Third-generation biorefineries as the means to produce fuels and chemicals from CO2


Concerns regarding petroleum depletion and global climate change caused by greenhouse gas emissions have spurred interest in renewable alternatives to fossil fuels. Third-generation (3G) biorefineries aim to utilize microbial cell factories to convert renewable energies and atmospheric CO2 into fuels and chemicals, and hence represent a route for assessing fuels and chemicals in a carbon-neutral manner. However, to establish processes competitive with the petroleum industry, it is important to clarify/evaluate/identify the most promising CO2 fixation pathways, the most appropriate CO2 utilization models and the necessary productivity levels. Here, we discuss the latest advances in 3G biorefineries. Following an overview of applications of CO2 feedstocks, mainly from flue gas and waste gasification, we review prominent opportunities and barriers in CO2 fixation and energy capture. We then summarize reported CO2-based products and industries, and describe trends and key challenges for future advancement of 3G biorefineries.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Milestones in 3G biorefineries.
Fig. 2: Key steps in 3G biorefineries.
Fig. 3: Existing CO2 fixation pathways.
Fig. 4: Theoretical CO2 fixation pathways proposed.
Fig. 5: Sketch of the different energy utilization systems for 3G biorefineries.


  1. 1.

    Petit, J.-R. et al. Climate and atmospheric history of the past 420,000 years from the Vostok ice core, Antarctica. Nature 399, 429 (1999).

    Article  CAS  Google Scholar 

  2. 2.

    Earth’s CO2 Home Page. CO (2019).

  3. 3.

    Xu, Y., Ramanathan, V. & Victor, D. G. Global warming will happen faster than we think. Nature 564, 30–32 (2018).

    Article  CAS  Google Scholar 

  4. 4.

    Glikson, A. The lungs of the Earth: review of the carbon cycle and mass extinction of species. Energy Procedia 146, 3–11 (2018).

    Article  CAS  Google Scholar 

  5. 5.

    Hughes, T. P. et al. Climate change, human impacts, and the resilience of coral reefs. Science 301, 929–933 (2003).

    Article  CAS  Google Scholar 

  6. 6.

    Enguídanos, M., Soria, A., Kavalov, B. & Jensen, P. Techno-Economic Analysis of Bio-alcohol Production in the EU: A Short Summary for Decision-Makers (European Commission, 2002);

  7. 7.

    Musa, S. D., Zhonghua, T., Ibrahim, A. O. & Habib, M. China’s energy status: a critical look at fossils and renewable options. Renew. Sust. Energ. Rev. 81, 2281–2290 (2017).

    Article  Google Scholar 

  8. 8.

    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 

  9. 9.

    Charubin, K. & Papoutsakis, E. T. Direct cell-to-cell exchange of matter in a synthetic Clostridium syntrophy enables CO2 fixation, superior metabolite yields, and an expanded metabolic space. Metab. Eng. 52, 9–19 (2019).

    Article  CAS  Google Scholar 

  10. 10.

    Global Energy and CO 2 Status Report (IEA, 2017);

  11. 11.

    Special Report on Carbon Dioxide Capture and Storage (IPCC, 2005);

  12. 12.

    Global Waste Generation Could Increase 70% by 2050 (World Bank, 2018);

  13. 13.

    Vuppaladadiyam, A. K. et al. Impact of flue gas compounds on microalgae and mechanisms for carbon assimilation and utilization. ChemSusChem 11, 334–355 (2018).

    Article  CAS  Google Scholar 

  14. 14.

    Chandolias, K., Richards, T. & Taherzadeh, M. J. Waste Biorefinery (Elsevier, 2018).

  15. 15.

    Chiu, S.-Y. et al. Microalgal biomass production and on-site bioremediation of carbon dioxide, nitrogen oxide and sulfur dioxide from flue gas using Chlorella sp. cultures. Bioresour. Technol. 102, 9135–9142 (2011).

    Article  CAS  Google Scholar 

  16. 16.

    Direct Air Capture of CO 2 with Chemicals (American Physical Society, 2016);

  17. 17.

    Liew, F., Koepke, M. & Simpson, S. Liquid, Gaseous and Solid Biofuels – Conversion Techniques (IntechOpen, 2013).

  18. 18.

    Hafenbradl, D. & Hein, M. Power-to-gas: a solution for energy storage. Gas. Energy 4, 26–29 (2015).

    Google Scholar 

  19. 19.

    Daniels, L., Fuchs, G., Thauer, R. K. & Zeikus, J. G. Carbon monoxide oxidation by methanogenic bacteria. J. Bacteriol. 132, 118–126 (1977).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Nithiya, E. M., Tamilmani, J., Vasumathi, K. K. & Premalatha, M. Improved CO2 fixation with Oscillatoria sp. in response to various supply frequencies of CO2 supply. J. CO2 Util. 18, 198–205 (2017).

    Article  CAS  Google Scholar 

  21. 21.

    Duarte, J. H., de Morais, E. G., Radmann, E. M. & Costa, J. A. V. Biological CO2 mitigation from coal power plant by Chlorella fusca and Spirulina sp. Bioresour. Technol. 234, 472–475 (2017).

    Article  CAS  Google Scholar 

  22. 22.

    Liang, F. et al. The effects of physicochemical factors and cell density on nitrite transformation in a lipid-rich Chlorella. J. Microbiol. Biotechnol. 25, 2116–2124 (2015).

