Strain identifier

BacDive ID: 164374

Type strain: Yes

Species: Stutzerimonas urumqiensis

Strain Designation: T3

Strain history: Y. Zou; Biotechnol. Res. Inst., CAAS, China; T3.

NCBI tax ID(s): 638269 (species)

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General

@ref: 67770

BacDive-ID: 164374

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, other, colony-forming

description: Stutzerimonas urumqiensis T3 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Rhizosphere soil of Alhagi sparsifolia collected from Xinjiang.

NCBI tax id

  • NCBI tax id: 638269
  • Matching level: species

strain history

  • @ref: 67770
  • history: Y. Zou; Biotechnol. Res. Inst., CAAS, China; T3.

doi: 10.13145/bacdive164374.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Stutzerimonas
  • species: Stutzerimonas urumqiensis
  • full scientific name: Stutzerimonas urumqiensis (Zou et al. 2019) Gomila et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas urumqiensis

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas urumqiensis

full scientific name: Pseudomonas urumqiensis Zou et al. 2019

strain designation: T3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
67888negative1.5-2.3 µm0.8-1.2 µmotheryes
125438negative100

colony morphology

  • @ref: 67888
  • colony color: yellow
  • colony shape: circular
  • medium used: LB (Luria-Bertani) agar

Culture and growth conditions

culture temp

@refgrowthtypetemperature
67770positivegrowth28
67888positivegrowth15-42
67888positiveoptimum30

culture pH

@refabilitytypepHPH range
67888positivegrowth4-9alkaliphile
67888positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 125438
  • oxygen tolerance: aerobe
  • confidence: 91.568

halophily

@refsaltgrowthtested relationconcentration
67888NaClpositivegrowth1-6 %(w/v)
67888NaClpositiveoptimum1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6788817632nitrate+reduction
678884853esculin+hydrolysis
6788823652dextrin+carbon source
6788853423tween 40+carbon source
6788817306maltose+carbon source
6788817464L-galactonic acid gamma-lactone+carbon source
678888391D-gluconate+carbon source
6788815748D-glucuronate+carbon source
6788816537galactarate+carbon source
6788830612D-glucarate+carbon source
6788815588D-malate+carbon source
67888370543-hydroxybutyrate+carbon source
67888167632-oxobutanoate-carbon source
6788813705acetoacetate+carbon source
6788832323glucuronamide-carbon source
6788816551D-trehalose-carbon source
6788817057cellobiose-carbon source
6788828066gentiobiose-carbon source
6788817992sucrose-carbon source
6788832528turanose-carbon source
6788817164stachyose-carbon source
6788816634raffinose-carbon source
6788836219alpha-lactose-carbon source
6788828053melibiose-carbon source
67888320055methyl beta-D-glucopyranoside-carbon source
6788817814salicin-carbon source
6788859640N-acetylglucosamine-carbon source
6788863153N-acetyl-D-mannosamine-carbon source
6788828800N-acetylgalactosamine-carbon source
6788835418n-acetylneuraminate-carbon source
6788817925alpha-D-glucose+carbon source
6788816024D-mannose-carbon source
6788815824D-fructose-carbon source
6788812936D-galactose-carbon source
67888739183-O-methyl-D-glucose-carbon source
6788828847D-fucose-carbon source
6788818287L-fucose-carbon source
6788862345L-rhamnose-carbon source
6788817596inosine-carbon source
6788817924D-sorbitol-carbon source
6788816899D-mannitol-carbon source
6788818333D-arabitol+carbon source
6788817268myo-inositol-carbon source
6788817754glycerol-carbon source
6788814314D-glucose 6-phosphate-carbon source
6788878697D-fructose 6-phosphate-carbon source
6788829990D-aspartate-carbon source
6788816523D-serine-carbon source
678885291gelatin-carbon source
6788870744glycine-proline-carbon source
6788816977L-alanine-carbon source
6788816467L-arginine-carbon source
6788829991L-aspartate-carbon source
6788829988L-glutamate+carbon source
6788815971L-histidine-carbon source
6788857606L-pyroglutamate-carbon source
6788817115L-serine-carbon source
6788817309pectin-carbon source
6788818024D-galacturonic acid-carbon source
6788826490quinate-carbon source
67888181014-hydroxyphenylacetic acid-carbon source
6788851850methyl pyruvate-carbon source
6788874611methyl (R)-lactate+carbon source
6788816651(S)-lactate+carbon source
6788816947citrate-carbon source
67888168102-oxoglutarate+carbon source
6788815589L-malate+carbon source
6788873706bromosuccinate+carbon source
6788816865gamma-aminobutyric acid-carbon source
67888645522-hydroxybutyrate+carbon source
6788817272propionate-carbon source
6788830089acetate+carbon source
6788815740formate-carbon source
6788816024D-mannose+assimilation
6788817634D-glucose+assimilation
6788830849L-arabinose-assimilation
6788816899D-mannitol+assimilation
6788859640N-acetylglucosamine-assimilation
6788817306maltose+assimilation
6788832032potassium gluconate+assimilation
6788827689decanoate-assimilation
6788817128adipate-assimilation
6788825115malate+assimilation
6788853258sodium citrate-assimilation
6788818401phenylacetate-assimilation
6788817634D-glucose-builds acid from
6788816467L-arginine-hydrolysis
6788816199urea-hydrolysis
678885291gelatin-hydrolysis
678883557154-nitrophenyl beta-D-galactopyranoside-hydrolysis

