F.L., R.N., R.O.J., L.W., C.L. and M.K. performed all strain engineering. A.P.M. and M.K. performed in silico analysis. J.S. and J.D. performed modeling. B.J.R. and A.S.K. performed all cell-free experiments. T.A., Z.R., L.T., J.C.B. and S.D.B. performed all fermentation experiments. C.C., A.G. and R.C. performed LCA. P.C., N.L.E., R.J.G. and R.L.H. performed all omics experiments. E.L., R.N., T.A., B.J.R., A.S.K., C.L. and M.K. performed data analysis and visualization. E.L., R.N., T.A., C.L., B.J.R., A.S.K, M.C.J. and M.K. wrote the manuscript. All authors edited and reviewed the manuscript.

Corresponding authors

Correspondence to Ching Leang, Michael C. Jewett or Michael Köpke.

Ethics declarations

Competing interests

F.L., R.N., T.A., C.C., R.O.J., L.W., J.S., S.T., A.P.M., A.G., L.T., J.C.B., J.D., R.C., S.D.S., S.D.B., C.L. and M.K. are current or former employees of LanzaTech, a for-profit company pursuing commercialization of the acetone and isopropanol gas fermentation process discussed here. M.C.J. consults for and has joint funding with LanzaTech. F.L. and M.K. are co-inventors on granted US patent 9,365,868 (assigned to LanzaTech) related to the production of acetone and isopropanol by fermentation of a gaseous substrate comprising CO that incorporates discoveries incorporated in this manuscript. M.K. is co-inventor on granted US patent 9,550,979 (assigned to LanzaTech) related to alcohol dehydrogenases with engineered metabolic activity that incorporates discoveries incorporated in this manuscript. R.O.J., A.P.M. and M.K. are co-inventors on US patent application 2015/0152445 (assigned to LanzaTech) related to inactivation of secondary alcohol dehydrogenases that incorporates discoveries incorporated in this manuscript. C.L. is an inventor on provisional US patent application 63/035,739 (assigned to LanzaTech) related to integration of acetone and isopropanol biosynthesis gene variants that incorporates discoveries incorporated in this manuscript. R.N. is an inventor on provisional US patent application 63/083,257 (assigned to LanzaTech) related to expressing multiple copies of acetone and isopropanol biosynthesis gene variants that incorporates discoveries incorporated in this manuscript. M.C.J. and A.S.K. are co-inventors on a US provisional patent application that incorporates discoveries described in this manuscript. Their interests are reviewed and managed by Northwestern University in accordance with their conflict of interest policies. All other authors declare no competing interests.

Peer review

Peer review information

Nature Biotechnology thanks Corinne Scown, Shang-Tian Yang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Text, Supplementary Figs. 1–12 and Material Transfer Agreement

Reporting Summary

Supplementary Data

Supplementary Tables 1–10

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liew, F.E., Nogle, R., Abdalla, T. et al. Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Nat Biotechnol 40, 335–344 (2022). https://doi.org/10.1038/s41587-021-01195-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41587-021-01195-w

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research