    Article  CAS  Google Scholar 

  23. 23.

    Calvin, M. & Benson, A. A. The path of carbon in photosynthesis. Science 107, 476–480 (1948).

    Article  CAS  Google Scholar 

  24. 24.

    Fuchs, G. Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu. Rev. Microbiol. 65, 631–658 (2011).

    Article  CAS  Google Scholar 

  25. 25.

    Ducat, D. C. & Silver, P. A. Improving carbon fixation pathways. Curr. Opin. Chem. Biol. 16, 337–344 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Kumar, M., Sundaram, S., Gnansounou, E., Larroche, C. & Thakur, I. S. Carbon dioxide capture, storage and production of biofuel and biomaterials by bacteria: a review. Bioresour. Technol. 247, 1059–1068 (2018).

    Article  CAS  Google Scholar 

  27. 27.

    Gleizer, S. et al. Conversion of Escherichia coli to generate all biomass carbon from CO2. Cell 179, 1255–1263 (2019). This work illustrates how to transform the heterotrophic mode of a microbial cell factory into the autotrophic mode, providing guidelines for future 3G biorefineries.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Schulman, M., Parker, D., Ljungdahl, L. G. & Wood, H. G. Total synthesis of acetate from CO2 V. determination by mass analysis of the different types of acetate formed from13CO2 by heterotrophic bacteria. J. Bacteriol. Parasitol. 109, 633–644 (1972).

    Article  CAS  Google Scholar 

  29. 29.

    Figueroa, I. A. et al. Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway. Proc. Natl Acad. Sci. USA 115, 92–101 (2018).

    Article  CAS  Google Scholar 

  30. 30.

    Kikuchi, G. The glycine cleavage system: composition, reaction mechanism, and physiological significance. Mol. Cell. Biochem. 1, 169–187 (1973).

    Article  CAS  Google Scholar 

  31. 31.

    Fast, A. G. & Papoutsakis, E. T. Functional expression of the Clostridium ljungdahlii acetyl-coenzyme A synthase in Clostridium acetobutylicum as demonstrated by a novel in vivo CO exchange activity en route to heterologous installation of a functional Wood-Ljungdahl pathway. Appl. Environ. Microbiol. 84, 2307–2317 (2018).

    Article  Google Scholar 

  32. 32.

    Bang, J. & Lee, S. Y. Assimilation of formic acid and CO2 by engineered Escherichia coli equipped with reconstructed one-carbon assimilation pathways. Proc. Natl Acad. Sci. USA 115, 9271–9279 (2018).

    Article  CAS  Google Scholar 

  33. 33.

    Bar-Even, A. Formate assimilation: the metabolic architecture of natural and synthetic pathways. Biochemistry 55, 3851–3863 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Döring, V., Darii, E., Yishai, O., Bar-Even, A. & Bouzon, M. Implementation of a reductive route of one-carbon assimilation in Escherichia coli through directed evolution. ACS Synth. Biol. 7, 2029–2036 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. 35.

    Tashiro, Y., Hirano, S., Matson, M. M., Atsumi, S. & Kondo, A. Electrical-biological hybrid system for CO2 reduction. Metab. Eng. 47, 211–218 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Yishai, O., Bouzon, M., Döring, V. & Bar-Even, A. In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in Escherichia coli. ACS Synth. Biol. 7, 2023–2028 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. 37.

    Gonzalez de la Cruz, J., Machens, F., Messerschmidt, K. & Bar-Even, A. Core catalysis of the reductive glycine pathway demonstrated in yeast. ACS Synth. Biol. 8, 911–917 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Huber, H. et al. A dicarboxylate/4-hydroxybutyrate autotrophic carbon assimilation cycle in the hyperthermophilic Archaeum Ignicoccus hospitalis. Proc. Natl Acad. Sci. USA 105, 7851–7856 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Berg, I. A., Kockelkorn, D., Buckel, W. & Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318, 1782–1786 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Hügler, M., Huber, H., Stetter, K. O. & Fuchs, G. Autotrophic CO2 fixation pathways in archaea (Crenarchaeota). Arch. Microbiol. 179, 160–173 (2003).

    Article  CAS  Google Scholar 

  41. 41.

    Holo, H. Chloroflexus aurantiacus secretes 3-hydroxypropionate, a possible intermediate in the assimilation of CO2 and acetate. Arch. Microbiol. 151, 252–256 (1989).

    Article  CAS  Google Scholar 

  42. 42.

    Strauss, G. & Fuchs, G. Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3‐hydroxypropionate cycle. Eur. J. Biochem. 215, 633–643 (1993).

    Article  CAS  Google Scholar 

  43. 43.

    Evans, M., Buchanan, B. B. & Arnon, D. I. A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Proc. Natl Acad. Sci. USA 55, 928–934 (1966).

    Article  CAS  Google Scholar 

  44. 44.

    Fuchs, G., Stupperich, E. & Eden, G. Autotrophic CO2 fixation in Chlorobium limicola. Evidence for the operation of a reductive tricarboxylic acid cycle in growing cells. Arch. Microbiol. 128, 64–71 (1980).

    Article  CAS  Google Scholar 

  45. 45.

    Ramos-Vera, W. H., Berg, I. A. & Fuchs, G. Autotrophic carbon dioxide assimilation in Thermoproteales revisited. J. Bacteriol. 191, 4286–4297 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. 46.

