Complete genome sequence of Planctomyces limnophilus type strain (Mü 290)

Abstract

Planctomyces limnophilus Hirsch and Müller 1986 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 which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. Besides Pirellula staleyi, this is the second completed genome sequence of the family Planctomycetaceae. P. limnophilus is of interest because it differs from Pirellula by the presence of a stalk and its structure of fibril bundles, its cell shape and size, the formation of multicellular rosettes, low salt tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304 protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords: GEBA; Gram negative; Planctomycetales; Planctomycetes; low salt tolerance; multicellular rosettes; stalk.

Figure 1

Scanning electron micrograph of P. limnophilus Mü 290^T

Figure 2

Phylogenetic tree highlighting the position of P. limnophilus Mü 290^T relative to the type strains of the other species within the genus and to the type strains of the other genera within the family Planctomycetaceae. The tree was inferred from 1,336 aligned characters [27,28] of the 16S rRNA gene sequence under the maximum likelihood criterion [29] and rooted in accordance with the current taxonomy [30]. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates [31] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [32] are shown in blue, published genomes in bold, e.g. the recently published GEBA genome of Pirellula staleyi [33]. 16S rRNA gene sequences are not available for strains of the species P. bekefii, P. guttaeformis or P. stranskae, all of which are typified by descriptions and were initially described as fungi [1,7]. The name P. gracilis was also initially described as a fungus, but the name has not been validly published under the Bacteriological Code. Starr et al. [34] considered this organism not be to a planctomycete.

Figure 3

Graphical circular map of the chromosome and the plasmid (not drawn to scale). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.