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Title: Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia

Abstract

Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847T, turned out to be misclassified and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pregenome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and an notation of the type strain, M3T. The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Authors:
 [1];  [2];  [1];  [3];  [4];  [3];  [3];  [3];  [2];  [2];  [2];  [3];  [3];  [3];  [3];  [3];  [3];  [3];  [5];  [5] more »;  [6];  [7];  [8];  [2];  [1];  [1];  [9];  [3];  [3];  [10];  [5];  [11];  [12];  [1] « less
  1. Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. St. Petersburg State Univ., St. Petersburg (Russia); St. Petersburg Academic Univ., St. Petersburg (Russia)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  7. CSIR - Institute of Microbial Technology, Chandigarh (India)
  8. HZI - Helmholtz Centre for Infection Research, Braunschweig (Germany)
  9. Univ. of Regensburg, Regensburg (Germany)
  10. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California Davis Genome Center, Davis, CA (United States)
  11. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); The Univ. of Queensland, Brisbane (Australia)
  12. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
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)
OSTI Identifier:
1378617
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 9; Journal Issue: 3; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; anaerobic; motile; mesophilic; methanogen; swamp; improved-high-quality draft; Methanomicrobiaceae; GEBA

Citation Formats

Goker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan -Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C., Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., and Klenk, Hans -Peter. Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. United States: N. p., 2014. Web. doi:10.4056/sigs.5138968.
Goker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan -Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C., Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., & Klenk, Hans -Peter. Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. United States. https://doi.org/10.4056/sigs.5138968
Goker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan -Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C., Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., and Klenk, Hans -Peter. 2014. "Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia". United States. https://doi.org/10.4056/sigs.5138968. https://www.osti.gov/servlets/purl/1378617.
@article{osti_1378617,
title = {Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia},
author = {Goker, Markus and Lu, Megan and Fiebig, Anne and Nolan, Matt and Lapidus, Alla and Tice, Hope and Del Rio, Tijana Glavina and Cheng, Jan -Fang and Han, Cliff and Tapia, Roxanne and Goodwin, Lynne A. and Pitluck, Sam and Liolios, Konstantinos and Mavromatis, Konstantinos and Pagani, Ioanna and Ivanova, Natalia and Mikhailova, Natalia and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Mayilraj, Shanmugam and Rohde, Manfred and Detter, John C. and Bunk, Boyke and Spring, Stefan and Wirth, Reinhard and Woyke, Tanja and Bristow, James and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans -Peter},
abstractNote = {Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847T, turned out to be misclassified and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pregenome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and an notation of the type strain, M3T. The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.},
doi = {10.4056/sigs.5138968},
url = {https://www.osti.gov/biblio/1378617}, journal = {Standards in Genomic Sciences},
issn = {1944-3277},
number = 3,
volume = 9,
place = {United States},
year = {Sun Jun 15 00:00:00 EDT 2014},
month = {Sun Jun 15 00:00:00 EDT 2014}
}

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When should a DDH experiment be mandatory in microbial taxonomy?
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Evaluation of Methanogenic Strains and Their Ability to Endure Aeration and Water Stress
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En route to a genome-based classification of Archaea and Bacteria?
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Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names
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A square bacterium
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A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
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GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
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Dietary palmitic acid promotes a prometastatic memory via Schwann cells
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Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
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A Rapid Bootstrap Algorithm for the RAxML Web Servers
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The DNA Bank Network: The Start from a German Initiative
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IMG ER: a system for microbial genome annotation expert review and curation
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The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011


Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


Methanoplanus petrolearius sp. nov., a novel methanogenic bacterium from an oil-producing well
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Isolation and Characterization of Methanomicrobium paynteri sp. nov., a Mesophilic Methanogen Isolated from Marine Sediments †
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Prodigal: prokaryotic gene recognition and translation initiation site identification
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Genome sequence-based species delimitation with confidence intervals and improved distance functions
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The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation
journal, December 2012


Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1T)
journal, August 2010


Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1
journal, September 2009


Complete genome sequence of Methanocorpusculum labreanum type strain Z
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Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
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Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison
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Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
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dataset, January 2013


Nomenclature Abstract for Methanolacinia Zellner et al. 1990 emend. Göker et al. 2014.
dataset, January 2013


Nomenclature Abstract for Methanoplanus Wildgruber et al. 1984 emend. Göker et al. 2014.
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Nomenclature Abstract for Methanoplanus limicola Wildgruber et al. 1984 emend. Göker et al. 2014.
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Nomenclature Abstract for Methanoplanus petrolearius Ollivier et al. 1998 emend. Göker et al. 2014.
dataset, January 2013


Taxonomic Abstract for the genera Methanolacinia
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