Genomics of cellulosic biofuels


The development of alternatives to fossil fuels as an energy source is an urgent global priority. Cellulosic biomass has the potential to contribute to meeting the demand for liquid fuel, but land-use requirements and process inefficiencies represent hurdles for large-scale deployment of biomass-to-biofuel technologies. Genomic information gathered from across the biosphere, including potential energy crops and microorganisms able to break down biomass, will be vital for improving the prospects of significant cellulosic biofuel production.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Biology of bioconversion of solar energy into biofuels.
Figure 2: Structure of lignocellulose.


  1. 1

    Hill, J., Nelson, E., Tilman, D., Polasky, S. & Tiffany, D. Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. Proc. Natl Acad. Sci. USA 103, 11206–11210 (2006)

    ADS  CAS  Article  Google Scholar 

  2. 2

    Tilman, D., Hill, J. & Lehman, C. Carbon-negative biofuels from low-input high-diversity grassland biomass. Science 314, 1598–1600 (2006)A demonstration of why grassland perennials, such as switchgrass, are superior for biofuel production when compared to crops that presently serve as food crops, such as soya bean or maize.

    ADS  CAS  Article  Google Scholar 

  3. 3

    Himmel, M. E. et al. Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315, 804–807 (2007)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Reddy, N. & Yang, Y. Biofibers from agricultural byproducts for industrial applications. Trends Biotechnol. 23, 22–27 (2005)

    CAS  Article  Google Scholar 

  5. 5

    van Wyk, J. P. Biotechnology and the utilization of biowaste as a resource for bioproduct development. Trends Biotechnol. 19, 172–177 (2001)A discussion of biowaste as a potential source of lignocellulose for biofuel production.

    CAS  Article  Google Scholar 

  6. 6

    Del Rio, J. C., Marques, G., Rencoret, J., Martinez, A. T. & Gutierrez, A. Occurrence of naturally acetylated lignin units. J. Agric. Food Chem. 55, 5461–5468 (2007)

    CAS  Article  Google Scholar 

  7. 7

    Sanderson, K. US biofuels: a field in ferment. Nature 444, 673–676 (2006)

    ADS  CAS  Article  Google Scholar 

  8. 8

    Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006)

    CAS  Article  Google Scholar 

  9. 9

    Tuskan, G. A. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604 (2006)

    ADS  CAS  Article  Google Scholar 

  10. 10

    Yu, J. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79–92 (2002)

    ADS  CAS  Article  Google Scholar 

  11. 11

    Goff, S. A. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92–100 (2002)

    ADS  CAS  Article  Google Scholar 

  12. 12

    The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana . Nature 408, 796–815 (2000)

    ADS  Article  Google Scholar 

  13. 13

    Kalluri, U. C., Difazio, S. P., Brunner, A. M. & Tuskan, G. A. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa . BMC Plant Biol. 7, 59 (2007)

    Article  Google Scholar 

  14. 14

    Busov, V. B., Brunner, A. M. & Strauss, S. H. Genes for control of plant stature and form. New Phytol. 177, 589–607 (2008)

    CAS  Article  Google Scholar 

  15. 15

    Ragauskas, A. J. et al. The path forward for biofuels and biomaterials. Science 311, 484–489 (2006)

    ADS  CAS  Article  Google Scholar 

  16. 16

    Filichkin, S. A. et al. Efficiency of gene silencing in Arabidopsis: direct inverted repeats vs. transitive RNAi vectors. Plant Biotechnol. J. 5, 615–626 (2007)

    CAS  Article  Google Scholar 

  17. 17

    Dinus, R. J., Payne, P., Sewell, M. M., Chiang, V. L. & Tuskan, G. A. Genetic modification of short rotation poplar wood properties for energy and fiber production. Crit. Rev. Plant Sci. 20, 51–69 (2001)

    CAS  Article  Google Scholar 

  18. 18

    LaForge, F. B. & Hudson, C. S. The preparation of several useful substances from corn cobs. J. Ind. Eng. Chem. 10, 925–927 (1918)

    CAS  Article  Google Scholar 

  19. 19

    Mosier, N. et al. Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresour. Technol. 96, 673–686 (2005)

    CAS  Article  Google Scholar 

  20. 20

    Gilbert, H. J. Cellulosomes: microbial nanomachines that display plasticity in quaternary structure. Mol. Microbiol. 63, 1568–1576 (2007)

    CAS  Article  Google Scholar 

  21. 21

    Viikari, L., Alapuranen, M., Puranen, T., Vehmaanpera, J. & Siika-Aho, M. Thermostable enzymes in lignocellulose hydrolysis. Adv. Biochem. Eng. Biotechnol. 108, 121–145 (2007)

    CAS  PubMed  Google Scholar 

  22. 22

    Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3, REVIEWS0003 (2002)

    Article  Google Scholar 

  23. 23

    Warnecke, F. et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450, 560–565 (2007)A metagenomic study of an invertebrate gut microbial community involved in lignocellulolytic degradation.

