Sphingobacterium deserti, Teng & Zhou & Molnár & Li & Tang & Chen & Wang & Su & Zhang & Lin, 2015

Teng, Chao, Zhou, Zhengfu, Molnár, István, Li, Xinna, Tang, Ran, Chen, Ming, Wang, Lin, Su, Shiyou, Zhang, Wei & Lin, Min, 2015, Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China, PLoS ONE (e 0122254) 10 (4), pp. 1-16 : 5-10

S. deserti sp. nov.

The cells of strain ZW T are Gram-negative, non-motile, non-spore-forming, strictly aerobic rods, approximately 0.6–1.7 μm in length and 0.3–0.6 μm in diameter ( Fig 1 ). After 48 h of incubation on TGY, ZW T colonies were 3–5 mm in diameter, lemon yellow, convex, circular, smooth and entire. The optimum growth temperature is 30°C (range: 5–42°C), and the optimum pH is 9 (range: pH 7.0–11.0). Growth occurs at NaCl concentrations ranging from 0 to 1%. Cells of strain ZW T are positive for catalase and oxidase activities, but negative for urease. Casein, starch, gelatin, Tween 20 and Tween 80 are not hydrolyzed. Cells of strain ZW T do not

show L-arginine dihydrolase activity, and are negative for citrate utilization, nitrate reduction, and the Voges-Proskauer reaction. They are able to assimilate D-glucose, D-mannose, D-maltose, and L-arabinose, but not xylose. Acid is produced from D-mannitol and L-arabinose, but not from D-fructose, D-xylose or salicin ( Table 1 ). The cells of strain ZW T exhibit resistance to kanamycin (50 μg/mL), ampicillin (50 μg/mL), hygromycin (50 μg/mL) and spectinomycin (35μg/mL), but are sensitive to rifampicin (50 μg/mL), chloramphenicol (50 μg/mL) and tetracycline (50 μg/mL). The predominant cellular fatty acids are summed feature 3 (C 16:1 ω7c / C 16:1 ω6c or C 16:1 ω6c/ C 16:1 ω7c) (39.22%), iso-C15:0 (27.91%), iso-C 17:0 3OH (15.21%), C 16:0 (4.98%), iso-C 15:0 3OH (3.03%), C16:0 3OH (5.39%) and C 14:0 (1.74%). This fatty acid profile is similar to those of several reference strains of sphingobacteria that were grown under identical conditions ( Table 2 ), suggesting that this newly isolated bacterium belongs to the genus Sphingobacterium . The polar lipid profile of strain ZW T includes phosphatidylethanolamine and several unidentified polar lipids (S1 Fig). Both strain ZW T and S. spiritivorum contain sphingolipids (S2 Fig), which are a distinct feature of members of the genus Sphingobacterium . The menaquinone of strain ZW T is MK-7 (>99%), consistent with all known members of the family Sphingobacterium . The GC content of the DNA of strain ZW T is 44.9 mol%, slightly higher than that of other Sphingobacterium strains.

The 16S rRNA gene sequence of strain ZW T (= KCTC 32092T = ACCC 05744T) is 1,311 bp in length (GenBank accession number JX403964). BLAST searches in the GenBank database and the EzTaxon server (http://www.ezbiocloud.net/eztaxon; [ 35]) indicated that strain ZW T belongs to the genus Sphingobacterium of the phylum Bacteroidetes. The 16S rRNA gene of strain ZW T exhibits the highest similarity to sequences from S. bambusae IBFC2009 T (95.65%), S. composti 4M24 T (95.57%), S. lactis WCC 4512 T (95.49%), S. mizutaii DSM 11724 T (95.11%), S. daejeonense TR 6-04 T (95.11%), S. kyonggiense KEMC 2241 -005 T (94.73%) and S. nematocida M-SX103 T (93.59%). DNA–DNA relatedness between strain ZW T and S. composti 4M24 T is 36.3%. Phylogenetic analysis confirmed that strain ZW T forms a coherent cluster with members of the genus Sphingobacterium , and an intra-genus clade with S. bambusae IBFC2009 T (Fig 2). According to Stackebrandt [ 36] and Wayne [ 37], 16S rRNA gene

finished genome sequence, to the best of our knowledge, for any species within the genus Sphingobacterium .

The length of the circular chromosome of strain ZW T was found to be 4,615,818 bp ( Fig 3 , GenBank accession number JJMU00000000). The GC content of the genome is 42.6 mol% ( Fig 4 ), in agreement with the value (44.9 mol%) established by DNA renaturation kinetics [ 16]. This is within the range of the published GC contents of the four other Sphingobacterium species for which draft genome sequences are publicly available.

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The genome of strain ZW T contains 48 tRNA genes and several rRNA gene clusters, including single copies of the 16S and the 23S rRNA genes and duplicate copies of the 5S rRNA gene. An estimated 88.6% of the genome contains coding sequences (CDSs), and these CDSs are predicted to encode 3,391 putative proteins. The predicted proteins belong to 1,238 conserved orthologous groups (COGs) from 23 COG categories. In addition, 1,408 predicted proteins were also annotated using the KEGG Orthology System (S2 Table).

Although many Sphingobacterium strains have been isolated in the last 30 years, no finished genome assemblies have been generated for any of those strains. In addition, few chromosomal features have been reported for any Sphingobacterium genome. The genomic data and the WGM restriction barcode of strain ZW T may facilitate the taxonomic characterization of further members of the genus Sphingobacterium ( Fig 5 ). Strain ZW T can also serve as a genome sequencing reference strain, with its WGM sequencing and annotation data available at NCBI for download and direct import into new draft genome sequences of other sphingobacteria.

Figures

Fig 1. Electron micrograph of the cell morphology of strain ZWT. doi:10.1371/journal.pone.0122254.g001

Fig 3. Optical mapping of the Sphingobacterium deserti sp. nov. ZWT genomic DNA with BamHI. The large chromosome restriction map was generated by shotgun optical mapping. The outer circle depicts the consensus map; the inner circles indicate the contigs from which the consensus map was generated. Colors are arbitrarily assigned to homologous overlapping fragments. doi:10.1371/journal.pone.0122254.g003

Fig 4. Genome map of Sphingobacterium deserti sp. nov. ZWT. Concentric tracks from the inside to the outside represent the GC nucleotide bias; the GC content; tRNA and rRNA genes on the reverse strand; tRNA and rRNA genes on the forward-strand; reverse-strand coding sequences (CDSs); and forwardstrand CDSs. doi:10.1371/journal. pone.0122254.g004

Fig 5. Whole-genome optical mapping barcode of Sphingobacterium deserti sp. nov. ZWT. Vertical lines represent restriction sites; distances between lines represent fragment sizes.