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

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.

doi:10.1186/s40793-015-0100-3

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

Abstract

Â© 2015 Billings et al. 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. 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:

Billings, Andrew F. ^[1]; Fortney, Julian L. ^[2]; Hazen, Terry C. ^[3]; Simmons, Blake ^[4]; Davenport, Karen W. ^[5]; Goodwin, Lynne ^[5]; Ivanova, Natalia ^[6]; Kyrpides, Nikos C. ^[6]; Mavromatis, Konstantinos ^[6]; Woyke, Tanja ^[6]; DeAngelis, Kristen M. ^[1]

Univ. of Massachusetts, Amherst, MA (United States)
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil & Environmental Engineering
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
Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Publication Date:: Thu Nov 19 00:00:00 EST 2015

Research Org.:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1259501

Alternate Identifier(s):: OSTI ID: 1378652

Grant/Contract Number:: AC02-05CH11231

Resource Type:: 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.

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                    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.  https://doi.org/10.1186/s40793-015-0100-3

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                    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.  https://doi.org/10.1186/s40793-015-0100-3.  https://www.osti.gov/servlets/purl/1259501.

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@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 = {Â© 2015 Billings et al. 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. 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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NamesforLife
DOI: 10.1601/ex.29337

Nomenclature Abstract for Tolumonas lignolytica (sic) Billings et al. 2016.
dataset, January 2016

Parker, Charles Thomas; Garrity, George M.
NamesforLife
DOI: 10.1601/nm.29337

Nomenclature Abstract for Tolumonas lignilytica corrig. Billings et al. 2016.
dataset, January 2016

Parker, Charles Thomas; Garrity, George M.
NamesforLife
DOI: 10.1601/nm.29338

Taxonomic Abstract for the species Tolumonas lignolytica (sic) Billings et al. 2016 and Tolumonas lignilytica corrig. Billings et al. 2016.
dataset, January 2016

Parker, Charles Thomas; Garrity, George M.
NamesforLife
DOI: 10.1601/tx.29337

Taxonomic Abstract for the genera Tolumonas Fischer-Romero et al. 1996 emend. Caldwell et al. 2011
dataset, January 2013

Parker, Charles Thomas; Wigley, Sarah; Garrity, George M.
NamesforLife
DOI: 10.1601/tx.3078

Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database
journal, April 2019

Brink, Daniel P.; Ravi, Krithika; Lidén, Gunnar
Applied Microbiology and Biotechnology, Vol. 103, Issue 10
DOI: 10.1007/s00253-019-09692-4

Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
journal, October 2017

Orellana, Roberto; Chaput, Gina; Markillie, Lye Meng
PLOS ONE, Vol. 12, Issue 10
DOI: 10.1371/journal.pone.0186440

Microbial communities mediating algal detritus turnover under anaerobic conditions
posted_content, September 2016

Morrison, Jessica M.; Murphy, Chelsea L.; Baker, Kristina
PeerJ Preprints
DOI: 10.7287/peerj.preprints.2453v1

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