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. 2015 Apr 1;10(4):e0122254. doi: 10.1371/journal.pone.0122254. eCollection 2015.

Abstract

A novel Gram-negative bacterium, designated ZWT, was isolated from a soil sample of the Western Desert of China, and its phenotypic properties and phylogenetic position were investigated using a polyphasic approach. Growth occurred on TGY medium at 5-42°C with an optimum of 30°C, and at pH 7.0-11.0 with an optimum of pH 9.0. The predominant cellular fatty acids were summed feature 3 (C16:1ω7c/C16:1ω6c or C16:1ω6c/C16:1ω7c) (39.22%), iso-C15:0 (27.91%), iso-C17:0 3OH (15.21%), C16:0 (4.98%), iso-C15:0 3OH (3.03%), C16:0 3OH (5.39%) and C14:0 (1.74%). The major polar lipid of strain ZWT is phosphatidylethanolamine. The only menaquinone observed was MK-7. The GC content of the DNA of strain ZWT is 44.9 mol%. rDNA phylogeny, genome relatedness and chemotaxonomic characteristics all indicate that strain ZWT represents a novel species of the genus Sphingobacterium. We propose the name S. deserti sp. nov., with ZWT (= KCTC 32092T = ACCC 05744T) as the type strain. Whole genome optical mapping and next-generation sequencing was used to derive a finished genome sequence for strain ZWT, consisting of a circular chromosome of 4,615,818 bp in size. The genome of strain ZWT features 3,391 protein-encoding and 48 tRNA-encoding genes. Comparison of the predicted proteome of ZWT with those of other sphingobacteria identified 925 species-unique proteins that may contribute to the adaptation of ZWT to its native, extremely arid and inhospitable environment. As the first finished genome sequence for any Sphingobacterium, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • China
  • Chromosome Mapping
  • Genome, Bacterial*
  • Sequence Analysis, DNA
  • Soil Microbiology*
  • Sphingobacterium / genetics*
  • Sphingobacterium / isolation & purification

Grant support

This work was supported by the Ministry of Science and Technology of China (National Basic Research Program 2015CB755701, 2013CB733900, 2010CB126504 and National High-Tech Program 2012AA063503), the National Natural Science Foundation of China (grant No. 31170105), the Important National Science &Technology Specific Projects (2014ZX0800301B, 2013ZX08012-001, 2013ZX08009-003), and the Special Fund for Agro-scientific Research in the Public Interest (201103007). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.