metabolite production

  • @ref: 67888
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
67888catalase+1.11.1.6
67888cytochrome oxidase+1.9.3.1
67888alkaline phosphatase+3.1.3.1
67888esterase (C 4)+
67888esterase Lipase (C 8)+
67888lipase (C 14)-
67888valine arylamidase+
67888cystine arylamidase+3.4.11.3
67888trypsin-3.4.21.4
67888leucine arylamidase+3.4.11.1
67888alpha-chymotrypsin-3.4.21.1
67888alpha-galactosidase-3.2.1.22
67888beta-galactosidase-3.2.1.23
67888beta-glucuronidase-3.2.1.31
67888beta-glucosidase-3.2.1.21
67888alpha-glucosidase+3.2.1.20
67888N-acetyl-beta-glucosaminidase-3.2.1.52
67888alpha-fucosidase-3.2.1.51
67888alpha-mannosidase-3.2.1.24
67888naphthol-AS-BI-phosphohydrolase+
67888acid phosphatase+3.1.3.2

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    67888C12:07.8
    67888C16:015.6
    67888C10:0 3OH3
    67888C12:0 3OH2.6
    67888C16:1 w6c/C16:1 w7c28.2
    67888C18:1 w6c and/or C18:1w7c37.7
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dategeographic locationenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
67770Rhizosphere soil of Alhagi sparsifolia collected from XinjiangAlhagi sparsifoliaChinaCHNAsia
67888rhizosphere soil of Alhagi sparsifoliaChinaCHNAsia2017-10-29Xinjiangmodified Döbereiner medium10 g sucrose; 5 g malic acid; 0.4 g KH2PO4 x H2O; 0.1 g, K2HPO4 x H2O; 0.2 g, MgSO4 x 7H2O; 0.1 g, NaCl; 0.02 g CaCl2 x 2H2O; 0.01 g FeCl3 x 6H2O; 0.002 g Na2MoO4 x H2O; 15 g agar powder; 1000 ml distilled water; pH 7.0-7.23 days28soil sample (10 g) collected was added to 100 ml sterile water and shaken with glass beads at room temperature for 15 min, followed by standing for 1 h. Supernatant was ten-fold diluted serially. Each diluted sample (100 µl) was separately spread on modified Döbereiner medium.

Sequence information

16S sequences

  • @ref: 67888
  • description: Stutzerimonas urumqiensis 16S ribosomal RNA gene, partial sequence
  • accession: MH355542
  • length: 1497
  • database: nuccore
  • NCBI tax ID: 638269

Genome sequences

  • @ref: 67770
  • description: [Pseudomonas] urumqiensis T3
  • accession: GCA_003640395
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 638269

GC content

  • @ref: 67888
  • GC-content: 65.3
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno100yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.91no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.568no
125438spore-formingspore-formingAbility to form endo- or exosporesno88.284no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.75yes
125438motile2+flagellatedAbility to perform flagellated movementyes87.927no

External links

@ref: 67770

culture collection no.: JCM 32830, ACCC 60124

literature

  • topic: Phylogeny
  • Pubmed-ID: 30950783
  • title: Pseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia.
  • authors: Zou Y, He S, Sun Y, Zhang X, Liu Y, Cheng Q
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003390
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67888Yuanyuan Zou, Shanwen He, Yuping Sun, Xiaoxia Zhang, Yang Liu, Qi ChengPseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia10.1099/ijsem.0.003390IJSEM 69: 1760-1766 2019
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695