title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae.
abstract: Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
authors.affiliation: DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
authors.forename: Carmen
authors.initials: C
authors.lastname: Scheuner
authors.affiliation: DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Tindall
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: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Matt
authors.initials: M
authors.lastname: Nolan
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
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: Lynne
authors.initials: L
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: Marcel
authors.initials: M
authors.lastname: Huntemann
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: Ioanna
authors.initials: I
authors.lastname: Pagani
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: Natalia
authors.initials: N
authors.lastname: Ivanova
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: Cynthia D
authors.initials: CD
authors.lastname: Jeffries
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
authors.forename: Loren
authors.initials: L
authors.lastname: Hauser
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: Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya.
authors.forename: Romano
authors.initials: R
authors.lastname: Mwirichia
authors.affiliation: HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Rohde
authors.affiliation: DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
authors.forename: Birte
authors.initials: B
authors.lastname: Abt
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: 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 ; 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: DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
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: DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
keywords: GEBA; Gram-negative; Halotolerant; Non-peptidoglycan bacteria; Planctomycetales; Planctomycetes; Stalked bacteria; Taxonomic descriptions