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Volume 70, Issue 7

sp. nov., isolated from the roots of rice Free

Abstract

A novel Gram-stain-negative strain, designated ZYY5, was isolated from rice roots. Results of 16S rRNA gene analysis indicated that strain ZYY5 was a member of the genus , with a highest similarity to DSM 18068 (98.5%). The major fatty acids were summed feature 3 (C ω7 and/or C ω6), C and summed feature 8 (C ω7 and/or C ω6). Multi-locus sequence analysis using five concatenated genes (16S rRNA, , , and ) and phylogenomic analysis based on 2940 core gene sequences showed that strain ZYY5 formed a robust cluster with strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of . The orthologous average nucleotide identity (ANI) and digital DNA–DNAhybridization (dDDH) values among these six strains ranged from 96.8–99.9% and 73.7–99.8%, which supported that they were belonged to the same species. However, strain ZYY5 shared 58.4 of dDDH and 94.5% of ANI values with type strain DSM 18068, which were lower than the proposed species boundary cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5 contained virulence-associated genes, which is same as the phylogenetic-related strains of the genus . Based on the results of the polyphasic approaches, we propose that strain ZYY5 represents a novel species in the genus , for which the name sp. nov. (=JCM 33020 =ACCC 61554 ) is proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be classified in the same genomospecies of same as ZYY5.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Dickeya , genome , polyphasic taxonomy and rice endophytic bacteria
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31670005)
    • Principle Award Recipient: Xiao-Xia Zhang
© 2020 The Authors
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2020-06-18
2024-04-16
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Dickeya oryzae sp. nov., isolated from the roots of rice
Int J Syst Evol Microbiol 70, 4171 (2020); https://doi.org/10.1099/ijsem.0.004265
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