    Blochl, E. Pyrolobus fumarii, gen. and sp. nov., represents and novel group of archaea, extending the upper temperature limit for life to 113°C. Extremophiles 1, 14–21 (1997).

    Article  CAS  Google Scholar 

  47. 47.

    Keller, M. W. et al. Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide. Proc. Natl Acad. Sci. USA 110, 5840–5845 (2013).

    Article  CAS  Google Scholar 

  48. 48.

    Hügler, M., Menendez, C., Schägger, H. & Fuchs, G. Malonyl-coenzyme A reductase from Chloroflexus aurantiacus, a key enzyme of the 3-hydroxypropionate cycle for autotrophic CO2 fixation. J. Bacteriol. 184, 2404–2410 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Alber, B. E. & Fuchs, G. Propionyl-coenzyme A synthase from Chloroflexus aurantiacus, a key enzyme of the 3-hydroxypropionate cycle for autotrophic CO2 fixation. J. Biol. Chem. 277, 12137–12143 (2002).

    Article  CAS  Google Scholar 

  50. 50.

    Mattozzi, M. D., Ziesack, M., Voges, M. J., Silver, P. A. & Way, J. C. Expression of the sub-pathways of the Chloroflexus aurantiacus 3-hydroxypropionate carbon fixation bicycle in E. coli: Toward horizontal transfer of autotrophic growth. Metab. Eng. 16, 130–139 (2013).

    Article  CAS  Google Scholar 

  51. 51.

    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). A comprehensive review comparing energetic efficiencies of four non-photosynthetic carbon fixation pathways for cell growth and production of ethanol, acetate, 2,3-butanediol and butyrate.

    Article  Google Scholar 

  52. 52.

    Ivanovsky, R., Sintsov, N. & Kondratieva, E. ATP-linked citrate lyase activity in the green sulfur bacterium Chlorobium limicola forma thiosulfatophilum. Arch. Microbiol. 128, 239–241 (1980).

    Article  Google Scholar 

  53. 53.

    Hügler, M., Huber, H., Molyneaux, S. J., Vetriani, C. & Sievert, S. M. Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage. Environ. Microbiol. 9, 81–92 (2007).

    Article  CAS  Google Scholar 

  54. 54.

    Mall, A. et al. Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium. Science 359, 563–567 (2018).

    Article  CAS  Google Scholar 

  55. 55.

    Nunoura, T. et al. A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile. Science 359, 559–563 (2018).

    Article  CAS  Google Scholar 

  56. 56.

    Guo, L. et al. Enhancement of malate production through engineering of the periplasmic rTCA pathway in Escherichia coli. Biotechnol. Bioeng. 115, 1571–1580 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Schwander, T. et al. A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354, 900–904 (2016). This work illustrates how the design and construction of a synthetic CO 2 fixation pathway that is in vitro much faster than the CBB cycle in cell extracts.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. 58.

    Gong, F. & Li, Y. Fixing carbon, unnaturally. Science 354, 830–831 (2016).

    Article  CAS  Google Scholar 

  59. 59.

    Erb, T. J., Brecht, V., Fuchs, G., Müller, M. & Alber, B. E. Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase. Proc. Natl Acad. Sci. USA 106, 8871–8876 (2009).

    Article  Google Scholar 

  60. 60.

    Schwander, T. & Erb, T. J. Do it your (path) way–synthetische Wege zur CO2-Fixierung. BIOspektrum 22, 590–592 (2016).

    Article  CAS  Google Scholar 

  61. 61.

    Stoffel, G. M. M. et al. Four amino acids define the CO2 binding pocket of enoyl-CoA carboxylases/reductases. Proc. Natl Acad. Sci. USA 116, 13964–13969 (2019).

    Article  CAS  Google Scholar 

  62. 62.

    Berg, I. A. et al. Autotrophic carbon fixation in archaea. Nat. Rev. Microbiol. 8, 447–460 (2010).

    Article  CAS  Google Scholar 

  63. 63.

    Bar-Even, A., Noor, E. & Milo, R. A survey of carbon fixation pathways through a quantitative lens. J. Exp. Bot. 63, 2325–2342 (2012). This work presents a thorough technoeconomic analysis of current identified carbon fixation pathways and suggests potential metabolic structures of yet to be identified CO 2 fixation pathways.

    Article  CAS  Google Scholar 

  64. 64.

    Bar-Even, A., Noor, E., Lewis, N. E. & Milo, R. Design and analysis of synthetic carbon fixation pathways. Proc. Natl Acad. Sci. USA 107, 8889–8894 (2010).

    Article  Google Scholar 

  65. 65.

    Näser, U. et al. Synthesis of 13C-labeled γ-hydroxybutyrates for EPR studies with 4-hydroxybutyryl-CoA dehydratase. Bioorg. Chem. 33, 53–66 (2005).

    Article  CAS  Google Scholar 

  66. 66.

    Könneke, M. et al. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proc. Natl Acad. Sci. USA 111, 8239–8244 (2014).

    Article  CAS  Google Scholar 

  67. 67.

    South, P. F., Cavanagh, A. P., Liu, H. W. & Ort, D. R. J. S. Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field. Science 363, eaat9077 (2019).

    Article  CAS  Google Scholar 

  68. 68.

    Arai, H., Kanbe, H., Ishii, M. & Igarashi, Y. Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6. J. Bacteriol. 192, 2651–2652 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. 69.

