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Title: The Genome Sequence of Methanohalophilus mahii SLP T Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments

Abstract

Methanohalophilus mahii is the type species of the genus Methanohalophilus , which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLP T was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.

Authors:
 [1];  [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [3];  [2];  [2];  [2];  [2];  [2];  [2];  [4];  [4];  [5] more »;  [5];  [5];  [5];  [3];  [6];  [6];  [7];  [1];  [2];  [2];  [8];  [4];  [2];  [2];  [1] « less
+ Show Author Affiliations
  1. DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
  2. DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
  3. DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA, Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
  4. Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
  5. DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA, Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
  6. Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
  7. HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
  8. DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA, Davis Genome Center, University of California, Davis, CA 95817, USA
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); German Research Foundation (DFG)
OSTI Identifier:
1198247
Alternate Identifier(s):
OSTI ID: 1630537
Grant/Contract Number:  
AC02-05CH11231; AC52-07NA27344; AC05-00OR22725; AC02-06NA25396; INST 599/1-2
Resource Type:
Published Article
Journal Name:
Archaea
Additional Journal Information:
Journal Name: Archaea Journal Volume: 2010; Journal ID: ISSN 1472-3646
Publisher:
Hindawi
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Spring, Stefan, Scheuner, Carmen, Lapidus, Alla, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Lykidis, Athanasios, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Goodwin, Lynne, Detter, John C., Brettin, Thomas, Rohde, Manfred, Göker, Markus, Woyke, Tanja, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., and Klenk, Hans-Peter. The Genome Sequence of Methanohalophilus mahii SLP T Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments. United States: N. p., 2010. Web. doi:10.1155/2010/690737.
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Spring, Stefan, Scheuner, Carmen, Lapidus, Alla, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Lykidis, Athanasios, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Goodwin, Lynne, Detter, John C., Brettin, Thomas, Rohde, Manfred, Göker, Markus, Woyke, Tanja, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., & Klenk, Hans-Peter. The Genome Sequence of Methanohalophilus mahii SLP T Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments. United States. https://doi.org/10.1155/2010/690737
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Spring, Stefan, Scheuner, Carmen, Lapidus, Alla, Lucas, Susan, Glavina Del Rio, Tijana, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Lykidis, Athanasios, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Goodwin, Lynne, Detter, John C., Brettin, Thomas, Rohde, Manfred, Göker, Markus, Woyke, Tanja, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., and Klenk, Hans-Peter. Fri . "The Genome Sequence of Methanohalophilus mahii SLP T Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments". United States. https://doi.org/10.1155/2010/690737.
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@article{osti_1198247,
title = {The Genome Sequence of Methanohalophilus mahii SLP T Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments},
author = {Spring, Stefan and Scheuner, Carmen and Lapidus, Alla and Lucas, Susan and Glavina Del Rio, Tijana and Tice, Hope and Copeland, Alex and Cheng, Jan-Fang and Chen, Feng and Nolan, Matt and Saunders, Elizabeth and Pitluck, Sam and Liolios, Konstantinos and Ivanova, Natalia and Mavromatis, Konstantinos and Lykidis, Athanasios and Pati, Amrita and Chen, Amy and Palaniappan, Krishna and Land, Miriam and Hauser, Loren and Chang, Yun-Juan and Jeffries, Cynthia D. and Goodwin, Lynne and Detter, John C. and Brettin, Thomas and Rohde, Manfred and Göker, Markus and Woyke, Tanja and Bristow, Jim and Eisen, Jonathan A. and Markowitz, Victor and Hugenholtz, Philip and Kyrpides, Nikos C. and Klenk, Hans-Peter},
abstractNote = {Methanohalophilus mahii is the type species of the genus Methanohalophilus , which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLP T was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.},
doi = {10.1155/2010/690737},
journal = {Archaea},
number = ,
volume = 2010,
place = {United States},
year = {2010},
month = {1}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1155/2010/690737
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Figures / Tables:

Figure 1 Figure 1: Scanning electron micrograph of cells of Mhp. mahii strain SLPT. Bar = 2 μm.
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Works referenced in this record:

Methanogenesis and Sulfate Reduction: Competitive and Noncompetitive Substrates in Estuarine Sediments
journal, January 1982

Methanohalophilus mahii gen. nov., sp. nov., a Methylotrophic Halophilic Methanogen
journal, January 1988

  • Paterek, J. R.; Smith, P. H.
  • International Journal of Systematic Bacteriology, Vol. 38, Issue 1
  • DOI: 10.1099/00207713-38-1-122

