Strain identifier

BacDive ID: 13077

Type strain: No

Species: Pseudomonas nitroreducens

Strain Designation: HBP1

Strain history: <- H.-P. E. Kohler; HBP1

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3432

BacDive-ID: 13077

DSM-Number: 8897

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Pseudomonas nitroreducens HBP1 is a mesophilic, motile bacterium that was isolated from sewage sludge.

NCBI tax id

NCBI tax idMatching level
1437882strain
46680species

strain history

  • @ref: 3432
  • history: <- H.-P. E. Kohler; HBP1

doi: 10.13145/bacdive13077.20230509.8.1

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 nitroreducens
  • full scientific name: Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Pseudomonas nitritireducens
    20215Pseudomonas multiresinivorans

@ref: 3432

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas nitroreducens

full scientific name: Pseudomonas nitroreducens Iizuka and Komagata 1964 emend. Lang et al. 2007

strain designation: HBP1

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes96.562
6948099.998negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3432MINERAL MEDIUM WITH 2-HYDROXYBIPHENYL (DSMZ Medium 465a)yeshttps://mediadive.dsmz.de/medium/465aName: MINERAL MEDIUM WITH 2-HYDROXYBIPHENYL (DSMZ Medium 465a) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l [1,1?-Biphenyl]-2-ol 0.5 g/l (NH4)2SO4 0.5 g/l MgCl2 x 6 H2O 0.1 g/l Ca(NO3)2 x 4 H2O 0.05 g/l EDTA 0.0005 g/l FeSO4 x 7 H2O 0.0002 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l MnCl2 x 4 H2O 3e-06 g/l Na2MoO4 x 2 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water
3432REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)yeshttps://mediadive.dsmz.de/medium/220aName: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

  • @ref: 3432
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.791

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
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
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
60262--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
60262+--+----+-----+++++++
3432+--+----+-----+++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3432sewage sludgeCaliforniaUSAUSANorth America
60262Sewage sludgeCaliforniaUSAUSANorth America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Sewage sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_295.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_203;97_221;98_250;99_295&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AM088479
  • Sequence Identity:
  • Total samples: 5736
  • soil counts: 862
  • aquatic counts: 2237
  • animal counts: 2039
  • plant counts: 598

Safety information

risk assessment

  • @ref: 3432
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Pseudomonas nitroreducens HBP1 partial 16S rRNA gene, strain DSM 8897
  • accession: AM088479
  • length: 1501
  • database: ena
  • NCBI tax ID: 1437882

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas nitroreducens HBP1GCA_011044415completencbi46680
66792Pseudomonas nitroreducens HBP1GCA_000518065contigncbi1437882
66792Pseudomonas nitroreducens HBP11437882.3wgspatric1437882
66792Pseudomonas nitroreducens HBP12579779010draftimg1437882

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.507no
flagellatedyes84.204no
gram-positiveno98.354no
anaerobicno97.186no
aerobicyes87.167no
halophileno85.932no
spore-formingno93.838no
thermophileno99.829yes
glucose-utilyes90.714no
glucose-fermentno90.678yes

External links

@ref: 3432

culture collection no.: CCUG 54620, DSM 8897

straininfo link

  • @ref: 82287
  • straininfo: 48545

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3432Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8897)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8897
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
60262Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54620)https://www.ccug.se/strain?id=54620
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)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82287Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48545.1StrainInfo: A central database for resolving microbial strain identifiers