    Ramos-Vera, W. H., Weiss, M., Strittmatter, E., Kockelkorn, D. & Fuchs, G. Identification of missing genes and enzymes for autotrophic carbon fixation in. Crenarchaeota. J. Bacteriol. 193, 1201–1211 (2011).

    Article  CAS  Google Scholar 

  70. 70.

    Emerson, D. F. & Stephanopoulos, G. Limitations in converting waste gases to fuels and chemicals. Curr. Opin. Biotechnol. 59, 39–45 (2019).

    Article  CAS  Google Scholar 

  71. 71.

    Li, F.-F. et al. Microalgae capture of CO2 from actual flue gas discharged from a combustion chamber. Ind. Eng. Chem. Res. 50, 6496–6502 (2011).

    Article  CAS  Google Scholar 

  72. 72.

    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 

  73. 73.

    Alberty, R. A. Thermodynamics of Biochemical Reactions (John Wiley and Sons, 2003).

  74. 74.

    Tran, Q. H. & Unden, G. Changes in the proton potential and the cellular energetics of Escherichia coli during growth by aerobic and anaerobic respiration or by fermentation. FEBS J. 251, 538–543 (1998).

    CAS  Google Scholar 

  75. 75.

    Boyle, N. R. & Morgan, J. A. Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation. Metab. Eng. 13, 150–158 (2011). This study provides a quantitative study of all six native CO 2 fixation pathways for their thermodynamic efficiencies for biomass production, and suggests that, when taking into account the cost of hydrogen production, photoautotrophic pathways are more efficient than chemoautotrophic pathways.

    Article  CAS  Google Scholar 

  76. 76.

    Lahtvee, P.-J. et al. Absolute quantification of protein and mRNA abundances demonstrate variability in gene-specific translation efficiency in yeast. Cell Syst. 4, 1–10 (2017).

    Article  CAS  Google Scholar 

  77. 77.

    Roger, M., Brown, F., Gabrielli, W. & Sargent, F. Efficient hydrogen-dependent carbon dioxide reduction by Escherichia coli. Curr. Biol. 28, 140–145 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. 78.

    Bennett, B. D. et al. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593–599 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. 79.

    Bar-Even, A., Noor, E., Flamholz, A., Buescher, J. M. & Milo, R. Hydrophobicity and charge shape cellular metabolite concentrations. PLoS Comput. Biol. 7, e1002166 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. 80.

    Bekers, K., Heijnen, J. & Van Gulik, W. Determination of the in vivo NAD: NADH ratio in Saccharomyces cerevisiae under anaerobic conditions, using alcohol dehydrogenase as sensor reaction. Yeast 32, 541–557 (2015).

    Article  CAS  Google Scholar 

  81. 81.

    Jinich, A. et al. Quantum chemistry reveals thermodynamic principles of redox biochemistry. PLoS Comput. Biol. 14, e1006471 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. 82.

    Perkins, C. & Weimer, A. W. Solar-thermal production of renewable hydrogen. AlChE J. 55, 286–293 (2009).

    Article  CAS  Google Scholar 

  83. 83.

    Angermayr, S. A., Rovira, A. G. & Hellingwerf, K. J. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends Biotechnol. 33, 352–361 (2015).

    Article  CAS  Google Scholar 

  84. 84.

    Bernhardsgrütter, I. et al. Awakening the sleeping carboxylase function of enzymes: engineering the natural CO2-binding potential of reductases. J. Am. Chem. Soc. 141, 9778–9782 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. 85.

    Sundaram, T. Physiological role of pyruvate carboxylase in a thermophilic Bacillus. J. Bacteriol. 113, 549–557 (1973).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. 86.

    Cotton, C. A., Edlich-Muth, C. & Bar-Even, A. Reinforcing carbon fixation: CO2 reduction replacing and supporting carboxylation. Curr. Opin. Biotechnol. 49, 49–56 (2018).

    Article  CAS  Google Scholar 

  87. 87.

    Garrastazu, C., Iniesta, M., Aranguez, M. & Ruiz, M. A. Comparative analysis of propionyl-CoA carboxylase from liver and mammary gland of mid-lactation cow. Comp. Biochem. Physiol. B 99, 613–617 (1991).

    Article  CAS  Google Scholar 

  88. 88.

    Kai, Y. et al. Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition. Proc. Natl Acad. Sci. USA 96, 823–828 (1999).

    Article  CAS  Google Scholar 

  89. 89.

    Erb, T. J. et al. Synthesis of C5-dicarboxylic acids from C2-units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway. Proc. Natl Acad. Sci. USA 104, 10631–10636 (2007).

    Article  CAS  Google Scholar 

  90. 90.

    Sage, R. F. Variation in the kcat of Rubisco in C3 and C4 plants and some implications for photosynthetic performance at high and low temperature. J. Exp. Bot. 53, 609–620 (2002).

    Article  CAS  Google Scholar 

  91. 91.

    Claassens, N. J. A warm welcome for alternative CO2 fixation pathways in microbial biotechnology. Microb. Biotechnol. 10, 31–34 (2017).

    Article  Google Scholar 

  92. 92.

    Varaljay, V. et al. Functional metagenomic selection of RuBisCO from uncultivated bacteria. Environ. Microbiol. 18, 1187–1199 (2015).

    Article  CAS  Google Scholar 

  93. 93.

    Bachu, S. & Adams, J. Sequestration of CO2 in geological media in response to climate change: capacity of deep saline aquifers to sequester CO2 in solution. Energy Convers. Manag. 44, 3151–3175 (2003).

