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

Markus Göker; Megan Lu; Anne Fiebig; Matt Nolan; Alla Lapidus; Hope Tice; Tijana Glavina Del Rio; Jan-Fang Cheng; Cliff Han; Roxanne Tapia; Lynne A Goodwin; Sam Pitluck; Konstantinos Liolios; Konstantinos Mavromatis; Ioanna Pagani; Natalia Ivanova; Natalia Mikhailova; Amrita Pati; Amy Chen; Krishna Palaniappan; Miriam Land; Shanmugam Mayilraj; Manfred Rohde; John C Detter; Boyke Bunk; Stefan Spring; Reinhard Wirth; Tanja Woyke; James Bristow; Jonathan A Eisen; Victor Markowitz; Philip Hugenholtz; Nikos C Kyrpides; Hans-Peter Klenk

doi:10.4056/sigs.5138968

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

Stand Genomic Sci. 2014 Mar 15;9(3):1076-88. doi: 10.4056/sigs.5138968. eCollection 2014 Jun 15.

Authors

Markus Göker¹, Megan Lu², Anne Fiebig¹, Matt Nolan³, Alla Lapidus⁴, Hope Tice³, Tijana Glavina Del Rio³, Jan-Fang Cheng³, Cliff Han², Roxanne Tapia², Lynne A Goodwin², Sam Pitluck³, Konstantinos Liolios³, Konstantinos Mavromatis³, Ioanna Pagani³, Natalia Ivanova³, Natalia Mikhailova³, Amrita Pati³, Amy Chen⁵, Krishna Palaniappan⁵, Miriam Land⁶, Shanmugam Mayilraj⁷, Manfred Rohde⁸, John C Detter², Boyke Bunk¹, Stefan Spring¹, Reinhard Wirth⁹, Tanja Woyke³, James Bristow³, Jonathan A Eisen¹⁰, Victor Markowitz⁵, Philip Hugenholtz¹¹, Nikos C Kyrpides¹², Hans-Peter Klenk¹

Affiliations

¹ Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
² DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
³ DOE Joint Genome Institute, Walnut Creek, California, USA.
⁴ T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
⁵ Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁶ DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
⁷ MTCC - Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India.
⁸ HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
⁹ University of Regensburg, Microbiology - Archaeenzentrum, Regensburg, Germany.
¹⁰ DOE Joint Genome Institute, Walnut Creek, California, USA ; University of California Davis Genome Center, Davis, California, USA.
¹¹ DOE Joint Genome Institute, Walnut Creek, California, USA ; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
¹² DOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.

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.

Keywords: GEBA; Methanomicrobiaceae; anaerobic; improved-high-quality draft; mesophilic; methanogen; motile; swamp.