Isolation and Characterization of a Halophilic Methanogen from Great Salt Lake †
journal, January 1985

EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
journal, October 2007

  • Kim, Byung Kwon; Lim, Young-Woon; Kim, Myungjin
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 10
  • DOI: 10.1099/ijs.0.64915-0

Diversity and Stratification of Archaea in a Hypersaline Microbial Mat
journal, December 2008

  • Robertson, Charles E.; Spear, John R.; Harris, J. Kirk
  • Applied and Environmental Microbiology, Vol. 75, Issue 7
  • DOI: 10.1128/AEM.01811-08

Community Composition of a Hypersaline Endoevaporitic Microbial Mat
journal, November 2005

  • Sørensen, Ketil Bernt; Canfield, Donald E.; Teske, Andreas P.
  • Applied and Environmental Microbiology, Vol. 71, Issue 11
  • DOI: 10.1128/AEM.71.11.7352-7365.2005

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009

  • Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
  • Nature, Vol. 462, Issue 7276
  • DOI: 10.1038/nature08656

En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
journal, November 2009

  • Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos
  • Nucleic Acids Research, Vol. 38, Issue suppl_1
  • DOI: 10.1093/nar/gkp848

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998

Base-Calling of Automated Sequencer Traces Using Phred.  I. Accuracy Assessment
journal, March 1998

  • Ewing, Brent; Hillier, LaDeana; Wendl, Michael C.
  • Genome Research, Vol. 8, Issue 3
  • DOI: 10.1101/gr.8.3.175

Consed: A Graphical Tool for Sequence Finishing
journal, March 1998

  • Gordon, David; Abajian, Chris; Green, Phil
  • Genome Research, Vol. 8, Issue 3
  • DOI: 10.1101/gr.8.3.195

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes
journal, May 2010

  • Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia
  • Nature Methods, Vol. 7, Issue 6
  • DOI: 10.1038/nmeth.1457

IMG ER: a system for microbial genome annotation expert review and curation
journal, June 2009

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
journal, September 2008

  • Yarza, Pablo; Richter, Michael; Peplies, Jörg
  • Systematic and Applied Microbiology, Vol. 31, Issue 4
  • DOI: 10.1016/j.syapm.2008.07.001

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

RASCAL: rapid scanning and correction of multiple sequence alignments
journal, June 2003

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
journal, August 2006

A Rapid Bootstrap Algorithm for the RAxML Web Servers
journal, October 2008

  • Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques
  • Systematic Biology, Vol. 57, Issue 5
  • DOI: 10.1080/10635150802429642

An Improved General Amino Acid Replacement Matrix
journal, April 2008

Multiple sequence alignment using partial order graphs
journal, March 2002

Isolation and Characterization of Methanohalophilus portucalensis sp. nov. and DNA Reassociation Study of the Genus Methanohalophilus
journal, July 1993

  • Boone, D. R.; Mathrani, I. M.; Liu, Y.
  • International Journal of Systematic Bacteriology, Vol. 43, Issue 3
  • DOI: 10.1099/00207713-43-3-430

Taxonomic Significance of the Distribution of Component Parts of Polar Ether Lipids in Methanogens
journal, November 1993

A dendrogram of archaea based on lipid component parts composition and its relationship to rRNA phylogeny
journal, August 2008

The minimum information about a genome sequence (MIGS) specification
journal, May 2008

  • Field, Dawn; Garrity, George; Gray, Tanya
  • Nature Biotechnology, Vol. 26, Issue 5
  • DOI: 10.1038/nbt1360

NOTES: Transfer of Methanolobus siciliae to the Genus Methanosarcina, Naming It Methanosarcina siciliae, and Emendation of the Genus Methanosarcina
journal, April 1994

  • Ni, S.; Woese, C. R.; Aldrich, H. C.
  • International Journal of Systematic Bacteriology, Vol. 44, Issue 2
  • DOI: 10.1099/00207713-44-2-357

Methanogenic archaea: ecologically relevant differences in energy conservation
journal, June 2008

  • Thauer, Rudolf K.; Kaster, Anne-Kristin; Seedorf, Henning
  • Nature Reviews Microbiology, Vol. 6, Issue 8
  • DOI: 10.1038/nrmicro1931

Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens
journal, June 2009

The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
journal, April 2002

RamA, a Protein Required for Reductive Activation of Corrinoid-dependent Methylamine Methyltransferase Reactions in Methanogenic Archaea
journal, November 2008

