title: Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2.
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.
authors.affiliation: 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.
authors.forename: Hannah L
authors.initials: HL
authors.lastname: Woo
authors.affiliation: Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Ballor
authors.affiliation: 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.
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.affiliation: Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Department of Civil & Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.
authors.forename: Julian L
authors.initials: JL
authors.lastname: Fortney
authors.affiliation: Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Sandia National Lab, Livermore, CA, USA.
authors.forename: Blake
authors.initials: B
authors.lastname: Simmons
authors.affiliation: Los Alamos National Laboratory, Los Alamos, NM, USA.
authors.forename: Karen Walston
authors.initials: KW
authors.lastname: Davenport
authors.affiliation: Los Alamos National Laboratory, Los Alamos, NM, USA.
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
authors.forename: Janet
authors.initials: J
authors.lastname: Jansson
authors.affiliation: Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA ; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
authors.forename: Jeff
authors.initials: J
authors.lastname: Kimbrel
authors.affiliation: Microbiology Department, University of Massachusetts, Amherst, MA, USA.
authors.forename: Kristen M
authors.initials: KM
authors.lastname: DeAngelis
keywords: Anaerobic lignin degradation; Facultative anaerobe; Tropical forest soil isolate