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Title: Complete genome sequence of “Enterobacter lignolyticus” SCF1

Abstract

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Ente-robacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest 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 net methane producers. Because of its ability to grow on lignin anae-robically, we sequenced the genome. The genome of "E. lignolyticus" SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohy-drate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster.

Authors:
 [1];  [2];  [1];  [3];  [4];  [5];  [1];  [1];  [6];  [6];  [7];  [7];  [7];  [7];  [7];  [1]
+ Show Author Affiliations
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  5. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  6. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23), Biological Systems Science Division (SC-23.2 )
OSTI Identifier:
1511334
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

DeAngelis, Kristen M., D’Haeseleer, Patrik, Chivian, Dylan, Fortney, Julian L., Khudyakov, Jane, Simmons, Blake, Woo, Hannah, Arkin, Adam P., Davenport, Karen Walston, Goodwin, Lynne, Chen, Amy, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja, and Hazen, Terry C. Complete genome sequence of “Enterobacter lignolyticus” SCF1. United States: N. p., 2011. Web. doi:10.4056/sigs.2104875.
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DeAngelis, Kristen M., D’Haeseleer, Patrik, Chivian, Dylan, Fortney, Julian L., Khudyakov, Jane, Simmons, Blake, Woo, Hannah, Arkin, Adam P., Davenport, Karen Walston, Goodwin, Lynne, Chen, Amy, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja, & Hazen, Terry C. Complete genome sequence of “Enterobacter lignolyticus” SCF1. United States. https://doi.org/10.4056/sigs.2104875
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DeAngelis, Kristen M., D’Haeseleer, Patrik, Chivian, Dylan, Fortney, Julian L., Khudyakov, Jane, Simmons, Blake, Woo, Hannah, Arkin, Adam P., Davenport, Karen Walston, Goodwin, Lynne, Chen, Amy, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja, and Hazen, Terry C. Sat . "Complete genome sequence of “Enterobacter lignolyticus” SCF1". United States. https://doi.org/10.4056/sigs.2104875. https://www.osti.gov/servlets/purl/1511334.
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@article{osti_1511334,
title = {Complete genome sequence of “Enterobacter lignolyticus” SCF1},
author = {DeAngelis, Kristen M. and D’Haeseleer, Patrik and Chivian, Dylan and Fortney, Julian L. and Khudyakov, Jane and Simmons, Blake and Woo, Hannah and Arkin, Adam P. and Davenport, Karen Walston and Goodwin, Lynne and Chen, Amy and Ivanova, Natalia and Kyrpides, Nikos C. and Mavromatis, Konstantinos and Woyke, Tanja and Hazen, Terry C.},
abstractNote = {In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "Ente-robacter lignolyticus" SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest 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 net methane producers. Because of its ability to grow on lignin anae-robically, we sequenced the genome. The genome of "E. lignolyticus" SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohy-drate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster.},
doi = {10.4056/sigs.2104875},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 5,
place = {United States},
year = {Sat Oct 15 00:00:00 EDT 2011},
month = {Sat Oct 15 00:00:00 EDT 2011}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.4056/sigs.2104875
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Cited by: 56 works
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Figures / Tables:

Figure 1 Figure 1: Phylogenetic tree highlighting the position of “Enterobacter lignolyticus” SCF1 relative to other type and non-type strains within the Enterobacteriaceae. Strains shown are those within the Enterobacteriaceae having corresponding NCBI genome project ids listed within. The tree is based on a concatenated MUSCLE alignment of 69 near-universal single-copy COGsmore » (COGs 12, 13, 16, 18, 30, 41, 46, 48, 49, 52, 60, 72, 80, 81, 86, 87, 88, 89, 90, 91, 92, 93, 94, 96, 97, 98, 99, 100, 102, 103, 104, 105, 124, 126, 127, 130, 143, 149, 150, 162, 164, 172, 184, 185, 186, 197, 198, 200, 201, 202, 215, 237, 244, 256, 284, 441, 442, 452, 461, 504, 519, 522, 525, 528, 532, 533, 540, 541, 552). The tree was constructed using FastTree-2 using the JTT model of amino acid evolution. FastTree-2 infers approximate maximum-likelihood phylogenetic placements and provides local support values based on the Shimodaira-Hasegawa test. Solid circles represent local support values over 90% and open circles over 80%. Erwinia tasmaniensis was used as an outgroup.« less
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