Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113)

Abstract

Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords: GEBA; Gram-negative; Sphingobacteriaceae; chemoorganotrophic; gliding motility; heparinolytic; mesophilic; strictly aerobic.

Figure 1

Phylogenetic tree highlighting the position of P. saltans relative to the other type strains within the genus Pedobacter. The tree was inferred from 1,402 aligned characters [22,23] of the 16S rRNA gene sequence under the maximum-likelihood (ML) criterion [24] and rooted with the type strain of the type species of the family Sphingobacteriaceae [25]. The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 550 ML bootstrap replicates [26] (left) and from 1,000 maximum-parsimony bootstrap replicates [27] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [28] as unpublished are marked with one asterisk, those listed as published with two asterisks [29]. Note that the taxon selection used in this figure does not allow conclusions about the monophyly of the genus Pedobacter. In an expanded analysis also including the genera Mucilaginibacter and Nubsella (data not shown), neither the Kishino-Hasegawa test as implemented in PAUP* [27] in conjunction with the maximum-parsimony criterion nor the Shimodaira-Hasegawa test as implemented in RAxML [24] in conjunction with the ML criterion indicated a significant difference between the respective globally best tree and the best tree after constraining for the monophyly of all four genera. (See, e.g. chapter 21 in [30] for an in-depth description of such paired-site tests.)

Figure 2

Scanning electron micrograph of P. saltans strain 113^T

Figure 3

Graphical circular map of genome. 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.

Figure 4

Venn diagram depicting the intersections of protein sets (total number of derived protein sequences in parentheses) of P. heparinus, P. saltans and N. aromaticivorans.