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Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica

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Abstract

During a study of endophytic bacteria from traditional Chinese medicinal plants, a bacterial strain, designated PTYR-5T, was isolated from the leaf of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTYR-5T is a member of the genus Rhizobium, exhibiting the highest sequence similarities to R. cellulosilyticum LMG 23642T (97.2 %), R. huautlense LMG 18254T (97.2 %) and R. alkalisoli CCBAU 01393T (97.1 %). The levels of 16S rRNA gene sequence similarity with respect to other Rhizobium species with validly published names were less than 97.0 %. Phylogenies of the housekeeping genes atpD, recA and glnII confirmed its distinct position, showing low similarity with respect to those of recognized Rhizobium species (no more than 94.1 , 90.0 and 88.0      % similarity, respectively). The DNA–DNA relatedness values of strain PTYR-5T with R. cellulosilyticum LMG 23642T, R. huautlense LMG 18254T and R. alkalisoli CCBAU 01393T were 33.6, 21.4 and 29.5 %, respectively. Based on phenotypic, phylogenetic and genotypic data, strain PTYR-5T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium smilacinae sp. nov. is proposed. The type strain is PTYR-5T (=CCTCC AB 2013016T=KCTC 32300T=LMG 27604T).

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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 31170100) and the Natural Science Foundation of Shaanxi Province, China (Grant No. 2012JQ3006).

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Authors and Affiliations

  1. State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People’s Republic of China

    Lei Zhang, Xu Shi, Meiru Si, Changfu Li, Lingfang Zhu, Liang Zhao, Xihui Shen & Yao Wang

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  1. Lei Zhang
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  2. Xu Shi
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  3. Meiru Si
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  4. Changfu Li
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  8. Yao Wang
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Correspondence to Yao Wang.

Additional information

Lei Zhang and Xu Shi have contributed equally to this work.

The GenBank/EMBL/DDBJ accession numbers for the partial 16S rRNA, atpD, recA and glnII gene sequences of strain PTYR-5T are KF551141, KF738707, KF738708 and KF738709, respectively.

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Zhang, L., Shi, X., Si, M. et al. Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica . Antonie van Leeuwenhoek 106, 715–723 (2014). https://doi.org/10.1007/s10482-014-0241-1

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