Biofuels: Microbially Generated Methane and Hydrogen


The production of methane (CH4) or hydrogen (H2) from renewable biomass by microorganisms growing anaerobically has the potential for contribution to independence from fossil fuels. Anaerobes function in Nature by converting biomass to CH4 through food chains comprised of fermentative and acetogenic species, which decompose the complex biomass to H2, formate and acetate that are further metabolised to CH4 by methanogens. Methanogens reduce the concentration of products to levels that permit the initial decomposition of biomass by fermentative and acetogenic species. Current H2 production relies extensively on energy‐intensive fossil fuel sources. Photosynthetic and fermentative species offer more efficient routes for H2 production. Although fermentatives have significantly higher production rates, they have lower yields of H2 but may be a source of other valuable compounds that are synthesised along with H2. Further research must be conducted on obtaining H2 from reductive pools of NAD(P)H to increase yields and increase economic competitiveness.

Key Concepts:

  • Methane production from biomass, an essential component of the global carbon cycle, requires a microbial food chain.

  • Methane‐producing species (methanogens) are terminal organisms of the food chain metabolising acetate, formate and H2 that are metabolic products of species initiating decomposition of the biomass.

  • The methyl group of acetate is reduced to methane with electrons derived from oxidation of the carbonyl group.

  • Carbon dioxide is reduced to methane with electrons derived from oxidation of H2 or formate.

  • Current hydrogen production relies on fossil fuel sources.

  • Photosynthetic hydrogen production yields are high, but rates are slow.

  • Dark hydrogen production rates are fast, but yields are low.

  • Higher yields through dark fermentation may be obtained using pathways that use NAD(P)H.

  • Additional products such as 1,3‐propanediol and ethanol may be obtained along with hydrogen in dark fermentations.

Keywords: food chain; anaerobic; aceticlastic; fermentation; NADPH; hydrogenase; nitrogenase

Figure 1.

The global carbon cycle. Aerobic O2‐requiring conversions are shown in solid red arrows and anaerobic conversions in solid blue arrows. Black dotted arrows symbolise diffusion of substrates and products across the interface of aerobic and anaerobic zones.

Figure 2.

Composite of CO2 reduction and aceticlastic methane‐producing pathways. The left arm leading to CH3‐H4M(S)PT shows reactions (1–4) unique to the aceticlastic pathway and the right arm leading to CH3‐H4M(S)PT shows reactions (5–9) unique to the CO2 reduction pathway. Both pathways have in common reactions (10, 11 and 12) leading to the formation of CH4 from the methyl groups of CH3‐H4M(S)PT. Abbreviations: ATP, adenosine triphosphate; H4SPT, tetrahydrosarcinapterin; H4MPT, tetrahydromethanopterin; Fd, ferredoxin; CoA, coenzyme A; CoM, coenzyme M; CoB, coenzyme B; MF, methanofuran; F420, coenzyme F420.

Figure 3.

Comparison of electron transport pathways in acetotrophic methanogens. (a) H2‐dependent. (b) H2‐independent. Abbreviations: Ech, Ech hydrogenase; Fdr, ferredoxin reduced; Fdo, ferredoxin oxidised; Vho, Vho hydrogenase; MP, methanophenazine; HdrDE, heterodisulfide reductase; CoM‐SH, coenzyme M; CoB‐SH, coenzyme B; Atp, ATP synthase; Cyt c, cytochrome c; MaRnf, Rnf complex from Methanosarcina acetivorans; Mrp, putative sodium/proton antiporter.

Figure 4.

Fermentative pathways leading to production of H2 and other important products. Metabolites shown in blue indicate carbon substrates, whereas those in red indicate final fermentation products. Abbreviations: Fdred, reduced ferredoxin; Fdox, oxidised ferredoxin; Pi, orthophosphate.



Angenent LT, Karim K, Al‐Dahhan MH, Wrenn BA and Domiguez‐Espinosa R (2004) Production of bioenergy and biochemicals from industrial and agricultural wastewater. Trends in Biotechnology 22: 477–485.

Balat M (2008) Potential importance of hydrogen as a future solution to environmental and transportation problems. International Journal of Hydrogen Energy 33: 4013–4029.

