Strain identifier

BacDive ID: 13080

Type strain: Yes

Species: Pseudomonas nitroreducens

Strain Designation: KS 0050, P-6

Strain history: CIP <- 2000, IAM <- S. Ikemoto: strain AJ 2282

NCBI tax ID(s): 1215112 (strain), 46680 (species)

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General

@ref: 5336

BacDive-ID: 13080

DSM-Number: 14399

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

description: Pseudomonas nitroreducens KS 0050 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oil-brine.

NCBI tax id

NCBI tax idMatching level
46680species
1215112strain

strain history

@refhistory
5336<- JCM <- K. Komagata; KS 0050 <- AJ <- IAM <- H. Iizuka and K. Komagata; P-6
67770K. Komagata KS 0050 <-- AJ 2282 <-- IAM 1439 <-- H. Iizuka and K. Komagata P-6.
121316CIP <- 2000, IAM <- S. Ikemoto: strain AJ 2282

doi: 10.13145/bacdive13080.20230509.8.1

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: 5336

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: KS 0050, P-6

type strain: yes

Morphology

cell morphology

  • @ref: 121316
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 121316
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5336CASO 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
40575MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121316CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5336positivegrowth28mesophilic
40575positivegrowth25mesophilic
45737positivegrowth22-42
67770positivegrowth30mesophilic
121316positivegrowth5-37
121316nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
45737aerobe
121316obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
121316NaClpositivegrowth0-8 %
121316NaClnogrowth10 %

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
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12131616947citrate+carbon source
1213164853esculin-hydrolysis
12131617632nitrate+reduction
12131616301nitrite+reduction
12131617632nitrate+respiration

antibiotic resistance

  • @ref: 121316
  • 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
12131635581indoleno

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
121316oxidase+
121316beta-galactosidase-3.2.1.23
121316alcohol dehydrogenase+1.1.1.1
121316gelatinase-
121316amylase-
121316DNase-
121316caseinase-3.4.21.50
121316catalase+1.11.1.6
121316tween esterase-
121316lecithinase-
121316lipase-
121316lysine decarboxylase-4.1.1.18
121316ornithine decarboxylase-4.1.1.17
121316protease-
121316tryptophan deaminase-
121316urease-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
121316-++++++-+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5336+--+----+-----+++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121316++----------------------------------------------++++++------+++++--+---+++++++-+++-+++-+++++++--+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
5336oil-brineJapanJPNAsia
45737Oil brineJapanJPNAsiaTokyo
67770Oil brineJapanJPNAsia
121316Oil brineJapanJPNAsia1957

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Condition#Saline

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: AM088474
  • Sequence Identity:
  • Total samples: 5736
  • soil counts: 862
  • aquatic counts: 2237
  • animal counts: 2039
  • plant counts: 598

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53361Risk group (German classification)
1213161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas nitroreducens partial 16S rRNA gene, type strain IAM 1439AM0884731523ena46680
20218Pseudomonas nitroreducens 16S rRNA geneD840211370ena46680
20218Pseudomonas nitroreducens gene for 16S rRNA, partial sequence, strain: NBRC 12694AB6803231462ena46680
5336Pseudomonas nitroreducens partial 16S rRNA gene, type strain: DSM 14399AM0884741521ena46680

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas nitroreducens NBRC 12694 strain NBRC 126941215112.3wgspatric1215112
66792Pseudomonas nitroreducens strain DSM 1439946680.53wgspatric46680
66792Pseudomonas nitroreducens strain LMG 2161446680.17wgspatric46680
66792Pseudomonas nitroreducens LMG 216142671180175draftimg46680
67770Pseudomonas nitroreducens NBRC 12694GCA_002091755contigncbi1215112
67770Pseudomonas nitroreducens LMG 21614GCA_900188285scaffoldncbi46680
67770Pseudomonas nitroreducens DSM 14399GCA_012986245contigncbi46680

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes92.85no
gram-positiveno98.334no
anaerobicno98.037yes
aerobicyes88.779yes
halophileno82.002no
spore-formingno94.433no
thermophileno99.782yes
glucose-utilyes91.953yes
flagellatedyes89.617no
glucose-fermentno90.035no

