Strain identifier

BacDive ID: 13108

Type strain: Yes

Species: Pseudomonas parafulva

Strain Designation: CB-1

Strain history: CIP <- 2002, JCM <- M. Uchino <- AJ 2127 <- H. Iizuka and K. Komagata: strain CB-1

NCBI tax ID(s): 1215114 (strain), 157782 (species)

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General

@ref: 6684

BacDive-ID: 13108

DSM-Number: 17004

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

description: Pseudomonas parafulva CB-1 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from Oryza sativa.

NCBI tax id

NCBI tax idMatching level
157782species
1215114strain

strain history

@refhistory
6684<- M. Uchino,Tokyo University of Agriculture; NRIC 0501
67770M. Uchino <-- AJ 2129 <-- H. Iizuka and K. Komagata CB-1.
121557CIP <- 2002, JCM <- M. Uchino <- AJ 2127 <- H. Iizuka and K. Komagata: strain CB-1

doi: 10.13145/bacdive13108.20230509.8.1

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 parafulva
  • full scientific name: Pseudomonas parafulva Uchino et al. 2002

@ref: 6684

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas parafulva

full scientific name: Pseudomonas parafulva Uchino et al. 2002

strain designation: CB-1

type strain: yes

Morphology

cell morphology

  • @ref: 121557
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 121557
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39907MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
6684NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
121557CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6684positivegrowth28mesophilic
39907positivegrowth30mesophilic
67770positivegrowth30mesophilic
121557positivegrowth10-37
121557nogrowth5psychrophilic
121557nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121557
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
121557NaClpositivegrowth0-4 %
121557NaClnogrowth6 %
121557NaClnogrowth8 %
121557NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836927897tryptophan-energy source
6836917632nitrate-reduction
12155716947citrate+carbon source
1215574853esculin-hydrolysis
12155717632nitrate-reduction
12155716301nitrite-reduction
12155717632nitrate-respiration

antibiotic resistance

  • @ref: 121557
  • 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
12155735581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
121557oxidase+
121557beta-galactosidase-3.2.1.23
121557alcohol dehydrogenase+1.1.1.1
121557gelatinase-
121557amylase-
121557DNase-
121557caseinase-3.4.21.50
121557catalase+1.11.1.6
121557tween esterase-
121557lecithinase-
121557lipase-
121557lysine decarboxylase-4.1.1.18
121557ornithine decarboxylase-4.1.1.17
121557protease-
121557tryptophan deaminase-
121557urease-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
121557--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6684---+----+-+---++-++++
6684--++----+-+---++-++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121557++--+--------------+-----------+-----+------+----++--+--+---+++++-----++++-+++++++-++---+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
6684Oryza sativaOryza sativaJapanJPNAsia
67770Japanese rice paddy
121557Food, Japanese rice paddyJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_278.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_203;99_278&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: LC507438
  • Sequence Identity:
  • Total samples: 250
  • soil counts: 47
  • aquatic counts: 36
  • animal counts: 93
  • plant counts: 74

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66841Risk group (German classification)
1215571Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas fulva gene for 16S rRNA, partial sequence, strain:AJ 2129AB0469961484ena47880
6684Pseudomonas parafulva gene for 16S rRNA, partial sequence, strain: AJ 2129AB0601321484ena1215114
67770Pseudomonas parafulva JCM 11244 gene for 16S ribosomal RNA, partial sequenceLC5074381459ena157782

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas parafulva DSM 170041292029.3wgspatric1215114
66792Pseudomonas parafulva NBRC 166361215114.3wgspatric1215114
66792Pseudomonas parafulva NBRC 166362585427683draftimg1215114
66792Pseudomonas parafulva DSM 170042523533547draftimg1215114
67770Pseudomonas parafulva NBRC 16636 = DSM 17004GCA_000425765scaffoldncbi1215114
67770Pseudomonas parafulva NBRC 16636 = DSM 17004GCA_000730645contigncbi1215114

GC content

  • @ref: 67770
  • GC-content: 60
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.947no
gram-positiveno98.497no
anaerobicno98.129no
aerobicyes94.768no
halophileno80.791no
spore-formingno94.943no
thermophileno99.849yes
glucose-utilyes93.067no
flagellatedyes81.697no
glucose-fermentno87.927no

External links

@ref: 6684

culture collection no.: DSM 17004, AJ 2129, IFO 16636, JCM 11244, NRIC 0501, BCRC 17511, CIP 107617, NBRC 16636

straininfo link

  • @ref: 82316
  • straininfo: 88072

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12483612Recharacterization of Pseudomonas fulva Iizuka and Komagata 1963, and proposals of Pseudomonas parafulva sp. nov. and Pseudomonas cremoricolorata sp. nov.Uchino M, Shida O, Uchimura T, Komagata KJ Gen Appl Microbiol10.2323/jgam.47.2472001
Phylogeny15774686Pseudomonas pachastrellae sp. nov., isolated from a marine sponge.Romanenko LA, Uchino M, Falsen E, Frolova GM, Zhukova NV, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.63176-02005Animals, Bacterial Typing Techniques, DNA, Bacterial, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, Porifera/*microbiology, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species SpecificityGenetics
Genetics27594974High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T) type strains.Pena A, Busquets A, Gomila M, Mulet M, Gomila RM, Reddy TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Garcia-Valdes E, Goker M, Woyke T, Klenk HP, Kyrpides N, Lalucat JStand Genomic Sci10.1186/s40793-016-0178-22016
Phylogeny31712900Pseudomonas jilinensis sp. nov., Isolated from Oil Production Water of Jilin Oilfield in China.Wang JW, Cai M, Nie Y, Hu B, Yang Y, Wu XLCurr Microbiol10.1007/s00284-019-01798-22019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6684Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17004)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17004
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
39907Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5073
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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
82316Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88072.1StrainInfo: A central database for resolving microbial strain identifiers
121557Curators of the CIPCollection of Institut Pasteur (CIP 107617)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107617