Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), 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 1448T, 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.

Paludisphaera borealis gen. nov., sp. nov., a hydrolytic planctomycete from northern wetlands, and proposal of Isosphaeraceae fam. nov.

“…The overall similarities between the genome of strain PX4 T (Ivanova and others, unpublished) and the genomes of I. pallida IS1B T and S. acidiphila DSM 18658 T estimated using formula 2 of the Genome-to-Genome-Distance-Calculator (Auch et al, 2010) are 19.8¡2.3 and 20.0¡2.3, respectively. These DNA-DNA hybridization values are similar to those calculated for members of different genera (Scheuner et al, 2014). Average nucleotide identity values generated by comparing the genome of strain PX4 T with the genomes of I. pallida IS1B T and S. acidiphila DSM 18658 T are also very low, i.e.…”

“…Table 3. Major characteristics that distinguish the genus Paludisphaera gen. nov. from the genera Isosphaera, Singulisphaera and Aquisphaera Genera: 1, Paludisphaera gen. nov.; 2, Isosphaera (data from Giovannoni et al, 1987 andGöker et al, 2011); 3, Singulisphaera (data from Kulichevskaya et al, 2008and Scheuner et al, 2014; 4, Aquisphaera (data from Bondoso et al, 2011). +, Positive; 2, negative; nd, not determined.…”

Genome-Based Taxonomic Classification of Bacteroidetes

“…G+C content values provided in species descriptions that deviate more than 1% from the value calculated from the genome sequence, or display a range of more than 1%, obscure species affiliations and should be corrected (Riedel et al, 2014). Emendations of higher taxa regarding their G+C content have also been conducted (Scheuner et al, 2014) but we abstain from accordingly redefining Bacteroidetes genera here because we opine that more type-strain genome sequences per genus would be needed. Moreover, the emendation of Flavobacterium suncheonense has recently been conducted (Panschin et al, 2016) and needs not be considered here.…”

“…Apparently the same holds if a range of G+C values was provided whose lower or upper bound deviates by more than 1% from the directly calculated G+C value, but a species description should also be restricted if a range of G+C values was provided that, unrealistically, exceeds 1%. Taxa of higher rank should accordingly be emended if their presumed range of G+C values turns out to be in conflict with the information from genome sequences (Scheuner et al, 2014). …”

Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea

“…Based on 16S rRNA gene sequence comparison, it branches within the former genus Planctomyces which was recently found to be polyphyletic. Consequently, it was further subdivided into the separate genera Gimesia, Planctopirus, Rubinisphaera , and Planctomyces , which all belong to the order Planctomycetales and the family Planctomycetaceae (Scheuner et al, 2014). Similar results were obtained by a MLSA phylogenetic analysis, while both approaches provided rather low bootstrap support.…”