PMID- 32552985
OWN - NLM
STAT- MEDLINE
DCOM- 20200824
LR  - 20200824
IS  - 1466-5034 (Electronic)
IS  - 1466-5026 (Linking)
VI  - 70
IP  - 7
DP  - 2020 Jul
TI  - Dickeya oryzae sp. nov., isolated from the roots of rice.
PG  - 4171-4178
LID - 10.1099/ijsem.0.004265 [doi]
AB  - A novel Gram-stain-negative strain, designated ZYY5(T), was isolated from rice 
      roots. Results of 16S rRNA gene analysis indicated that strain ZYY5(T) was a 
      member of the genus Dickeya, with a highest similarity to Dickeya zeae DSM 
      18068(T) (98.5%). The major fatty acids were summed feature 3 (C(16:1) omega7c and/or 
      C(16:1) omega6c), C(16:0) and summed feature 8 (C(18:1) omega7c and/or C(18:1) omega6c). 
      Multi-locus sequence analysis using five concatenated genes (16S rRNA, atpD, 
      infB, recA and gyrB) and phylogenomic analysis based on 2940 core gene sequences 
      showed that strain ZYY5(T) formed a robust cluster with strains EC1, ZJU1202, 
      DZ2Q, NCPPB 3531 and CSL RW192, while separated from the other strains of D. 
      zeae. 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(T) shared 58.4 of dDDH and 94.5% of ANI values with type 
      strain D. zeae DSM 18068(T), which were lower than the proposed species boundary 
      cut-off for dDDH and ANI. The genomic analysis revealed that strain ZYY5(T) 
      contained virulence-associated genes, which is same as the phylogenetic-related 
      strains of the genus Dickeya. Based on the results of the polyphasic approaches, 
      we propose that strain ZYY5(T) represents a novel species in the genus Dickeya, 
      for which the name Dickeya oryzae sp. nov. (=JCM 33020 (T)=ACCC 61554 (T)) is 
      proposed. Strains EC1, ZJU1202, DZ2Q, NCPPB 3531 and CSL RW192 should also be 
      classified in the same genomospecies of D. oryzae same as ZYY5(T).
FAU - Wang, Xing
AU  - Wang X
AD  - Key Laboratory of Microbial Resources Collection and Preservation, Ministry of 
      Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional 
      Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
FAU - He, Shan-Wen
AU  - He SW
AD  - College of life science, The Yangtze University, Jingzhou, 434025, PR China.
AD  - Key Laboratory of Microbial Resources Collection and Preservation, Ministry of 
      Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional 
      Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
FAU - Guo, He-Bao
AU  - Guo HB
AD  - Key Laboratory of Microbial Resources Collection and Preservation, Ministry of 
      Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional 
      Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
FAU - Han, Ji-Gang
AU  - Han JG
AD  - Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, 
      PR China.
FAU - Thin, Kyu Kyu
AU  - Thin KK
AD  - Key Laboratory of Microbial Resources Collection and Preservation, Ministry of 
      Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional 
      Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
FAU - Gao, Ju-Sheng
AU  - Gao JS
AD  - Qiyang Agro-ecosystem of National Field Experimental Station, Institute of 
      Agricultural Resources and Regional, Chinese Academy of Agricultural Sciences, 
      Qiyang 426182, PR China.
AD  - Key Laboratory of Microbial Resources Collection and Preservation, Ministry of 
      Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional 
      Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
FAU - Wang, Yao
AU  - Wang Y
AD  - College of life science, The Yangtze University, Jingzhou, 434025, PR China.
AD  - Key Laboratory of Microbial Resources Collection and Preservation, Ministry of 
      Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional 
      Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
FAU - Zhang, Xiao-Xia
AU  - Zhang XX
AD  - Key Laboratory of Microbial Resources Collection and Preservation, Ministry of 
      Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional 
      Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
LA  - eng
PT  - Journal Article
PL  - England
TA  - Int J Syst Evol Microbiol
JT  - International journal of systematic and evolutionary microbiology
JID - 100899600
RN  - 0 (DNA, Bacterial)
RN  - 0 (Fatty Acids)
RN  - 0 (RNA, Ribosomal, 16S)
SB  - IM
MH  - Bacterial Typing Techniques
MH  - Base Composition
MH  - China
MH  - DNA, Bacterial/genetics
MH  - Enterobacteriaceae/*classification/isolation & purification
MH  - Fatty Acids/chemistry
MH  - Genes, Bacterial
MH  - Nucleic Acid Hybridization
MH  - Oryza/*microbiology
MH  - *Phylogeny
MH  - Plant Roots/*microbiology
MH  - RNA, Ribosomal, 16S/genetics
MH  - Sequence Analysis, DNA
OTO - NOTNLM
OT  - Dickeya
OT  - genome
OT  - polyphasic taxonomy
OT  - rice endophytic bacteria
EDAT- 2020/06/20 06:00
MHDA- 2020/08/25 06:00
CRDT- 2020/06/20 06:00
PHST- 2020/06/20 06:00 [pubmed]
PHST- 2020/08/25 06:00 [medline]
PHST- 2020/06/20 06:00 [entrez]
AID - 10.1099/ijsem.0.004265 [doi]
PST - ppublish
SO  - Int J Syst Evol Microbiol. 2020 Jul;70(7):4171-4178. doi: 10.1099/ijsem.0.004265.