Bacteria Use Multiple Enzymes to Degrade Plant Biomass

Analyses reveal how bacteria degrade lignin and provide better understanding for producing biofuels.

The Science

The production of biofuels from plant biomass is a highly promising source of energy, but researchers are trying to find microbes that readily degrade recalcitrant lignin found in plant biomass. Recent comprehensive genomic and metabolomic analysis of a known lignin-degrading bacterium provides insight into how this degradation is accomplished.

The Impact

Because the initial step of manufacturing biofuels from plant matter is the decomposition of complex lignocellulose into more manageable “building blocks,” an understanding of how nature achieves biomass breakdown is critical. The findings from a new study reveal some of the basic tools used by a specific microbe to break down lignocellulose. This work provides insight into how industrial processes might achieve degradation during biofuel production, and how side processes such as hydrogen production might be harnessed as well.


Lignocellulosic biomass represents nearly 90 percent of the dry weight of total plant biomass material, and is composed of cellulose and lignin. Lignin lends rigidity and rot-resistance to cell walls in wood and bark. It is a complex, cross-linked phenolic structure that makes lignocellulosic-derived biofuels a promising source of alternative energy, provided the recalcitrant material can be degraded and toxic by-products can be managed. Microbial species that grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing lignin in a way that protects cellulose for improved conversion of lignin to fuel precursors. One candidate species that can use lignin for growth in the absence of oxygen is Enterobacter lignolyticus SCF1, a bacterium isolated from tropical rain forest soil. A team of researchers from the University of Massachusetts, Amherst; Santa Maria University in Valparaiso, Chile; and EMSL, the Environmental Molecular Sciences Laboratory conducted whole gene-expression analysis of E. lignolyticus SCF1 using next generation sequencing for transcriptomic analysis. The experiments were conducted on cells grown in the presence of lignin, with samples taken at three different times during growth. Cultures with lignin achieved twice the cell biomass as cultures grown without lignin, and E. lignolyticus SCF1 degraded 60 percent of the available lignin. A complement of enzymes consistent with disruption of the chemical structures present in lignin were up-regulated in lignin-amended conditions. Additionally, the association of hydrogen production with lignin degradation suggests a possible value added stream to lignin degradation in the future.

Principal Investigator

Kristin DeAngelis
University of Massachusetts–Amherst
[email protected]

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This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research (BER)), including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science User Facility, and the Joint BioEnergy Institute (; and the University of Massachusetts Amherst.


Orellana, R., G. Chaput, L. M. Markillie, H. D. Mitchell, M. J. Gaffrey, G. Orr, and K. M. DeAngelis. 2017. “Multi-time Series RNA-Seq Analysis of Enterobacter lignolyticus SCF1 During Growth in Lignin-Amended Medium,” PLoS One, 12(10). DOI:10.1371/journal.pone.0186440.