Genomic analysis of Skermanella stibiiresistens type strain SB22T
© The Author(s) 2014
Published: 15 June 2014
Members of genus Skermanella were described as Gram-negative, motile, aerobic, rod-shaped, obligate-heterotrophic bacteria and unable to fix nitrogen. In this study, the genome sequence of Skermanella stibiiresistens SB22T is reported. Phylogenetic analysis using core proteins confirmed the phylogenetic assignment based on 16S rRNA gene sequences. Strain SB22T has all the proteins for complete glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The RuBisCO encoding genes cbbL1S1 and nitrogenase delta subunit gene anfG are absent, consistent with its inability to fix carbon and nitrogen, respectively. In addition, the genome possesses a series of flagellar assembly and chemotaxis genes to ensure its motility.
KeywordsSkermanella stibiiresistens genome sequence metabolism flagella chemotaxis
The type species for the genus Skermanella is Skermanella parooens ACM 2042T, which was originally proposed as Conglomeromonas largomobilis subsp. parooensis by Skerman et al. in 1983 . Later, it was transferred to the genus Skermanella (family Rhodospirillaceae) on the basis of phylogenetic evidence and phenotypic characteristics, especially the inability to fix nitrogen [2,3]. At present, this genus comprises four validly published species, Skermanella parooensis , Skermanella aerolata , Skermanella xinjiangensis  and Skermanella stibiiresistens , which were isolated from fresh water, air, sandy soil and a coal mine, respectively.
Skermanella was characterized as a Gram-negative, non-spore-forming bacterium with unicellular and multicellular phases of growth, an obligate chemo-organotroph and facultative anaerobe, unable to fix nitrogen, and with a high DNA G+C content. To the best of our knowledge, genome information for Skermanella members is still not available. In this study, we present the draft genome sequence of a Skermanella type strain S. stibiiresistens SB22T and compare it with the members of the related genera Azospirillum and Rhodospirillum.
Classification and features
Classification and general features of S. stibiiresistens SB22T according to the MIGS recommendations .
Species Skermanella stibiiresistens
Type strain SB22T
D-glucose, D-ribose, rhamnose, L-proline, salicin, inositol, DL-lactate, L-alanine, malic acid, potassium 2-ketogluconate and 3-hydroxybutyric acid
Terminal electron receptor
Jixi coal mine of Jixi City, Heilongjiang Province, northeast China
Sample collection time
Surface sandy soil
Genome sequencing information
Genome project history
Genome sequencing project information of S. stibiiresistens SB22T
Illumina Paired-End library (300 bp insert size)
Gene calling method
GenBank date of release
February 23, 2014
NCBI project ID
Source material identifier
Growth condition and DNA isolation
S. stibiiresistens SB22T was grown aerobically in R2A medium at 28°C for 2 days. It can also grow on LB medium under the same conditions. The strain was apricot-colored after incubated 72 h at 28°C on R2A agar. The DNA was isolated using the QiAamp kit according to the manufacturer’s instruction (Qiagen, German).
Genome sequencing and assembly
The Illumina Hiseq2000 technology with Paired-End (PE) library strategy was used to determine the sequence of S. stibiiresistens SB22T. A total of 7,588,874 × 2 high quality reads totaling 1,454,191,294 bp data with an average coverage 184.5 × was generated. Illumina sequencing data was assembled with SOAPdenovo, version 1.05 (http://soap.genomics.org.cn/). The initial draft assembly contained 7,879,677 bp in 257 contigs. Then the draft genome sequence was deposited to the NCBI with contigs less than 200 bp nucleotides cut off.
The draft genome sequence was deposited to NCBI and was annotated though the Prokaryotic Genome Annotation Pipeline (PGAP), using the Best-placed reference protein set and the gene caller GeneMarkS+. Signal peptides and transmembrane helices were predicted by SignalP  and SOSUI , respectively. The WebMGA-server  was used to identify the Clusters of Orthologs Groups (COG).
Nucleotide content and gene count level in genome of S. stibiiresistens SB22T
% of Totala
Genome size (bp)
Number of contigs
Frame shifted genes
DNA coding region (bp)
Protein-coding genes with function prediction
Protein-coding genes assigned to COGs
Protein-coding genes with transmembrane helices
Protein-coding genes with signal peptides
Number of protein-coding genes associated with the 25 general COG functional categories in S. stibiiresistens SB22T genome.
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane/envelope biogenesis
Intracellular trafficking, secretion, and vesicular transport
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGS
Insights from the genome sequence
Profiles of metabolic networks and pathways
Genes involved in carbon fixation
Genus Skermanella belongs to family Rhodospirillaceae, but Skermanella species cannot fix carbon as Rhodospirillum centenum  and Azospirillum amazonense  do. Genomic analysis of S. stibiiresistens SB22T, shows that the RuBisCO encoding genes cbbL1S1 [24,25] are not present, which is in agreement with the strain’s inability to fix carbon.
Genes involved in nitrogen metabolism
Strain S. stibiiresistens SB22T is closely related to some species of genera Azospirillum and Rhodospirillum . Genus Rhodospirillum is described as a photosynthetic non-sulfur purple bacterium that favors growth in an anoxygenic, photosynthetic, nitrogen-fixing environment . Some aerobic nitrogen fixing strains of Azospirillum have significant effects on crop plants . But genus Skermanella is unable to fix nitrogen under microaerophilic conditions [3,4,6]. Even though nitrogenase genes nifDKH are present in the genome of S. stibiiresistens SB22T, we found that the nitrogenase delta subunit gene anfG is absent.
Flagella and chemotaxis
This work was supported by the National Natural Science Foundation of China (31170106).
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