Strain identifier

BacDive ID: 13096

Type strain: Yes

Species: Pseudomonas rhizosphaerae

Strain Designation: IH5

Strain history: CIP <- 2004, CECT <- A. Peix, CSIC, Salamanca, Spain: strain IH5

NCBI tax ID(s): 216142 (species)

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General

@ref: 6349

BacDive-ID: 13096

DSM-Number: 16299

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

description: Pseudomonas rhizosphaerae IH5 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of grasses.

NCBI tax id

  • NCBI tax id: 216142
  • Matching level: species

strain history

@refhistory
6349<- E. Velázquez; IH5 <- A. Peix
122211CIP <- 2004, CECT <- A. Peix, CSIC, Salamanca, Spain: strain IH5

doi: 10.13145/bacdive13096.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas rhizosphaerae
  • full scientific name: Pseudomonas rhizosphaerae Peix et al. 2003

@ref: 6349

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas rhizosphaerae

full scientific name: Pseudomonas rhizosphaerae Peix et al. 2003

strain designation: IH5

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122211negativerod-shapedyes
125439negative98.8
125438negative99

pigmentation

  • @ref: 122211
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6349NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
32908MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122211CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122211CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
6349positivegrowth25
32908positivegrowth30
122211positivegrowth5-30
122211nogrowth37
122211nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
122211obligate aerobe
125438aerobe91.028

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.3

halophily

@refsaltgrowthtested relationconcentration
122211NaClpositivegrowth0-6 %
122211NaClnogrowth8 %
122211NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12221116947citrate-carbon source
1222114853esculin-hydrolysis
12221117632nitrate-reduction
12221116301nitrite-reduction
12221117632nitrate-respiration
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
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

  • @ref: 122211
  • 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
12221135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
122211oxidase-
122211beta-galactosidase-3.2.1.23
122211alcohol dehydrogenase-1.1.1.1
122211gelatinase-
122211amylase+
122211DNase-
122211caseinase-3.4.21.50
122211catalase+1.11.1.6
122211tween esterase-
122211lecithinase-
122211lipase-
122211lysine decarboxylase-4.1.1.18
122211ornithine decarboxylase-4.1.1.17
122211protease-
122211tryptophan deaminase-
122211urease-3.5.1.5
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122211--++-++---++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6349--------++++--++-++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122211+++-+--------------++-----+----+-+--+------++--+++++-++++---+-+++-----++-+-+++-+++-+---+-++++++-+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6349rhizosphere of grassesSalamancaSpainESPEurope
59228Rhizosphere of grassesSalamancaSpainESPEurope1997
122211Environment, SoilSalamancaSpainESPEurope1997

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63491Risk group (German classification)
1222111Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6349
  • description: Pseudomonas rhizosphaerae 16S ribosomal RNA gene, complete sequence
  • accession: AY152673
  • length: 1531
  • database: nuccore
  • NCBI tax ID: 216142

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas rhizosphaerae DSM 16299GCA_000761155completencbi216142
66792Pseudomonas rhizosphaerae DSM 16299216142.3completepatric216142

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.84yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.028yes
125438spore-formingspore-formingAbility to form endo- or exosporesno83.045no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98yes
125438motile2+flagellatedAbility to perform flagellated movementyes86.193no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.3
125439BacteriaNetmotilityAbility to perform movementyes82.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe86.7

External links

@ref: 6349

culture collection no.: CCUG 51518, CIP 108243, DSM 16299, CECT 5726, LMG 21640

straininfo link

  • @ref: 82306
  • straininfo: 87494

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657147Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro.Peix A, Rivas R, Mateos PF, Martinez-Molina E, Rodriguez-Barrueco C, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.02703-02003Base Composition, Burkholderia/classification, Catalase/metabolism, Molecular Sequence Data, Phosphates/*metabolism, *Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/metabolism, RNA, Bacterial/chemistry/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny15143034Pseudomonas lutea sp. nov., a novel phosphate-solubilizing bacterium isolated from the rhizosphere of grasses.Peix A, Rivas R, Santa-Regina I, Mateos PF, Martinez-Molina E, Rodriguez-Barrueco C, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.02966-02004Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phosphates/metabolism, Phylogeny, Poaceae/microbiology, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Solubility, SpainGenetics
Genetics25483321Complete genome sequence of Pseudomonas rhizosphaerae IH5T (=DSM 16299T), a phosphate-solubilizing rhizobacterium for bacterial biofertilizer.Kwak Y, Jung BK, Shin JHJ Biotechnol10.1016/j.jbiotec.2014.11.0312014*Biofuels, Bioreactors/microbiology, Genome, Bacterial/*genetics, Hydrolysis, Molecular Sequence Data, Phosphates, Pseudomonas/*genetics/*metabolism, Sequence Analysis, DNA, SewageTranscriptome
Phylogeny33620302Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov., isolated from raw milk in Germany.Gieschler S, Fiedler G, Bohnlein C, Grimmler C, Franz CMAP, Kabisch JInt J Syst Evol Microbiol10.1099/ijsem.0.0047172021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6349Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16299)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16299
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
32908Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5844
59228Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51518)https://www.ccug.se/strain?id=51518
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
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
82306Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87494.1StrainInfo: A central database for resolving microbial strain identifiers
122211Curators of the CIPCollection of Institut Pasteur (CIP 108243)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108243
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1