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Title: Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.

Abstract

Tolumonas lignolytica BRL6-1 T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1 T are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involved in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. Finally, by characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material.

Authors:
 [1];  [2];  [3];  [4];  [5];  [5];  [6];  [6];  [6];  [6];  [1]
  1. Univ. of Massachusetts, Amherst, MA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil & Environmental Engineering
  3. Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil & Environmental Engineering; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Earth & Planetary Sciences
  4. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1259501
Alternate Identifier(s):
OSTI ID: 1378652
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Anaerobic lignin degradation; Tropical forest soil isolate; Tolumonas

Citation Formats

Billings, Andrew F., Fortney, Julian L., Hazen, Terry C., Simmons, Blake, Davenport, Karen W., Goodwin, Lynne, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja, and DeAngelis, Kristen M. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.. United States: N. p., 2015. Web. doi:10.1186/s40793-015-0100-3.
Billings, Andrew F., Fortney, Julian L., Hazen, Terry C., Simmons, Blake, Davenport, Karen W., Goodwin, Lynne, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja, & DeAngelis, Kristen M. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.. United States. doi:10.1186/s40793-015-0100-3.
Billings, Andrew F., Fortney, Julian L., Hazen, Terry C., Simmons, Blake, Davenport, Karen W., Goodwin, Lynne, Ivanova, Natalia, Kyrpides, Nikos C., Mavromatis, Konstantinos, Woyke, Tanja, and DeAngelis, Kristen M. Thu . "Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.". United States. doi:10.1186/s40793-015-0100-3. https://www.osti.gov/servlets/purl/1259501.
@article{osti_1259501,
title = {Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.},
author = {Billings, Andrew F. and Fortney, Julian L. and Hazen, Terry C. and Simmons, Blake and Davenport, Karen W. and Goodwin, Lynne and Ivanova, Natalia and Kyrpides, Nikos C. and Mavromatis, Konstantinos and Woyke, Tanja and DeAngelis, Kristen M.},
abstractNote = {Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involved in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. Finally, by characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material.},
doi = {10.1186/s40793-015-0100-3},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {Thu Nov 19 00:00:00 EST 2015},
month = {Thu Nov 19 00:00:00 EST 2015}
}

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