Edited by Steven E. Lindow, University of California, Berkeley, CA, and approved April 9, 2012 (received for review August 6, 2011)
To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.
Author contributions: J.I.K., K.M.D., T.C.H., B.A.S., and M.P.T. designed research; J.I.K., S.E.B., K.M.D., and H.W. performed research; P.D., S.E.B., K.M.D., H.W., and E.A.L. contributed new reagents/analytic tools; J.I.K., P.D., S.E.B., H.W., E.A.L., and M.P.T. analyzed data; and J.I.K., P.D., and M.P.T. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The genome sequence reported in this paper has been deposited in the GenBank database (accession no. CP002272.1). [This organism was previously called Enterobacter cloacae SCF1 and has been renamed Enterobacter lignolyticus SCF1. The name has not yet been changed in the National Center for Biotechnology Information (NCBI) database.] The data reported in this paper have been deposited in the Sequence Read Archive (SRA) database, http://www.ncbi.nlm.nih.gov/sra [accession nos. SRX059720–SRX059739 (raw Illumina RNA deep sequencing data)].
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1112750109/-/DCSupplemental.
Freely available online through the PNAS open access option.