  • Ferguson, Tsuneo; Soares, Jitesh A.; Lienard, Tanja
  • Journal of Biological Chemistry, Vol. 284, Issue 4
  • DOI: 10.1074/jbc.M807392200

The direct genetic encoding of pyrrolysine
journal, December 2005

The Na+-translocating methyltransferase complex from methanogenic archaea
journal, May 2001

  • Gottschalk, Gerhard; Thauer, Rudolf K.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1505, Issue 1
  • DOI: 10.1016/S0005-2728(00)00274-7

Hydrogen is a preferred intermediate in the energy-conserving electron transport chain of Methanosarcina barkeri
journal, September 2009

  • Kulkarni, Gargi; Kridelbaugh, Donna M.; Guss, Adam M.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 37
  • DOI: 10.1073/pnas.0905914106

Function of Ech Hydrogenase in Ferredoxin-Dependent, Membrane-Bound Electron Transport in Methanosarcina mazei
journal, November 2009

  • Welte, Cornelia; Kallnik, Verena; Grapp, Marcel
  • Journal of Bacteriology, Vol. 192, Issue 3
  • DOI: 10.1128/JB.01307-09

Differences in Hydrogenase Gene Expression between Methanosarcina acetivorans and Methanosarcina barkeri
journal, February 2009

  • Guss, A. M.; Kulkarni, G.; Metcalf, W. W.
  • Journal of Bacteriology, Vol. 191, Issue 8
  • DOI: 10.1128/JB.00563-08

Electron Transport in the Pathway of Acetate Conversion to Methane in the Marine Archaeon Methanosarcina acetivorans
journal, December 2005

Methanogenesis by Methanosarcina acetivorans involves two structurally and functionally distinct classes of heterodisulfide reductase
journal, February 2010

The Membrane-Bound Electron Transport System of Methanosarcina Species
journal, February 2004

The F 420 H 2 Dehydrogenase from Methanosarcina mazei Is a Redox-driven Proton Pump Closely Related to NADH Dehydrogenases
journal, April 2000

  • Bäumer, Sebastian; Ide, Tina; Jacobi, Carsten
  • Journal of Biological Chemistry, Vol. 275, Issue 24
  • DOI: 10.1074/jbc.M000650200

The Mrp system: a giant among monovalent cation/proton antiporters?
journal, June 2005

Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)
journal, June 2010

  • Spring, Stefan; Rachel, Reinhard; Lapidus, Alla
  • Standards in Genomic Sciences, Vol. 2, Issue 3
  • DOI: 10.4056/sigs.821804

The coupling ion in the methanoarchaeal ATP synthases: H + vs. Na + in the A 1 A o ATP synthase from the archaeon Methanosarcina mazei Gö1
journal, December 2007

Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics
journal, December 2001

  • Graham, David E.; White, Robert H.
  • Natural Product Reports, Vol. 19, Issue 2
  • DOI: 10.1039/b103714p

Identification of Coenzyme M Biosynthetic Phosphosulfolactate Synthase: A NEW FAMILY OF SULFONATE-BIOSYNTHESIZING ENZYMES
journal, February 2002

  • Graham, David E.; Xu, Huimin; White, Robert H.
  • Journal of Biological Chemistry, Vol. 277, Issue 16
  • DOI: 10.1074/jbc.M201011200

Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: Different role, different evolution
journal, February 2010

  • Ogawa, Takuya; Yoshimura, Tohru; Hemmi, Hisashi
  • Biochemical and Biophysical Research Communications, Vol. 393, Issue 1
  • DOI: 10.1016/j.bbrc.2010.01.063

Composition, Variation, and Dynamics of Major Osmotic Solutes in Methanohalophilus Strain FDF1
journal, January 1992

Gating the bacterial mechanosensitive channels: MscS a new paradigm?
journal, April 2004

  • Edwards, Michelle D.; Booth, Ian R.; Miller, Samantha
  • Current Opinion in Microbiology, Vol. 7, Issue 2
  • DOI: 10.1016/j.mib.2004.02.006

Inhibition of methanogenesis by sulphate reducing bacteria competing for transferred hydrogen
journal, April 1978

  • Abram, Jeremy W.; Nedwell, David B.
  • Archives of Microbiology, Vol. 117, Issue 1
  • DOI: 10.1007/BF00689356

Influence of oxygen on sulfate reduction and growth of sulfate-reducing bacteria
journal, February 1993

  • Marschall, Christoph; Frenzel, Peter; Cypionka, Heribert
  • Archives of Microbiology, Vol. 159, Issue 2
  • DOI: 10.1007/BF00250278
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