    Article  CAS  Google Scholar 

  94. 94.

    Berg, I. A. Ecological aspects of the distribution of different autotrophic CO2 fixation pathways. Appl. Environ. Microbiol. 77, 1925–1936 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. 95.

    Comotti, A. et al. Porous dipeptide crystals as selective CO2 adsorbents: experimental isotherms vs. grand canonical Monte Carlo simulations and MAS NMR spectroscopy. CrystEngComm 15, 1503–1507 (2013).

    Article  CAS  Google Scholar 

  96. 96.

    Jajesniak, P., Ali, H. E. M. O. & Wong, T. S. Carbon dioxide capture and utilization using biological systems: opportunities and challenges. J. Bioprocess. Biotech. 4, 3 (2014).

    Google Scholar 

  97. 97.

    Mackinder, L. C. et al. A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle. Proc. Natl Acad. Sci. USA 113, 5958–5963 (2016).

    Article  CAS  Google Scholar 

  98. 98.

    Yeates, T. O., Crowley, C. S. & Tanaka, S. Bacterial microcompartment organelles: protein shell structure and evolution. Annu. Rev. Biophys. 39, 185–205 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. 99.

    Rosenberg, E., DeLong, E. F., Lory, S., Stackebrandt, E. & Thompson, F. The Prokaryotes (Springer, 2006).

  100. 100.

    Claassens, N. J., Sousa, D. Z., dos Santos, V. A. M., de Vos, W. M. & van der Oost, J. Harnessing the power of microbial autotrophy. Nat. Rev. Microbiol. 14, 692–706 (2016). A comprehensive review discussing advances and bottlenecks for engineering autotrophic microbial cell factories, focusing on the energy harvesting perspective.

    Article  CAS  Google Scholar 

  101. 101.

    Liu, C., Colón, B. C., Ziesack, M., Silver, P. A. & Nocera, D. G. Water splitting–biosynthetic system with CO2 reduction efficiencies exceeding photosynthesis. Science 352, 1210–1213 (2016).

    Article  CAS  Google Scholar 

  102. 102.

    Yu, J. Bio-based products from solar energy and carbon dioxide. Trends Biotechnol. 32, 5–10 (2014).

    Article  CAS  Google Scholar 

  103. 103.

    Mohan, S. V., Modestra, J. A., Amulya, K., Butti, S. K. & Velvizhi, G. A circular bioeconomy with biobased products from CO2 sequestration. Trends Biotechnol. 34, 506–519 (2016). This review provides a comprehensive summary of different energy harvesting techniques for 3G biorefinery and proposes an integrated CO 2 biorefinery model that interlinks multiple processes and circulates resources and waste.

  104. 104.

    Tabita, F. R. Anoxygenic Photosynthetic Bacteria (Springer, 1995).

  105. 105.

    Raven, J. A. Contributions of anoxygenic and oxygenic phototrophy and chemolithotrophy to carbon and oxygen fluxes in aquatic environments. Aquat. Microb. Ecol. 56, 177–192 (2009).

    Article  Google Scholar 

  106. 106.

    Frost-Christensen, H. & Sand-Jensen, K. The quantum efficiency of photosynthesis in macroalgae and submerged angiosperms. Oecologia 91, 337–384 (1992).

    Article  Google Scholar 

  107. 107.

    Larsen, H., Yocum, C. S. & Niel, C. Bv On the energetics of the photosynthesis in green sulfur bacteria. J. Gen. Physiol. 36, 161–171 (1952).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. 108.

    Martinez, A., Bradley, A., Waldbauer, J., Summons, R. & DeLong, E. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc. Natl Acad. Sci. USA 104, 5590–5595 (2007).

    Article  CAS  Google Scholar 

  109. 109.

    Guo, J. et al. Light-driven fine chemical production in yeast biohybrids. Science 362, 813–816 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. 110.

    Zhao, T.-T. et al. Artificial bioconversion of carbon dioxide. Chin. J. Catal. 40, 1421–1437 (2019).

    Article  CAS  Google Scholar 

  111. 111.

    Shen, Y. Carbon dioxide bio-fixation and wastewater treatment via algae photochemical synthesis for biofuels production. RSC Adv. 4, 49672–49722 (2014).

    Article  CAS  Google Scholar 

  112. 112.

    Nürnberg, D. J. et al. Photochemistry beyond the red limit in chlorophyll f–containing photosystems. Science 360, 1210–1213 (2018).

    Article  CAS  Google Scholar 

  113. 113.

    Ort, D. R. et al. Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proc. Natl Acad. Sci. USA 112, 8529–8536 (2015).

    Article  CAS  Google Scholar 

  114. 114.

    Sakimoto, K. K., Wong, A. B. & Yang, P. Self-photosensitization of nonphotosynthetic bacteria for solar-to-chemical production. Science 351, 74–77 (2016).

    Article  CAS  Google Scholar 

  115. 115.

    Zhang, H. et al. Bacteria photosensitized by intracellular gold nanoclusters for solar fuel production. Nat. Nanotechnol. 13, 900–905 (2018).

    Article  CAS  Google Scholar 

  116. 116.

    Hauska, G., Schoedl, T., Remigy, H. & Tsiotis, G. The reaction center of green sulfur bacteria (1). Biochim. Biophys. Acta 1507, 260–277 (2001).

    Article  CAS  Google Scholar 

  117. 117.

