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Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2
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...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273726/ https://www.ncbi.nlm.nih.gov/pubmed/25566348 http://dx.doi.org/10.1186/1944-3277-9-19 |
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author | Woo, Hannah L Ballor, Nicholas R Hazen, Terry C Fortney, Julian L Simmons, Blake Davenport, Karen Walston Goodwin, Lynne Ivanova, Natalia Kyrpides, Nikos C Mavromatis, Konstantinos Woyke, Tanja Jansson, Janet Kimbrel, Jeff DeAngelis, Kristen M |
author_facet | Woo, Hannah L Ballor, Nicholas R Hazen, Terry C Fortney, Julian L Simmons, Blake Davenport, Karen Walston Goodwin, Lynne Ivanova, Natalia Kyrpides, Nikos C Mavromatis, Konstantinos Woyke, Tanja Jansson, Janet Kimbrel, Jeff DeAngelis, Kristen M |
author_sort | Woo, Hannah L |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4273726 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-42737262015-01-06 Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 Woo, Hannah L Ballor, Nicholas R Hazen, Terry C Fortney, Julian L Simmons, Blake Davenport, Karen Walston Goodwin, Lynne Ivanova, Natalia Kyrpides, Nikos C Mavromatis, Konstantinos Woyke, Tanja Jansson, Janet Kimbrel, Jeff DeAngelis, Kristen M Stand Genomic Sci Short Genome Report 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. BioMed Central 2014-12-08 /pmc/articles/PMC4273726/ /pubmed/25566348 http://dx.doi.org/10.1186/1944-3277-9-19 Text en Copyright © 2014 Woo et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Short Genome Report Woo, Hannah L Ballor, Nicholas R Hazen, Terry C Fortney, Julian L Simmons, Blake Davenport, Karen Walston Goodwin, Lynne Ivanova, Natalia Kyrpides, Nikos C Mavromatis, Konstantinos Woyke, Tanja Jansson, Janet Kimbrel, Jeff DeAngelis, Kristen M Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 |
title | Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 |
title_full | Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 |
title_fullStr | Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 |
title_full_unstemmed | Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 |
title_short | Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 |
title_sort | complete genome sequence of the lignin-degrading bacterium klebsiella sp. strain brl6-2 |
topic | Short Genome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273726/ https://www.ncbi.nlm.nih.gov/pubmed/25566348 http://dx.doi.org/10.1186/1944-3277-9-19 |
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