Costa KC, Wong PM, Wang T et al. (2010) Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proceedings of the National Academy of Sciences of the USA 107: 11050–11055.

da Costa JCD, Reed GP and Thambimuthu K (2009) High temperature gas separation membranes in coal gasification. Energy Procedia 1: 295–302.

Deppenmeier U and Muller V (2008) Life close to the thermodynamic limit: how methanogenic archaea conserve energy. Results and Problems in Cell Differentiation 45: 123–152.

Dixon R and Kahn D (2004) Genetic regulation of biological nitrogen fixation. Nature Reviews Microbiology 2: 621–631.

Ghosh D, Sobro IF and Hallenbeck PC (2012) Stoichiometric conversion of biodiesel derived crude glycerol to hydrogen: response surface methodology study of the effects of light intensity and crude glycerol and glutamate concentration. Bioresource Technology 106: 154–160.

Haeseldonckx D and D'haeseleer W (2007) The use of the natural‐gas pipeline infrastructure for hydrogen transport in a changing market structure. International Journal of Hydrogen Energy 32: 1381–1386.

Hallenbeck PC, Abo‐Hashesh M and Ghosh D (2012) Strategies for improving biological hydrogen production. Bioresource Technology 110: 1–9.

Hendrickson EL and Leigh JA (2008) Roles of coenzyme F420‐reducing hydrogenases and hydrogen‐ and F420‐dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F420 and production of hydrogen during methanogenesis. Journal of Bacteriology 190: 4818–4821.

Henry CS, Jankowski MD, Broadbelt LJ and Hatzimanikatis V (2006) Genome‐scale thermodynamic analysis of E. coli metabolism. Biophysical Journal 90: 1453–1461.

Hu H and Wood TK (2010) An evolved E. coli strain for producing hydrogen and ethanol from glycerol. Biochemical and Biophysical Research Communications 391: 1033–1038.

Jin HG, Xu YJ, Lin RM and Han W (2008) A proposal for a novel multi‐functional energy system for the production of hydrogen and power. International Journal of Hydrogen Energy 33: 9–19.

Kim YM, Cho HS, Jung GY and Park JM (2011) Engineering the pentose phosphate pathway to improve hydrogen yield in recombinant E. coli. Biotechnology and Bioengineering 108: 2941–2946.

Konieczny A, Mondal K, Wiltowski T and Dydo P (2008) Catalyst development for thermocatalytic decomposition of methane to hydrogen. International Journal of Hydrogen Energy 33: 264–272.

Lessner DJ, Lhu L, Wahal CS and Ferry JG (2010) An engineered methanogenic pathway derived from the domains Bacteria and Archaea. MBio 1: e00243–e00210.

Lessner DJ, Li L, Li Q et al. (2006) An unconventional pathway for reduction of CO2 to methane in COgrown Methanosarcina acetivorans revealed by proteomics. Proceedings of the National Academy of Sciences of the USA 103: 17921–17926.

Lupa B, Hendrickson EL, Leigh JA and Whitman WB (2008) Formate‐dependent H2 production by the mesophilic methanogen Methanococcus maripaludis. Applied and Environmental Microbiology 74: 6584–6590.

Miller TL and Wolin MJ (1979) Fermentations by saccharolytic intestinal bacteria. American Journal of Clinical Nutrition 32: 164–172.

Smith KS and Ingram‐Smith C (2007) Methanosaeta, the forgotten methanogen? Trends in Microbiology 7: 150–155.

Smith PR, Bingham AS and Swartz JR (2012) Generation of hydrogen from NADPH using an [FeFe] hydrogenase. International Journal of Hydrogen Energy 37: 2977–2983.

Temudo MF, Poldermans R, Kleerebezem R and van Loosdrecht MC (2008) Glycerol fermentation by (open) mixed cultures: a chemostat study. Biotechnology and Bioengineering 100: 1088–1098.

Thauer RK (2010) Functionalization of methane in anaerobic microorganisms. Angewandte Chemie International Edition (English) 49: 6712–6713.

Thauer RK (2012) The Wolfe cycle comes full circle. Proceedings of the National Academy of Sciences of the USA 109: 15084–15085.

Thauer RK, Kaster AK, Seedorf H, Buckel W and Hedderich R (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Reviews Microbiology 6: 579–591.