    Manske, A. K., Glaeser, J., Kuypers, M. M. & Overmann, J. Physiology and phylogeny of green sulfur bacteria forming a monospecific phototrophic assemblage at a depth of 100 meters in the Black Sea. Appl. Environ. Microbiol. 71, 8049–8060 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. 118.

    Wang, J. et al. Field study on attached cultivation of Arthrospira (Spirulina) with carbon dioxide as carbon source. Bioresour. Technol. 283, 270–276 (2019).

    Article  CAS  Google Scholar 

  119. 119.

    Chen, J. et al. Microalgal industry in China: challenges and prospects. J. Appl. Phycol. 28, 715–725 (2016).

    Article  CAS  Google Scholar 

  120. 120.

    Bhola, V., Swalaha, F., Ranjith Kumar, R., Singh, M. & Bux, F. Overview of the potential of microalgae for CO2 sequestration. Int. J. Environ. Sci. Technol. 11, 2103–2118 (2014).

    Article  CAS  Google Scholar 

  121. 121.

    Liu, Y. & Whitman, W. B. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann. N. Y. Acad. Sci. 1125, 171–189 (2008).

    Article  CAS  Google Scholar 

  122. 122.

    Lamont, C. M. & Sargent, F. Design and characterisation of synthetic operons for biohydrogen technology. Arch. Microbiol. 199, 495–503 (2017).

    Article  CAS  Google Scholar 

  123. 123.

    Laurinavichene, T. V. & Tsygankov, A. A. H2 consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors. FEMS Microbiol. Lett. 202, 121–124 (2001).

    Article  CAS  Google Scholar 

  124. 124.

    Gong, F., Zhu, H., Zhang, Y. & Li, Y. Biological carbon fixation: From natural to synthetic. J. CO 2 Util. 28, 221–227 (2018).

  125. 125.

    Claassens, N. J., Sánchez-Andrea, I., Sousa, D. Z. & Bar-Even, A. Towards sustainable feedstocks: A guide to electron donors for microbial carbon fixation. Curr. Opin. Biotechnol. 50, 195–205 (2018). This review systematically evaluates different electron donors, and suggests that formate, H 2 and CO are the most promising for growth and bioproduction.

    Article  CAS  Google Scholar 

  126. 126.

    Guzman, M. S. et al. Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris. Nat. Commun. 10, 1355 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. 127.

    Nevin, K. P., Woodard, T. L., Franks, A. E., Summers, Z. M. & Lovley, D. R. Microbial electrosynthesis: feeding microbes electricity to convert carbon dioxide and water to multicarbon extracellular organic compounds. mBio 1, e00103-10 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. 128.

    Tremblay, P.-L., Angenent, L. T. & Zhang, T. Extracellular electron uptake: among autotrophs and mediated by surfaces. Trends Biotechnol. 35, 360–371 (2017).

    Article  CAS  Google Scholar 

  129. 129.

    Chen, X., Cao, Y., Li, F., Tian, Y. & Song, H. Enzyme-assisted microbial electrosynthesis of poly (3-hydroxybutyrate) via CO2 bioreduction by engineered Ralstonia eutropha. ACS Catal. 8, 4429–4437 (2018).

    Article  CAS  Google Scholar 

  130. 130.

    Jiang, Y. et al. Carbon dioxide and organic waste valorization by microbial electrosynthesis and electro-fermentation. Water Res. 149, 42–55 (2018).

    Article  CAS  Google Scholar 

  131. 131.

    Holmes, D. E., Bond, D. R. & Lovley, D. R. Electron transfer by Desulfobulbus propionicus to Fe (III) and graphite electrodes. Appl. Environ. Microbiol. 70, 1234–1237 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. 132.

    Liao, J. C., Mi, L., Pontrelli, S. & Luo, S. Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat. Rev. Microbiol. 14, 288–304 (2016). This study thoroughly discusses 2G biorefinery, 3G biorefinery and methane biorefinery on their strength on bioproduction.

    Article  CAS  Google Scholar 

  133. 133.

    Rodrigues, R. M. et al. Perfluorocarbon nanoemulsion promotes the delivery of reducing equivalents for electricity-driven microbial CO2 reduction. Nat. Catal. 2, 407–414 (2019).

    Article  CAS  Google Scholar 

  134. 134.

    Haas, T., Krause, R., Weber, R., Demler, M. & Schmid, G. Technical photosynthesis involving CO2 electrolysis and fermentation. Nat. Catal. 1, 32–39 (2018).

    Article  CAS  Google Scholar 

  135. 135.

    Su, L. & Ajo-Franklin, C. M. Reaching full potential: bioelectrochemical systems for storing renewable energy in chemical bonds. Curr. Opin. Biotechnol. 57, 66–72 (2019). This review comprehensively summarizes state-of-the-art technologies of bioelectrochemical systems and biohybrid systems.

    Article  CAS  Google Scholar 

  136. 136.

    Woo, H. M. Solar-to-chemical and solar-to-fuel production from CO2 by metabolically engineered microorganisms. Curr. Opin. Biotechnol. 45, 1–7 (2017).

    Article  CAS  Google Scholar 

  137. 137.

    Cornejo, J. A., Sheng, H., Edri, E., Ajo-Franklin, C. & Frei, H. Nanoscale membranes that chemically isolate and electronically wire up the abiotic/biotic interface. Nat. Commun. 9, 2263 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. 138.

