Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2

Hannah L Woo; Nicholas R Ballor; Terry C Hazen; Julian L Fortney; Blake Simmons; Karen Walston Davenport; Lynne Goodwin; Natalia Ivanova; Nikos C Kyrpides; Konstantinos Mavromatis; Tanja Woyke; Janet Jansson; Jeff Kimbrel; Kristen M DeAngelis

doi:10.1186/1944-3277-9-19

Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2

Stand Genomic Sci. 2014 Dec 8:9:19. doi: 10.1186/1944-3277-9-19. eCollection 2014.

Authors

Affiliations

¹ Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.
² Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA.
³ Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN, USA ; Department of Microbiology, The University of Tennessee, Knoxville, TN, USA ; Department of Earth & Planetary Sciences, The University of Tennessee, Knoxville, TN, USA.
⁴ Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.
⁵ Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Sandia National Lab, Livermore, CA, USA.
⁶ Los Alamos National Laboratory, Los Alamos, NM, USA.
⁷ Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
⁸ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
⁹ Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁰ Microbiology Department, University of Massachusetts, Amherst, MA, USA.

Abstract

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M.

Keywords: Anaerobic lignin degradation; Facultative anaerobe; Tropical forest soil isolate.