Thauer RK, Kaster AK, Goenrich M et al. (2010) Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage. Annual Review of Biochemistry 79: 507–536.

Ursua A, Gandia LM and Sanchis P (2012) Hydrogen production from water electrolysis: current status and future trends. Proceedings of the Institute of Electrical and Electronics Engineers 100: 410–426.

Veit A, Akhtar MK, Mizutani T and Jones PR (2008) Constructing and testing the thermodynamic limits of synthetic NAD(P)H:H2 pathways. Microbial Biotechnology 1: 382–394.

Vignais PM, Billoud B and Meyer J (2001) Classification and phylogeny of hydrogenases. FEMS Microbiology Reviews 25: 455–501.

Wang M, Tomb JF and Ferry JG (2011) Electron transport in acetate‐grown Methanosarcina acetivorans. BMC Microbiology 11: 165.

Wells MA, Mercer J, Mott RA et al. (2011) Engineering a non‐native hydrogen production pathway into E. coli via a cyanobacterial [NiFe] hydrogenase. Metabolic Engineering 13: 445–453.

Wheeler C, Jhalani A, Klein EJ, Tummala S and Schmidt LD (2004) The water‐gas‐shift reaction at short contact times. Journal of Catalysis 223: 191–199.

Wong CH and Whitesides GM (1981) Enzyme‐catalyzed organic‐synthesis – Nad(P)h cofactor regeneration by using glucose‐6‐phosphate and the glucose‐6‐phosphate‐dehydrogenase from Leuconostoc mesenteroides. Journal of the American Chemical Society 103: 4890–4899.

Woodward J and Orr M (1998) Enzymatic conversion of sucrose to hydrogen. Biotechnology Progress 14: 897–902.

Woodward J, Cordray KA, Edmonston RJ et al. (2000a) Enzymatic hydrogen production: Conversion of renewable resources for energy production. Energy and Fuels 14: 197–201.

Woodward J, Orr M, Cordray K and Greenbaum E (2000b) Biotechnology – enzymatic production of biohydrogen. Nature 405: 1014–1015.

Yamane T, Sirirote P and Shimizu S (1987) Evaluation of half‐life of immobilized enzyme during continuous reaction in bioreactors: A theoretical study. Biotechnology and Bioengineering 30: 963–969.

Zhang C, Lv FX and Xing XH (2011) Bioengineering of the Enterobacter aerogenes strain for biohydrogen production. Bioresource Technology 102: 8344–8349.

Zhang YH, Evans BR, Mielenz JR, Hopkins RC and Adams MW (2007) High‐yield hydrogen production from starch and water by a synthetic enzymatic pathway. PloS One 2: e456.

Zhu H, Gonzalez R and Bobik TA (2011) Coproduction of acetaldehyde and hydrogen during glucose fermentation by E. coli. Applied and Environmental Microbiology 77: 6441–6450.

Zimmerman SA, Tomb JF and Ferry JG (2010) Characterization of CamH from Methanosarcina thermophila, founding member of a subclass of the g class of carbonic anhydrases. Journal of Bacteriology 192: 1353–1360.

Further Reading

Cavicchioli R (2010) Archaea: time line of the third domain. Nature Reviews Microbiology 9: 51–61.

Ferry JG (2010) How to make a living exhaling methane. Annual Review of Microbiology 64: 453–473.

Kim DH and Kim MS (2011) Hydrogenases for biological hydrogen production. Bioresource Technology 102: 8423–8431.

Maeda T, Sanchez‐Torres V and Wood TK (2012) Hydrogen production by recombinant E. coli strains. Microbial Biotechnology 5: 214–225.

Nicolet Y and Fontecilla‐Camps JC (2012) Structure‐function relationships in [FeFe]‐hydrogenase active site maturation. Journal of Biological Chemistry 287: 13532–13540.

Rother M, Sattler C and Stock T (2011) Studying gene regulation in methanogenic archaea. Methods in Enzymology 494: 91–110.

Welte C and Deppenmeier U (2011) Proton translocation in methanogens. Methods in Enzymology 494: 257–280.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
McAnulty, Michael J, Vepachedu, Venkata R, Wood, Thomas K, and Ferry, James G(Mar 2013) Biofuels: Microbially Generated Methane and Hydrogen. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020375]