    Lai, M. J. & Lan, E. I. Photoautotrophic synthesis of butyrate by metabolically engineered cyanobacteria. Biotechnol. Bioeng. 116, 893–903 (2019).

    CAS  PubMed  Google Scholar 

  139. 139.

    Tran, M., Zhou, B., Pettersson, P. L., Gonzalez, M. J. & Mayfield, S. P. Synthesis and assembly of a full‐length human monoclonal antibody in algal chloroplasts. Biotechnol. Bioeng. 104, 663–673 (2009).

    CAS  PubMed  Google Scholar 

  140. 140.

    Ni, J., Liu, H.-Y., Tao, F., Wu, Y.-T. & Xu, P. Remodeling of the photosynthetic chain promotes direct CO2 conversion to valuable aromatics. Angew. Chem. 57, 15990–15994 (2018).

    Article  CAS  Google Scholar 

  141. 141.

    Ferreira, G., Pinto, L. R., Maciel Filho, R. & Fregolente, L. A review on lipid production from microalgae: Association between cultivation using waste streams and fatty acid profiles. Renew. Sust. Energ. Rev. 109, 448–466 (2019).

    Article  CAS  Google Scholar 

  142. 142.

    Yunus, I. S. et al. Synthetic metabolic pathways for photobiological conversion of CO2 into hydrocarbon fuel. Metab. Eng. 49, 201–211 (2018).

    Article  CAS  Google Scholar 

  143. 143.

    Humphreys, C. M. & Minton, N. P. Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas. Curr. Opin. Biotechnol. 50, 174–181 (2018).

    Article  CAS  Google Scholar 

  144. 144.

    Ishizaki, A., Tanaka, K. & Taga, N. Microbial production of poly-d-3-hydroxybutyrate from CO2. Appl. Microbiol. Biotechnol. 57, 6–12 (2001).

    Article  CAS  Google Scholar 

  145. 145.

    Ammam, F., Tremblay, P.-L., Lizak, D. M. & Zhang, T. Effect of tungstate on acetate and ethanol production by the electrosynthetic bacterium Sporomusa ovata. Biotechnol. Biofuels 9, 163 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. 146.

    Bajracharya, S., Vanbroekhoven, K., Buisman, C. J. N., Strik, D. & Pant, D. Bioelectrochemical conversion of CO2 to chemicals: CO2 as a next generation feedstock for electricity-driven bioproduction in batch and continuous modes. Faraday Discuss. 202, 433–449 (2017).

    Article  CAS  Google Scholar 

  147. 147.

    Vassilev, I. et al. Microbial electrosynthesis of isobutyric, butyric, caproic acids, and corresponding alcohols from carbon dioxide. ACS Sustain. Chem. Eng. 6, 8485–8493 (2018).

    Article  CAS  Google Scholar 

  148. 148.

    LaBelle, E. V. & May, H. D. Energy efficiency and productivity enhancement of microbial electrosynthesis of acetate. Front. Microbiol. 8, 756 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  149. 149.

    Ganigué, R., Puig, S., Batlle-Vilanova, P., Balaguer, M. D. & Colprim, J. Microbial electrosynthesis of butyrate from carbon dioxide. Chem. Commun. 51, 3235–3238 (2015).

    Article  CAS  Google Scholar 

  150. 150.

    Jourdin, L., Raes, S. M., Buisman, C. J. & Strik, D. P. Critical biofilm growth throughout unmodified carbon felts allows continuous bioelectrochemical chain elongation from CO2 up to caproate at high current density. Front. Energy Res. 6, 7 (2018).

    Article  Google Scholar 

  151. 151.

    Krieg, T., Sydow, A., Faust, S., Huth, I. & Holtmann, D. CO2 to terpenes: autotrophic and electroautotrophic α‐humulene production with Cupriavidus necator. Angew. Chem. Int. Ed. 57, 1879–1882 (2018).

    Article  CAS  Google Scholar 

  152. 152.

    Full Final Report Section Synopsis (National Alliance for Advanced Biofuels and Bioproducts, 2017);

  153. 153.

    Campbell, P. K., Beer, T. & Batten, D. Life cycle assessment of biodiesel production from microalgae in ponds. Bioresour. Technol. 102, 50–56 (2011).

    Article  CAS  Google Scholar 

  154. 154.

    May, H. D., Evans, P. J. & LaBelle, E. V. The bioelectrosynthesis of acetate. Curr. Opin. Biotechnol. 42, 225–233 (2016).

    Article  CAS  Google Scholar 

  155. 155.

    Christodoulou, X. & Velasquez-Orta, S. B. Microbial electrosynthesis and anaerobic fermentation: an economic evaluation for acetic acid production from CO2 and CO. Environ. Sci. Technol. 50, 11234–11242 (2016).

    Article  CAS  Google Scholar 

  156. 156.

    De Luna, P. et al. What would it take for renewably powered electrosynthesis to displace petrochemical processes? Science 364, eaav3506 (2019).

    Article  CAS  Google Scholar 

  157. 157.

    Khan, N. E., Myers, J. A., Tuerk, A. L. & Curtis, W. R. A process economic assessment of hydrocarbon biofuels production using chemoautotrophic organisms. Bioresour. Technol. 172, 201–211 (2014).

    Article  CAS  Google Scholar 

  158. 158.

    Renewable Power: Climate-Safe Eneryg Competes on Cost Alone (IRENA, 2018);

  159. 159.

