Strain identifier

BacDive ID: 13048

Type strain: Yes

Species: Pseudomonas oryzihabitans

Strain Designation: KS0036, L-1, KS 0036

Strain history: CIP <- 1987, IAM <- JCM, Pseudomonas oryzihabitans <- K. Kodama: strain KS 0036 <- Ajinomoto Co. Inc.: strain AJ 2197 <- K. Komagata: strain L-1

NCBI tax ID(s): 1215113 (strain), 47885 (species)

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General

@ref: 2845

BacDive-ID: 13048

DSM-Number: 6835

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Pseudomonas oryzihabitans KS0036 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from rice paddy.

NCBI tax id

NCBI tax idMatching level
47885species
1215113strain

strain history

@refhistory
2845<- ATCC (Flavimonas oryzihabitans) <- JCM <- K. Kodama; KS0036 <- Ajinomoto Co. Inc.; AJ 2197 <- K. Komagata; L-1
67770K. Kodama KS 0036 <-- AJ 2197 <-- K. Komagata L-1.
121455CIP <- 1987, IAM <- JCM, Pseudomonas oryzihabitans <- K. Kodama: strain KS 0036 <- Ajinomoto Co. Inc.: strain AJ 2197 <- K. Komagata: strain L-1

doi: 10.13145/bacdive13048.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas oryzihabitans
  • full scientific name: Pseudomonas oryzihabitans Kodama et al. 1985

  • synonyms

    @refsynonym
    20215Pseudomonas psychrotolerans
    20215Flavimonas oryzihabitans

@ref: 2845

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas oryzihabitans

full scientific name: Pseudomonas oryzihabitans Kodama et al. 1985

strain designation: KS0036, L-1, KS 0036

type strain: yes

Morphology

cell morphology

  • @ref: 121455
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 121455
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2845COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
2845CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
33754MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121455CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2845positivegrowth28mesophilic
33754positivegrowth30mesophilic
67770positivegrowth30mesophilic
121455positivegrowth10-41
121455nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121455
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
121455NaClpositivegrowth0-4 %
121455NaClnogrowth6 %
121455NaClnogrowth8 %
121455NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12145516947citrate+carbon source
1214554853esculin-hydrolysis
12145517632nitrate-reduction
12145516301nitrite-reduction
12145517632nitrate-respiration

antibiotic resistance

  • @ref: 121455
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12145535581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121455oxidase-
121455beta-galactosidase-3.2.1.23
121455alcohol dehydrogenase-1.1.1.1
121455gelatinase-
121455amylase-
121455DNase-
121455caseinase-3.4.21.50
121455catalase+1.11.1.6
121455tween esterase+
121455lecithinase-
121455lipase-
121455lysine decarboxylase-4.1.1.18
121455ornithine decarboxylase-4.1.1.17
121455protease+
121455tryptophan deaminase-
121455urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121455-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2845--------++++-+++-++--
2845--------++/-++-+/-++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121455+++++----++--------+++-++-+----+++--+--+---+++-+++++-++++---+-+++------+++-+++-++++++--++++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
2845rice paddyJapanJPNAsia
45739Normal rice paddy,Oryza sativaJapanJPNAsiaTokyo
121455Plant, RiceJapanJPNAsia1963

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
28452Risk group (German classification)
1214551Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas oryzihabitans gene for 16S rRNAD840041527ena47885
20218Pseudomonas oryzihabitans strain LMG 7040 16S ribosomal RNA gene, partial sequenceGQ2505981527ena47885
20218Pseudomonas oryzihabitans gene for 16S rRNA, partial sequence, strain: NBRC 102199AB6817261463ena47885
2845Pseudomonas oryzihabitans partial 16S rRNA gene, type strain IAM 1568TAM2629731466ena47885

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas oryzihabitans NBRC 102199GCA_000730625contigncbi1215113
66792Pseudomonas oryzihabitans NBRC 1021991215113.3wgspatric1215113
66792Pseudomonas oryzihabitans strain DSM 683547885.39wgspatric47885
66792Pseudomonas oryzihabitans strain LMG7040 strain RIT 41147885.22wgspatric47885
66792Pseudomonas oryzihabitans NBRC 1021992585427682draftimg1215113
67770Pseudomonas oryzihabitans DSM 6835GCA_012986195contigncbi47885

GC content

  • @ref: 2845
  • GC-content: 65.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.369no
gram-positiveno98.098no
anaerobicno98.299no
aerobicyes93.295no
halophileno89.008no
spore-formingno95.561no
thermophileno99.691yes
glucose-utilyes94.926yes
flagellatedyes54.812no
glucose-fermentno89.184yes

External links

@ref: 2845

culture collection no.: DSM 6835, ATCC 43272, IAM 1568, JCM 2952, CCUG 12540, LMG 7040, CIP 102996, CCM 8845, AJ 2197, CGMCC 1.3392, NBRC 102199, NCIMB 12521

straininfo link

  • @ref: 82259
  • straininfo: 2812

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism17910097Regulation of pyrimidine formation in Pseudomonas oryzihabitans.West TPJ Basic Microbiol10.1002/jobm.2007103332007Aspartate Carbamoyltransferase/metabolism, Dihydroorotase/metabolism, Dihydroorotate Dehydrogenase, Enzyme Repression, Orotate Phosphoribosyltransferase/metabolism, Orotidine-5'-Phosphate Decarboxylase/metabolism, Oxidoreductases Acting on CH-CH Group Donors/metabolism, Pseudomonas/enzymology/genetics/*metabolism, Pyrimidines/*biosynthesis, Uracil/metabolismEnzymology
Phylogeny31751195Pseudomonas rhizoryzae sp. nov., isolated from rice.Wang X, He SW, Guo HB, Thin KK, Gao JS, Wang Y, Zhang XXInt J Syst Evol Microbiol10.1099/ijsem.0.0038522020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2845Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6835)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6835
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
33754Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14743
45739Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12540)https://www.ccug.se/strain?id=12540
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
82259Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2812.1StrainInfo: A central database for resolving microbial strain identifiers
121455Curators of the CIPCollection of Institut Pasteur (CIP 102996)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102996