Strain identifier

BacDive ID: 17495

Type strain: Yes

Species: Lysobacter oryzae

Strain Designation: YC6269, Z 3-12

Strain history: <- Y. R. Chung, Dept. of Microbiology, Gyeongsang National University <- Z. Aslam, dto.

NCBI tax ID(s): 1122187 (strain), 498057 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15535

BacDive-ID: 17495

DSM-Number: 21044

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Lysobacter oryzae YC6269 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of rice , no-tillage field.

NCBI tax id

NCBI tax idMatching level
1122187strain
498057species

strain history

  • @ref: 15535
  • history: <- Y. R. Chung, Dept. of Microbiology, Gyeongsang National University <- Z. Aslam, dto.

doi: 10.13145/bacdive17495.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Lysobacter
  • species: Lysobacter oryzae
  • full scientific name: Lysobacter oryzae Aslam et al. 2009

@ref: 15535

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Lysobacter

species: Lysobacter oryzae

full scientific name: Lysobacter oryzae Aslam et al. 2009

strain designation: YC6269, Z 3-12

type strain: yes

Morphology

cell morphology

  • @ref: 28889
  • gram stain: negative
  • cell length: 1.9 µm
  • cell width: 0.4 µm
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

  • @ref: 15535
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15535positivegrowth28mesophilic
28889positivegrowth15-42
28889positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
28889positivegrowth5.5-11alkaliphile
28889positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 28889
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 28889
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
288895291gelatin+carbon source
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
28889alkaline phosphatase+3.1.3.1
28889catalase+1.11.1.6
28889cytochrome oxidase+1.9.3.1
68368cytochrome oxidase-1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
15535----------+----------

Isolation, sampling and environmental information

isolation

  • @ref: 15535
  • sample type: rhizosphere of rice (Oryza sativa L.), no-tillage field
  • host species: Oryza sativa
  • geographic location: Jinju
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_81053.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_1523;97_23341;98_29484;99_81053&stattab=map
  • Last taxonomy: Lysobacter oryzae
  • 16S sequence: EU376963
  • Sequence Identity:
  • Total samples: 13914
  • soil counts: 10683
  • aquatic counts: 842
  • animal counts: 439
  • plant counts: 1950

Safety information

risk assessment

  • @ref: 15535
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15535
  • description: Lysobacter oryzae strain YC6269 16S ribosomal RNA gene, partial sequence
  • accession: EU376963
  • length: 1415
  • database: ena
  • NCBI tax ID: 498057

Genome sequences

  • @ref: 66792
  • description: Lysobacter oryzae DSM 21044
  • accession: 2571042365
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1122187

GC content

@refGC-contentmethod
1553567.4high performance liquid chromatography (HPLC)
2888967.4

External links

@ref: 15535

culture collection no.: DSM 21044, KCTC 22249

straininfo link

  • @ref: 86492
  • straininfo: 407366

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329586Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.).Aslam Z, Yasir M, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.000588-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny25406233Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil.Ngo HTT, Won K, Du J, Son HM, Park Y, Kook M, Kim KY, Jin FX, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.067397-02014Aglaia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lysobacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny25828767Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant.Singh H, Du J, Ngo HT, Won K, Yang JE, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0439-x2015Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fragaria/*microbiology, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Plant Roots/microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny26025168Lysobacter tyrosinelyticus sp. nov. isolated from Gyeryongsan national park soil.Du J, Singh H, Ngo HT, Won K, Kim KY, Yi THJ Microbiol10.1007/s12275-015-4729-92015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Parks, Recreational, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny26111851Lysobacter agri sp. nov., a bacterium isolated from soil.Singh H, Won K, Du J, Yang JE, Akter S, Kim KY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0510-72015Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Lysobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, TemperatureGenetics
Phylogeny26763907Lysobacter terricola sp. nov., isolated from greenhouse soil.Kim SJ, Ahn JH, Weon HY, Hong SB, Seok SJ, Kim JS, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0008932016
Phylogeny27377971Lysobacter humi sp. nov., a bacterium isolated from rice field.Akter S, Huq MA, Yi THArch Microbiol10.1007/s00203-016-1262-02016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Lysobacter/*classification/genetics/growth & development/*isolation & purification, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/metabolismTranscriptome
Phylogeny27521144Lysobacter rhizophilus sp. nov., isolated from rhizosphere soil of mugunghwa, the national flower of South Korea.Yan ZF, Trinh H, Moya G, Lin P, Li CT, Kook MC, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0014222016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Lysobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny35076363Lysobacter terrestris sp. nov., isolated from soil.Woo CY, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0052042022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Lysobacter/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15535Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21044)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21044
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
28889Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2532928776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68368Automatically annotated from API 20E
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86492Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407366.1StrainInfo: A central database for resolving microbial strain identifiers