    Karamanev, D. et al. Biological conversion of hydrogen to electricity for energy storage. Energy 129, 237–245 (2017).

    Article  CAS  Google Scholar 

  160. 160.

    Pricing Carbon Emissions through Taxes and Emissions Trading (OECD, 2018);

  161. 161.

    Junne, S. & Kabisch, J. Fueling the future with biomass: processes and pathways for a sustainable supply of hydrocarbon fuels and biogas. Eng. Life Sci. 17, 14–26 (2016).

    Article  CAS  Google Scholar 

  162. 162.

    Gross, M. Counting carbon costs. Curr. Biol. 28, 1221–1224 (2018).

    Article  CAS  Google Scholar 

  163. 163.

    Ricke, K., Drouet, L., Caldeira, K. & Tavoni, M. Country-level social cost of carbon. Nat. Clim. Change 8, 895–900 (2018).

    Article  CAS  Google Scholar 

  164. 164.

    Coma, M. et al. Organic waste as a sustainable feedstock for platform chemicals. Faraday Discuss. 202, 175–195 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. 165.

    Du, K. et al. Integrated lipid production, CO2 fixation, and removal of SO2 and NO from simulated flue gas by oleaginous Chlorella pyrenoidosa. Environ. Sci. Pollut. Res. 26, 16195–16209 (2019).

    Article  CAS  Google Scholar 

  166. 166.

    Yu, J. et al. Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2. Sci. Rep. 5, 8132 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. 167.

    Charubin, K., Bennett, R. K., Fast, A. G. & Papoutsakis, E. T. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab. Eng. 50, 173–191 (2018).

    Article  CAS  Google Scholar 

  168. 168.

    Liu, C. et al. Nanowire–bacteria hybrids for unassisted solar carbon dioxide fixation to value-added chemicals. Nano Lett. 15, 3634–3639 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. 169.

    Subhash, G. V. & Mohan, S. V. Deoiled algal cake as feedstock for dark fermentative biohydrogen production: an integrated biorefinery approach. Int. J. Hydrog. Energ. 39, 9573–9579 (2014).

    Article  CAS  Google Scholar 

  170. 170.

    ElMekawy, A. et al. Food and agricultural wastes as substrates for bioelectrochemical system (BES): the synchronized recovery of sustainable energy and waste treatment. Food Res. Int. 73, 213–225 (2015).

    Article  CAS  Google Scholar 

  171. 171.

    Hermida-Carrera, C., Kapralov, M. V. & Galmés, J. Rubisco catalytic properties and temperature response in crops. Plant Physiol. 171, 2549–2561 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  172. 172.

    Altaş, N. et al. Heterologous production of extreme alkaline thermostable NAD+-dependent formate dehydrogenase with wide-range pH activity from Myceliophthora thermophila. Process Biochem. 61, 110–118 (2017).

    Article  CAS  Google Scholar 

  173. 173.

    Wilcoxen, J., Snider, S. & Hille, R. Substitution of silver for copper in the binuclear Mo/Cu center of carbon monoxide dehydrogenase from Oligotropha carboxidovorans. J. Am. Chem. Soc. 133, 12934–12936 (2011).

    Article  CAS  Google Scholar 

  174. 174.

    Hawkins, A. B., Adams, M. W. W. & Kelly, R. M. Conversion of 4-hydroxybutyrate to acetyl coenzyme A and its anapleurosis in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway. Appl. Environ. Microbiol. 80, 2536–2545 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. 175.

    Liu, C., Wang, Q., Xian, M., Ding, Y. & Zhao, G. Dissection of malonyl-coenzyme A reductase of Chloroflexus aurantiacus results in enzyme activity improvement. PLoS ONE 8, e75554 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. 176.

    Fan, F. et al. On the catalytic mechanism of human ATP citrate lyase. Biochemistry 51, 5198–211 (2012).

    Article  CAS  Google Scholar 

  177. 177.

    Yoo, H. G. et al. Characterization of 2-octenoyl-CoA carboxylase/reductase utilizing pteB from Streptomyce avermitilis. Biosci. Biotechnol. Biochem. 75, 1191–1193 (2011).

    Article  CAS  Google Scholar 

  178. 178.

    ElMekawy, A. et al. Technological advances in CO2 conversion electro-biorefinery: a step toward commercialization. Bioresour. Technol. 215, 357–370 (2016).

    Article  CAS  Google Scholar 

Download references


This work was supported by the Beijing Advanced Innovation Center for Soft Matter Science and Engineering, National Natural Science Foundation of China (21811530003), National Key Research and Development Program (2018YFA0903000 and 2018YFA0900100), the Double First-Rate Program (ylkxj03), the Novo Nordisk Foundation (NNF10CC1016517) and the Knut and Alice Wallenberg Foundation.

Author information




Z.L., T.T. and J.N. drafted the outline. Z.L., K.W., Y.C., T.T. and J.N. wrote the manuscript. T.T. and J.N. supervised the research. All authors have read and approved the final manuscript.

Corresponding authors

Correspondence to Tianwei Tan or Jens Nielsen.

Ethics declarations

Competing interests

The authors declare no competing interests.

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 Table 1, Supplementary References

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Liu, Z., Wang, K., Chen, Y. et al. Third-generation biorefineries as the means to produce fuels and chemicals from CO2. Nat Catal 3, 274–288 (2020).

Download citation

Further reading


Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing