Towards sustainable feedstocks: A guide to electron donors for microbial carbon fixation

Current Opinion in Biotechnology

Volumn 50, Issue , 2018, Pages 195-205

  Claassens, Nico Joannes ^a   Sánchez Andrea, Irene ^b   Sousa, Diana Zita ^b   Bar Even, Arren ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON DIOXIDE; CARBON INORGANIC COMPOUNDS; FEEDSTOCKS;

CARBON COMPOUNDS; ELECTRON CARRIER; ELECTRON DONORS; HIGH-EFFICIENCY; MICROBIAL CARBONS; PHYSICOCHEMICAL PROPERTY; PRODUCTION METHODS; REDUCTION POTENTIAL;

ELECTRONS;

AMMONIA; CARBON; CARBON MONOXIDE; FERROUS ION; FORMIC ACID; HYDROGEN; METHANE; METHANOL; NITROGEN OXIDE; PHOSPHITE; SULFIDE; SULFUR;

ANAEROBIC DIGESTION; BIOTECHNOLOGICAL PRODUCTION; CARBON FIXATION; DIFFUSION; ELECTROCHEMISTRY; ELECTRON DONOR; ENVIRONMENTAL PARAMETERS; ENZYME ACTIVITY; METABOLIC PARAMETERS; MICROBIAL METABOLISM; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; REDUCTION POTENTIAL; REVIEW; SOLUBILITY; SUSTAINABLE FEEDSTOCK; TRANSPORT KINETICS; BACTERIUM; BIOREACTOR; BIOTECHNOLOGY; CARBON CYCLE; ELECTRON; METABOLISM; MICROBIOLOGY;

BACTERIA; BIOREACTORS; BIOTECHNOLOGY; CARBON CYCLE; ELECTROCHEMISTRY; ELECTRONS;

EID: 85041899657     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2018.01.019     Document Type: Review

References (67)

1. Zhu, X.-G., Long, S.P., Ort, D.R., What is the maximum efficiency with which photosynthesis can convert solar energy into biomass?. Curr Opin Biotechnol 19 (2008), 153–159.
2. Cotton, C.A.R., Douglass, J.S., De Causmaecker, S., Brinkert, K., Cardona, T., Fantuzzi, A., Rutherford, A.W., Murray, J.W., Photosynthetic constraints on fuel from microbes. Front Bioeng Biotechnol 3 (2015), 1–5.
3. Wijffels, R.H., Kruse, O., Hellingwerf, K.J., Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae. Curr Opin Biotechnol 24 (2013), 405–413.
4. Xu, K., Lv, B., Huo, Y.X., Li, C., Toward the lowest energy consumption and emission in biofuel production: combination of ideal reactors and robust hosts. Curr Opin Biotechnol 50 (2018), 19–24.
5. Chistoserdova, L., Applications of methylotrophs: Can single carbon be harnessed for biotechnology?. Curr Opin Biotechnol 50 (2018), 189–194.
6. Claassens, N.J., Sousa, D.Z., Dos Santos, V.A.P.M., de Vos, W.M., van der Oost, J., Harnessing the power of microbial autotrophy. Nat Rev Microbiol 14 (2016), 692–706 This review gives a broad overview on the potential of microbial autotrophy for biotechnology. It discusses recent advances and provides future strategies to apply synthetic biology principles for improved microbial autotrophy.
7. Nybo, S.E., Khan, N.E., Woolston, B.M., Curtis, W.R., Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals. Metab Eng 30 (2015), 105–120 This review provides an excellent discussion on the most promising chemoautotrophic hosts and describes how they can be engineered. It also describes the potential engineering of heterotrophs into synthetic autotrophs.
8. Bar-Even, A., Noor, E., Flamholz, A., Milo, R., Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes. Biochim Biophys Acta 1827 (2013), 1039–1047.
9. Diender, M., Stams, A.J.M., Sousa, D.Z., Pathways and bioenergetics of anaerobic carbon monoxide fermentation. Front Microbiol 6 (2015), 1–18.
10. Whitaker, W.B., Sandoval, N.R., Bennett, R.K., Fast, A.G., Papoutsakis, E.T., Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization. Curr Opin Biotechnol 33 (2015), 165–175.
11. 2 from ambient air. Chem Rev 116 (2016), 11840–11876.
12. 2 to C1-compounds.
13. Badwal, S.P.S., Kulkarni, A.P., And, H.J., Giddey, S., Abstract: solar fuels. Electrochemical Science for a sustainable society, 2017.
14. 2 . Annu Rev Phys Chem 63 (2012), 541–569.
15. Dürre, P., Eikmanns, B.J., C1-carbon sources for chemical and fuel production by microbial gas fermentation. Curr Opin Biotechnol 35 (2015), 63–72 Several gaseous C1-substrates and their microbial utilization and production are clearly discussed, both for anaerobic and aerobic processes.
16. Yishai, O., Lindner, S.N., Gonzalez de la Cruz, J., Tenenboim, H., Bar-Even, A., The formate bio-economy. Curr Opin Chem Biol 35 (2016), 1–9 This review provides an outlook on the opportunities and challenges of using formate as an electron donor for biotechnology.
17. Grunwald, S., Mottet, A., Grousseau, E., Plassmeier, J.K., Popović, M.K., Uribelarrea J-LL, Gorret, N., Guillouet, S.E., Sinskey, A., Kinetic and stoichiometric characterization of organoautotrophic growth of Ralstonia eutropha on formic acid in fed-batch and continuous cultures. Microb Biotechnol 8 (2015), 155–163.
18. 2 to organic products. Sci Rep, 5, 2015, 16168 This study provides a good example on how laboratory evolution can be successfully applied to evolve tolerance towards a toxic electron donor, in this case methanol consumed by the acetogen Sporomusa ovata.
19. Bar-Even, A., Flamholz, A., Noor, E., Milo, R., Thermodynamic constraints shape the structure of carbon fixation pathways. Biochim Biophys Acta 1817 (2012), 1646–1659.
20. 2 fixation pathways. Appl Environ Microbiol 77 (2011), 1925–1936.
21. 2 -fixation pathways to support synthetic biology strategies for production of fuels and chemicals. Curr Opin Chem Eng 1 (2012), 380–395.
22. Diender, M., Stams, A.J.M., Sousa, D.Z., Production of medium-chain fatty acids and higher alcohols by a synthetic co-culture grown on carbon monoxide or syngas. Biotechnol Biofuels, 9, 2016, 82.
23. Liu, C., Gallagher, J.J., Sakimoto, K.K., Nichols, E.M., Chang, C.J., Chang, M.C.Y., Yang, P., Nanowire–bacteria hybrids for unassisted solar carbon dioxide fixation to value-added chemicals. Nano Lett 15 (2015), 3634–3639 This study presents a highly innovative approach, where the cathode of a photochemical semiconductor system is interfaced with the acetogen Sporomusa for light-to-acetate conversion. The acetate is subsequently consumed by genetically engineered E. coli for the production of several value-added products in aerobic conditions.
24. Bar-Even, A., Noor, E., Lewis, N.E., Milo, R., Design and analysis of synthetic carbon fixation pathways. Proc Natl Acad Sci U S A 107 (2010), 8889–8894.
25. Schwander, T., Schada von Borzyskowski, L., Burgener, S., Cortina, N.S., Erb, T.J., A synthetic pathway for the fixation of carbon dioxide in vitro. Science 354 (2016), 900–904.
26. 2 fixation pathways in microbial biotechnology. Microb Biotechnol, 2017, 10.
27. 2 reduction efficiencies exceeding photosynthesis. Science 352 (2016), 1210–1213 This study demonstrates an integrated electrobioreactor in which a hydrogen-producing cathode is interfaced with Ralstonia eutropha for the production of several chemicals.
28. Tremblay, P.L., Angenent, L.T., Zhang, T., Extracellular electron uptake: among autotrophs and mediated by surfaces. Trends Biotechnol 35 (2017), 360–371.
29. 2 to higher alcohols. Science, 335, 2012, 1596.
30. Nichols, E.M., Gallagher, J.J., Liu, C., Su, Y., Resasco, J., Yu, Y., Sun, Y., Yang, P., Chang, M.C.Y., Chang, C.J., Hybrid bioinorganic approach to solar-to-chemical conversion. Proc Natl Acad Sci U S A 112 (2015), 11461–11466 This paper demonstrates an integrated electrobioreactor chamber in which a hydrogen-producing cathode is coupled with the methanogen M. barkeri, showing a very high solar-to-methane efficiency.
31. Khunjar, W.O., Sahin, A., West, A.C., Chandran, K., Banta, S., Biomass production from electricity using ammonia as an electron carrier in a reverse microbial fuel cell. PLoS ONE, 2012, 7.
32. 2+ regeneration coupled to a bioreactor with A. ferrooxidans production strains.
33. Torella, J.P., Gagliardi, C.J., Chen, J.S., Bediako, D.K., Colon, B., Way, J.C., Silver, P.A., Nocera, D.G., Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system. Proc Natl Acad Sci U S A 112 (2015), 2337–2342.
34. Ueki, T., Nevin, K.P., Woodard, T.L., Lovley, D.R., Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii. MBio 5 (2014), 19–23.
35. Khan, N.E., Nybo, S.E., Chappell, J., Curtis, W.R., Triterpene hydrocarbon production engineered into a metabolically versatile host — Rhodobacter capsulatus. Biotechnol Bioeng 112 (2015), 1523–1532.
36. Schiffels, J., Pinkenburg, O., Schelden, M., Aboulnaga, E.H.A.A., Baumann, M.E.M., Selmer, T., An innovative cloning platform enables large-scale production and maturation of an oxygen-tolerant [NiFe]-hydrogenase from Cupriavidus necator in Escherichia coli. PLoS ONE, 2013, 8.
37. Drake, H.L., Kusel, K., Matthies, C., Acetogenic prokaryotes. The Prokaryotes, 2013, 1–662.
38. Schut, G.J., Lipscomb, G.L., Nguyen, D.M.N., Kelly, R.M., Adams, M.W.W., Heterologous production of an energy-conserving carbon monoxide dehydrogenase complex in the hyperthermophile Pyrococcus furiosus. Front Microbiol 7 (2016), 1–9.
39. King, G.M., Weber, C.F., Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat Rev Microbiol 5 (2007), 107–118.
40. 2 to formic acid utilizing Sustainion™ membranes. J CO2 Util 20 (2017), 208–217.
41. 2 to formate. FEBS J 280 (2013), 6083–6096.
42. Liao, J.C., Mi, L., Pontrelli, S., Luo, S., Fuelling the future: microbial engineering for the production of sustainable biofuels. Nat Rev Microbiol 14 (2016), 288–304.
43. Ettwig, K.F., Butler, M.K., Le Paslier, D., Pelletier, E., Mangenot, S., Kuypers, M.M.M., Schreiber, F., Dutilh, B.E., Zedelius, J., de Beer, D., et al. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464 (2010), 543–548.
44. Timmers, P.H.A., Welte, C.U., Koehorst, J.J., Plugge, C.M., Jetten, M.S.M., Stams, A.J.M., Reverse methanogenesis and respiration in methanotrophic archaea. Archaea, 2017, 2017.
45. Visser, M., Pieterse, M.M., Pinkse, M.W.H., Nijsse, B., Verhaert, P.D.E.M., de Vos, W.M., Schaap, P.J., Stams, A.J.M., Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by genome and proteome analysis. Environ Microbiol 18 (2016), 2843–2855.
46. Kuenen, J.G., Anammox bacteria: from discovery to application. Nat Rev Microbiol 6 (2008), 320–326.
47. Matsumoto, N., Yoshinaga, H., Ohmura, N., Ando, A., Saiki, H., Extension of logarithmic growth of Thiobacillus ferrooxidans using potential controlled electrochemical cultivation system. Process Metall 9 (1999), 757–766.
48. Kernan, T., Majumdar, S., Li, X., Guan, J., West, A.C., Banta, S., Engineering the iron-oxidizing chemolithoautotroph Acidithiobacillus ferrooxidans for biochemical production. Biotechnol Bioeng 113 (2016), 189–197.
49. Ilbert, M., Bonnefoy, V., Insight into the evolution of the iron oxidation pathways. Biochim Biophys Acta Bioenerg 1827 (2013), 161–175.
50. Widdel, F., Schnell, S., Heising, S., Ehrenreich, A., Assmus, B., Schink, B., Ferrous iron oxdation by anoxygenic phototrophic bacteria. Nature 362 (1993), 834–836.
51. Li, X., West, A.C., Banta, S., Enhancing isobutyric acid production from engineered Acidithiobacillus ferrooxidans cells via media optimization. Biotechnol Bioeng 113 (2016), 790–796.
52. Banerjee, I., Burrell, B., Reed, C., West, A.C., Banta, S., Metals and minerals as a biotechnology feedstock: engineering biomining microbiology for bioenergy applications. Curr Opin Biotechnol 45 (2017), 144–155 This review discusses the potential of sulfur and sulphide residues from metal mining as a microbial feedstock for autotrophic production.
53. Relyea, H.A., Van Der Donk, W.A., Mechanism and applications of phosphite dehydrogenase. Bioorg Chem 33 (2005), 171–189.
54. Schink, B., Friedrich, M., Phosphite oxidation by sulphate reduction. Nature, 406, 2000, 37.
55. 2 fixation pathway. Proc Natl Acad Sci U S A, 2017, 10.1073/pnas.1715549114.
56. Costas, A.M.G., White, A.K., Metcalf, W.W., Purification and characterization of a novel phosphorus-oxidizing enzyme from Pseudomonas stutzeri WM88. J Biol Chem 276 (2001), 17429–17436.
57. Tremblay, P.L., Zhang, T., Electrifying microbes for the production of chemicals. Front Microbiol 6 (2015), 1–10.
58. Lovley, D.R., Nevin, K.P., Electrobiocommodities: powering microbial production of fuels and commodity chemicals from carbon dioxide with electricity. Curr Opin Biotechnol 24 (2013), 385–390.
59. Krieg, T., Sydow, A., Schröder, U., Schrader, J., Holtmann, D., Reactor concepts for bioelectrochemical syntheses and energy conversion. Trends Biotechnol 32 (2014), 645–655.
60. Sakimoto, K.K., Wong, A.B., Yang, P., Self-photosensitization of nonphotosynthetic bacteria for solar-to-chemical production. Science 351 (2016), 74–77.
61. May, H.D., Evans, P.J., LaBelle, E.V., The bioelectrosynthesis of acetate. Curr Opin Biotechnol 42 (2016), 225–233.
62. Flamholz, A., Noor, E., Bar-Even, A., Milo, R., EQuilibrator — the biochemical thermodynamics calculator. Nucleic Acids Res 40 (2012), D770–D775.
63. Thauer, R.K., Jungermann, K., Decker, K., Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41 (1977), 100–180.
64. Crowther, G.J., Kosaly, G., Lidstrom, M.E., Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. J Bacteriol 190 (2008), 5057–5062.
65. Müller, J.E.N., Heggeset, T.M.B., Wendisch, V.F., Vorholt, J.A., Brautaset, T., Methylotrophy in the thermophilic Bacillus methanolicus, basic insights and application for commodity production from methanol. Appl Microbiol Biotechnol 99 (2014), 535–551.
66. Ochsner, A.M., Sonntag, F., Buchhaupt, M., Schrader, J., Vorholt, J.A., Methylobacterium extorquens: methylotrophy and biotechnological applications. Appl Microbiol Biotechnol 99 (2014), 517–534.
67. Doud, D.F.R., Angenent, L.T., Toward electrosynthesis with uncoupled extracellular electron uptake and metabolic growth: enhancing current uptake with Rhodopseudomonas palustris. Environ Sci Technol Lett 1 (2014), 351–355.