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Strain identifier

BacDive ID: 13001

Type strain: No

Species: Pseudomonas stutzeri

Strain Designation: JM300

Strain history: IAM 15110 <-- DSM 10701 <-- E. Moore <-- G. J. Stewart <-- B. A. Bryan.

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

@ref: 4044

BacDive-ID: 13001

DSM-Number: 10701

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, human pathogen

description: Pseudomonas stutzeri JM300 is a mesophilic human pathogen that was isolated from anaerobic enrichment from soil.

NCBI tax id

NCBI tax idMatching level
1123519strain
203192species
316species

strain history

doi: 10.13145/bacdive13001.20221219.7.1

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 stutzeri
  • full scientific name: Pseudomonas stutzeri (Lehmann and Neumann 1896) Sijderius 1946 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Stutzerimonas chloritidismutans
    20215Pseudomonas perfectomarinus
    20215Bacterium stutzeri
    20215Pseudomonas kunmingensis
    20215Pseudomonas chloritidismutans
    20215Stutzerimonas kunmingensis
    20215Stutzerimonas stutzeri
    20215Stutzerimonas perfectomarina
    20215Pseudomonas perfectomarina

@ref: 4044

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas stutzeri

full scientific name: Pseudomonas stutzeri (Lehmann and Neumann 1896) Sijderius 1946

strain designation: JM300

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes93.617
6948099.659negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4044TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 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
4044TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
4044CASO 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

culture temp

@refgrowthtypetemperaturerange
4044positivegrowth28mesophilic
4044positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 97.561

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 87.223

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4044+-------+-++-+++-++-+
4044+-------+-++-+++-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4044anaerobic enrichment from soilCaliforniaUSAUSANorth America
67770SoilCAUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Terrestrial#Soil
#Condition#Anoxic (anaerobic)

Safety information

risk assessment

  • @ref: 4044
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas stutzeri 16S rRNA gene, partial sequenceU586611344ena316
20218P.stutzeri 16S ribosomal RNA geneX986071492ena316

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas stutzeri DSM 10701 DSM 10701GCA_000279165completencbi1123519
66792Pseudomonas stutzeri DSM 107011123519.7completepatric1123519
66792Pseudomonas stutzeri JM3000, DSM 107012519899778completeimg1123519
66792Acinetobacter baumannii 1032241 1032241GCA_000580455contigpatric1310571

External links

@ref: 4044

culture collection no.: DSM 10701, JCM 21571, IAM 15110

straininfo link

@refpassport
20218http://www.straininfo.net/strains/162124
20218http://www.straininfo.net/strains/162125

