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Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil

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Abstract

One Gram-negative, aerobic, motile, rod-shaped bacterium, designated as FH14T, was isolated from nodules of Phaseolus vulgaris grown in Hidalgo State of Mexico. Results based upon 16S rRNA gene (≥99.8 % similarities to known species), concatenated sequence (recA, atpD and glnII) analysis of three housekeeping genes (≤93.4 % similarities to known species) and average nucleotide identity (ANI) values of genome sequence (ranged from 87.6 to 90.0 % to related species) indicated the distinct position of strain FH14T within the genus Rhizobium. In analyses of symbiotic genes, only nitrogen fixation gene nifH was amplified that had nucleotide sequence identical to those of the bean-nodulating strains in R. phaseoli and R. vallis, while nodulation gene nodC gene was not amplified. The failure of nodulation to its original host P. vulgaris and other legumes evidenced the loss of its nodulation capability. Strain FH14T contained summed feature 8 (C18:1 ω6c/C18:1 ω7c, 59.96 %), C16:0 (10.6 %) and summed feature 2 (C12:0 aldehyde/unknown 10.928, 10.24 %) as the major components of cellular fatty acids. Failure to utilize alaninamide, and utilizing l-alanine, l-asparagine and γ-amino butyric acid as carbon source, distinguished the strain FH14T from the type strains for the related species. The genome size and DNA G+C content of FH14T were 6.94 Mbp and 60.8 mol %, respectively. Based on those results, a novel specie in Rhizobium, named Rhizobium hidalgonense sp. nov., was proposed, with FH14T (=HAMBI 3636T = LMG 29288T) as the type strain.

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Acknowledgments

This study was financially supported by the National Natural Science Foundation of China (41371296). ETW was supported by the projects SIP20150597 authorized by Instituto Politecnico Nacional, México.

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Authors and Affiliations

  1. Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, People’s Republic of China

    Jun Yan & Xiao Zeng Han

  2. State Key Laboratory for Agro-Biotechnology, Beijing, 100193, People’s Republic of China

    Hui Yan, Li Xue Liu & Wen Feng Chen

  3. Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China

    Xiao Xia Zhang

  4. Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Mexico DF, Mexico

    Myrthala M. Verástegui-Valdés & En Tao Wang

  5. Rhizobium Research Center and College of Biological Sciences, China Agricultural University, Beijing, 100193, People’s Republic of China

    Hui Yan, Li Xue Liu & Wen Feng Chen

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  1. Jun Yan
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Correspondence to En Tao Wang or Xiao Zeng Han.

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Communicated by Erko Stackebrandt.

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Yan, J., Yan, H., Liu, L.X. et al. Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil. Arch Microbiol 199, 97–104 (2017). https://doi.org/10.1007/s00203-016-1281-x

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