External links

@ref: 5336

culture collection no.: DSM 14399, ATCC 33634, IAM 1439, JCM 2782, CCUG 12538, IFO 12694, AJ 2282, CGMCC 1.1796, CIP 106747, LMG 21614, MTCC 7932, NBRC 12694

straininfo link

  • @ref: 82290
  • straininfo: 46760

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656147Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea.Kwon SW, Kim JS, Park IC, Yoon SH, Park DH, Lim CK, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.02326-02003Agriculture, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics
Phylogeny17329778Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant.Prakash O, Kumari K, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.64456-02007Acyclic Monoterpenes, *Carbon, Coal Ash, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, India, Molecular Sequence Data, Monoterpenes/metabolism, *Particulate Matter, Phenanthrenes/metabolism, Phylogeny, *Power Plants, Pseudomonas/*classification/genetics/isolation & purification/metabolism, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny17329787Pseudomonas knackmussii sp. nov.Stolz A, Busse HJ, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.64761-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Pseudomonas/chemistry/*classification/genetics/physiology, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18523175Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site.Gupta SK, Kumari R, Prakash O, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.65401-02008Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species SpecificityGenetics
Enzymology20834145Molecular cloning and characterization of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens IFO12694.Imaoka M, Yano S, Okumura M, Hibi T, Wakayama MBiosci Biotechnol Biochem10.1271/bbb.1001992010Amines/metabolism, Amino Acids, Catalysis, Cloning, Molecular/*methods, Hydrolysis, Pseudomonas/*enzymology, Substrate Specificity, *gamma-Glutamyltransferase/chemistry/genetics/metabolismMetabolism
Phylogeny22918457Pseudomonas nitritireducens sp. nov., a nitrite reduction bacterium isolated from wheat soil.Wang YN, He WH, He H, Du X, Jia B, Zeng ZP, An ML, Chen GCArch Microbiol10.1007/s00203-012-0838-62012Base Composition, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/*genetics/isolation & purification/ultrastructure, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity, TriticumGenetics
Metabolism24867376Pyrimidine nucleotide synthesis in Pseudomonas nitroreducens and the regulatory role of pyrimidines.West TPMicrobiol Res10.1016/j.micres.2014.04.0032014Aspartate Carbamoyltransferase/metabolism, Pseudomonas/*metabolism, Pyrimidine Nucleotides/*biosynthesis, Pyrimidines/*biosynthesis
Enzymology27299717Purification and Some Properties of Glutaminase from Pseudomonas nitroreducens IFO 12694.Takashi T, Takeshi Y, Masashi U, Yasuki N, Nobuo I, Yu-Ichi H, Ju-Ichi SBiosci Biotechnol Biochem10.1271/bbb.60.11601996
27396994gamma-Glutamyl Transfer Reactions by Glutaminase from Pseudomonas nitroreducens IFO 12694 and Their Application for the Syntheses of Theanine and gamma-Glutamylmethylamide.Tachiki T, Yamada T, Mizuno K, Ueda M, Shiode J, Fukami HBiosci Biotechnol Biochem10.1271/bbb.62.12791998
Metabolism30507352Crystal structure analysis and enzymatic characterization of gamma-glutamyltranspeptidase from Pseudomonas nitroreducens.Hibi T, Imaoka M, Shimizu Y, Itoh T, Wakayama MBiosci Biotechnol Biochem10.1080/09168451.2018.15471042018Amino Acid Sequence, Amino Acids/metabolism, Bacterial Proteins/*chemistry/genetics/*metabolism, Catalytic Domain, Crystallography, X-Ray/*methods, Hydrolysis, Mutagenesis, Site-Directed, Protein Conformation, Pseudomonas/*enzymology, Sequence Homology, Amino Acid, Substrate Specificity, gamma-Glutamyltransferase/*chemistry/genetics/*metabolismEnzymology
Phylogeny33411665Pseudomonas nicosulfuronedens sp. nov., a nicosulfuron degrading bacterium, isolated from a microbial consortium.Li M, Ma Q, Kong D, Han X, Che J, Zhou Y, Jiang X, Ruan Z, Zhang QInt J Syst Evol Microbiol10.1099/ijsem.0.0046322021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, *Microbial Consortia, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, Pyridines/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfonylurea Compounds/*metabolism, Ubiquinone/chemistryMetabolism
Genetics35547011Whole genome sequencing and phylogenomic analyses of a novel glufosinate-tolerant Pseudomonas species.Wee WY, Chew XY, Taheri S, Tan XL, Teo CH3 Biotech10.1007/s13205-022-03185-42022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5336Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14399)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14399
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
40575Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18912
45737Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12538)https://www.ccug.se/strain?id=12538
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
82290Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46760.1StrainInfo: A central database for resolving microbial strain identifiers
121316Curators of the CIPCollection of Institut Pasteur (CIP 106747)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106747