title: Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), 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 4847(T), 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 (pre-genome-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 annotation of the type strain, M3(T). 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 G enomic E ncyclopedia of B acteria and Archaea project.
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
authors.forename: Megan
authors.initials: M
authors.lastname: Lu
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Anne
authors.initials: A
authors.lastname: Fiebig
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Matt
authors.initials: M
authors.lastname: Nolan
authors.affiliation: T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Hope
authors.initials: H
authors.lastname: Tice
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Tijana Glavina
authors.initials: TG
authors.lastname: Del Rio
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
authors.forename: Cliff
authors.initials: C
authors.lastname: Han
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
authors.forename: Roxanne
authors.initials: R
authors.lastname: Tapia
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
authors.forename: Lynne A
authors.initials: LA
authors.lastname: Goodwin
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Sam
authors.initials: S
authors.lastname: Pitluck
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Liolios
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Ioanna
authors.initials: I
authors.lastname: Pagani
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Natalia
authors.initials: N
authors.lastname: Mikhailova
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Amy
authors.initials: A
authors.lastname: Chen
authors.affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Krishna
authors.initials: K
authors.lastname: Palaniappan
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.affiliation: MTCC - Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India.
authors.forename: Shanmugam
authors.initials: S
authors.lastname: Mayilraj
authors.affiliation: HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Rohde
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Detter
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Boyke
authors.initials: B
authors.lastname: Bunk
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Spring
authors.affiliation: University of Regensburg, Microbiology - Archaeenzentrum, Regensburg, Germany.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Wirth
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: James
authors.initials: J
authors.lastname: Bristow
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; University of California Davis Genome Center, Davis, California, USA.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
authors.affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Markowitz
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
keywords: GEBA; Methanomicrobiaceae; anaerobic; improved-high-quality draft; mesophilic; methanogen; motile; swamp