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Sphingobium endophyticus sp. nov., isolated from the root of Hylomecon japonica

Abstract

A yellow-pigmented bacterium, designated strain GZGR-4T, was isolated from the root of Hylomecon japonica (Thunb.) Prantl et Kündig collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain GZGR-4T were Gram-negative, rod-shaped, strictly aerobic, non-endospore-forming and non-motile. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GZGR-4T is a member of the genus Sphingobium, exhibiting the highest sequence similarity to Sphingobium aromaticiconvertens DSM 12677T (97.3 %). 16S rRNA gene sequence similarities between strain GZGR-4T and the type strains of other Sphingobium species with validly published names ranged from 93.4–96.5 %. The predominant respiratory quinone of strain GZGR-4T was ubiquinone-10 (Q-10) and the major cellular fatty acids were summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c), summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c), C16:0 and C14:0 2-OH. Spermidine was the major polyamine. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, one unidentified phosphoglycolipid, one unidentified phospholipid, one unidentified aminolipid and one unidentified lipid. The DNA G+C content was 63.6 mol%. DNA–DNA relatedness for strain GZGR-4T with respect to its closest phylogenetic relative S. aromaticiconvertens DSM 12677T was 22.6 ± 5.3 %. On the basis of the polyphasic taxonomic data presented, strain GZGR-4T is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium endophyticus sp. nov. is proposed. The type strain is GZGR-4T (=CCTCC AB 2013305T = KCTC 32447T).

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Acknowledgments

This work was supported by the National High Technology Research and Development Program of China (863 program, grant 2013AA102802), the National Natural Science Foundation of China (Grant No. 31100001 and 31300158), the Natural Science Foundation of Shaanxi Province, China (Grant No. 2012JQ3006), the Fundamental Research Funds for the Central Universities (Grant No. QN2012020) and the Specialized Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20120204120032).

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Correspondence to Lei Zhang or Xihui Shen.

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Lingfang Zhu and Kaiyun Xin have contributed equally to this work.

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain GZGR-4T is KF551123.

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Zhu, L., Xin, K., Chen, C. et al. Sphingobium endophyticus sp. nov., isolated from the root of Hylomecon japonica . Antonie van Leeuwenhoek 107, 1001–1008 (2015). https://doi.org/10.1007/s10482-015-0392-8

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Keywords

  • Sphingobium endophyticus sp. nov.
  • Root of Hylomecon japonica
  • North-west China