    ADS  CAS  Article  Google Scholar 

  24. 24

    van Maris, A. J. et al. Alcoholic fermentation of carbon sources in biomass hydrolysates by Saccharomyces cerevisiae: current status. Antonie Van Leeuwenhoek 90, 391–418 (2006)

    Article  Google Scholar 

  25. 25

    Wang, M., Zhao, J., Yang, Z. & Du, Z. Electrochemical insights into the ethanol tolerance of Saccharomyces cerevisiae . Bioelectrochemistry 71, 107–112 (2007)

    CAS  Article  Google Scholar 

  26. 26

    Georgieva, T. I., Mikkelsen, M. J. & Ahring, B. K. High ethanol tolerance of the thermophilic anaerobic ethanol producer Thermoanaerobacter BG1L1. Central Eur. J. Biol. 2, 364–377 (2007)

    CAS  Google Scholar 

  27. 27

    Jeffries, T. W. et al. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis . Nature Biotechnol. 25, 319–326 (2007)

    CAS  Article  Google Scholar 

  28. 28

    Ohta, K., Beall, D. S., Mejia, J. P., Shanmugam, K. T. & Ingram, L. O. Genetic improvement of Escherichia coli for ethanol production: chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Appl. Environ. Microbiol. 57, 893–900 (1991)A description of the genetic modification of E. coli , yielding a strain capable of fermenting pentose and hexose sugars—which are present in lignocellulose—into ethanol.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. 29

    Jarboe, L. R., Grabar, T. B., Yomano, L. P., Shanmugan, K. T. & Ingram, L. O. Development of ethanologenic bacteria. Adv. Biochem. Eng. Biotechnol. 108, 237–261 (2007)

    CAS  PubMed  Google Scholar 

  30. 30

    Yomano, L. P., York, S. W. & Ingram, L. O. Isolation and characterization of ethanol-tolerant mutants of Escherichia coli KO11 for fuel ethanol production. J. Ind. Microbiol. Biotechnol. 20, 132–138 (1998)

    CAS  Article  Google Scholar 

  31. 31

    Durre, P. Biobutanol: an attractive biofuel. Biotechnol. J. 2, 1525–1534 (2007)

    Article  Google Scholar 

  32. 32

    Atsumi, S., Hanai, T. & Liao, J. C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451, 86–89 (2008)

    ADS  CAS  Article  Google Scholar 

  33. 33

    Lartigue, C. et al. Genome transplantation in bacteria: changing one species to another. Science 317, 632–638 (2007)

    ADS  CAS  Article  Google Scholar 

  34. 34

    Merchant, S. S. et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245–250 (2007)

    ADS  CAS  Article  Google Scholar 

  35. 35

    Gioia, J. et al. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS ONE 2, e928 (2007)

    ADS  Article  Google Scholar 

  36. 36

    Taylor, L. E. et al. Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T. J. Bacteriol. 188, 3849–3861 (2006)

    CAS  Article  Google Scholar 

  37. 37

    Lykidis, A. et al. Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J. Bacteriol. 189, 2477–2486 (2007)

    CAS  Article  Google Scholar 

  38. 38

    Nolling, J. et al. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183, 4823–4838 (2001)

    CAS  Article  Google Scholar 

  39. 39

    Bao, Q. et al. A complete sequence of the T. tengcongensis genome. Genome Res 12, 689–700 (2002)

    CAS  Article  Google Scholar 

  40. 40

    Seo, J. S. et al. The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nature Biotechnol. 23, 63–68 (2005)

    CAS  Article  Google Scholar 

Download references


I would like to thank S. Tringe, M. Hess, J. Tuskan, P. Hugenholtz, J. Bristow, B. Simmons, S. Long, J. Fruchart-Najib and H. Blanch for their input to the manuscript. This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract number DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract number DE-AC52-07NA27344, and Los Alamos National Laboratory under contract number DE-AC02-06NA25396.

Author information



Corresponding author

Correspondence to Edward M. Rubin.

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Rubin, E. Genomics of cellulosic biofuels. Nature 454, 841–845 (2008).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.