Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.
Keywords: decomposition, anaerobic metabolism, phenol degradation, 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, glutathione S-transferase proteins
Citation: DeAngelis KM, Sharma D, Varney R, Simmons B, Isern NG, Markillie LM, Nicora C, Norbeck AD, Taylor RC, Aldrich JT and Robinson EW (2013) Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1. Front. Microbiol. 4:280. doi: 10.3389/fmicb.2013.00280
Received: 14 June 2013; Accepted: 29 August 2013;
Published online: 19 September 2013.
Edited by:Yinjie Tang, Washington University, USA
Reviewed by:Dong-Woo Lee, Kyungpook National University, South Korea
Copyright © 2013 DeAngelis, Sharma, Varney, Simmons, Isern, Markillie, Nicora, Norbeck, Taylor, Aldrich and Robinson. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Kristen M. DeAngelis, Department of Microbiology, University of Massachusetts Amherst, 639 North Pleasant Street, 203N Morrill IVN, Amherst, MA 01003-9298, USA e-mail: firstname.lastname@example.org