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology1539983Isolation and characterization of a nitrite reductase gene and its use as a probe for denitrifying bacteria.Smith GB, Tiedje JMAppl Environ Microbiol10.1128/aem.58.1.376-384.19921992Amino Acid Sequence, Bacteria/isolation & purification/metabolism, Base Sequence, Blotting, Southern, *DNA Probes, DNA, Bacterial, Molecular Sequence Data, Nitrate Reductase, Nitrate Reductases/*genetics/isolation & purification/metabolism, Nitrates/metabolism, Polymerase Chain Reaction, Pseudomonas/*enzymology/genetics, Restriction Mapping, Sequence AlignmentPhylogeny
Enzymology1850410Purification of cytochrome cd1 nitrite reductase from Pseudomonas stutzeri JM300 and reconstitution with native and synthetic heme d1.Weeg-Aerssens E, Wu WS, Ye RW, Tiedje JM, Chang CKJ Biol ChemS0021-9258(20)89474-51991Amino Acid Sequence, Cells, Cultured, Cytochromes, Electron Transport Complex IV/*isolation & purification, Electrophoresis, Polyacrylamide Gel, Heme/*analogs & derivatives/chemistry, Molecular Sequence Data, Molecular Weight, Nitric Oxide/metabolism, *Nitrite Reductases, Nitrous Oxide/metabolism, Protein Conformation, Pseudomonas/*enzymology, Sequence Homology, Nucleic Acid, Spectrophotometry, UltravioletGenetics
Metabolism2059008Exchange of chromosomal markers by natural transformation between the soil isolate, Pseudomonas stutzeri JM300, and the marine isolate, Pseudomonas stutzeri strain ZoBell.Stewart GJ, Sinigalliano CDAntonie Van Leeuwenhoek10.1007/BF005821151991Deoxyribonuclease I/metabolism, Drug Resistance, Microbial/genetics, Genes, Bacterial, *Genetic Markers, Nalidixic Acid/pharmacology, Pseudomonas/*genetics, Rifampin/pharmacology, Streptomycin/pharmacology, *Transformation, Bacterial
Metabolism2365685Steady-state nitric oxide concentrations during denitrification.Goretski J, Zafiriou OC, Hollocher TCJ Biol ChemS0021-9258(19)38430-31990Alcaligenes/*metabolism, Anaerobiosis, Asparagine/metabolism, Kinetics, Nitrates/*metabolism, Nitric Oxide/*metabolism, Nitrites/*metabolism, Paracoccus denitrificans/*metabolism, Pseudomonas/*metabolism, Species SpecificityEnzymology
Enzymology7747927Isolation, sequencing and mutational analysis of a gene cluster involved in nitrite reduction in Paracoccus denitrificans.de Boer AP, Reijnders WN, Kuenen JG, Stouthamer AH, van Spanning RJAntonie Van Leeuwenhoek10.1007/BF008716351994Amino Acid Sequence, Base Sequence, Cloning, Molecular, Frameshift Mutation/genetics, Gene Expression Regulation, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, *Multigene Family, Nitrite Reductases/chemistry/*genetics, Nitrites/*metabolism, Oxidation-Reduction, Paracoccus denitrificans/enzymology/*genetics, Pyrroles/chemistry, Sequence Alignment, Sequence Homology, Amino Acid, TetrapyrrolesGenetics
7961508Inducible cell lysis system for the study of natural transformation and environmental fate of DNA released by cell death.Kloos DU, Stratz M, Guttler A, Steffan RJ, Timmis KNJ Bacteriol10.1128/jb.176.23.7352-7361.19941994Acinetobacter calcoaceticus/genetics, Bacteriolysis/genetics, DNA, Bacterial/*genetics, *Environmental Microbiology, Escherichia coli/genetics, Gram-Negative Bacteria/*genetics, Plasmids/genetics, Pseudomonas/genetics, *Transformation, Genetic
Enzymology8169201Structure and regulation of the carAB operon in Pseudomonas aeruginosa and Pseudomonas stutzeri: no untranslated region exists.Kwon DH, Lu CD, Walthall DA, Brown TM, Houghton JE, Abdelal ATJ Bacteriol10.1128/jb.176.9.2532-2542.19941994Amino Acid Sequence, Base Sequence, Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/biosynthesis/*genetics, Cloning, Molecular, DNA Mutational Analysis, *Gene Expression Regulation, Bacterial, Molecular Sequence Data, Operon/*genetics, *Protein Biosynthesis, Pseudomonas/enzymology/*genetics, Pseudomonas aeruginosa/enzymology/genetics, RNA, Messenger/metabolism, Recombinant Fusion Proteins/biosynthesis, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, Transcription, GeneticGenetics
Enzymology8439151Characterization of the structural gene encoding a copper-containing nitrite reductase and homology of this gene to DNA of other denitrifiers.Ye RW, Fries MR, Bezborodnikov SG, Averill BA, Tiedje JMAppl Environ Microbiol10.1128/aem.59.1.250-254.19931993Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics, Base Sequence, Copper/*chemistry, DNA, Bacterial/chemistry/*isolation & purification, *Genes, Bacterial, Molecular Sequence Data, Nitrite Reductases/*genetics/isolation & purification/physiology, Nitrites/*metabolism, Pseudomonas/chemistry/enzymology/genetics, Sequence Homology, Nucleic Acid, Species SpecificityPhylogeny
Phylogeny8875907The naturally transformable marine bacterium WJT-1C formally identified as "Vibrio" is a pseudomonad.Frischer ME, Williams HG, Bennison B, Drake GR, Balkwill DL, Paul JHCurr Microbiol10.1007/s0028499001151996Bacteriophage Typing, Carbon/metabolism, Fatty Acids/analysis, Flagella/chemistry, Phylogeny, Pseudomonas/*classification, RNA, Ribosomal, 16S/analysis, Staining and Labeling, Transformation, Bacterial, Vibrio/*chemistry/classification, Water MicrobiologyMetabolism
Phylogeny8995815Genome organization of Pseudomonas stutzeri and resulting taxonomic and evolutionary considerations.Ginard M, Lalucat J, Tummler B, Romling UInt J Syst Bacteriol10.1099/00207713-47-1-1321997Blotting, Southern, Chromosome Mapping, Chromosomes/genetics, DNA, Bacterial/analysis, Electrophoresis, Gel, Pulsed-Field, Genes, Bacterial, *Genome, Bacterial, Nucleic Acid Hybridization, Operon/genetics, Plasmids, Polymorphism, Restriction Fragment Length, Pseudomonas/*classification/*genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, *Restriction MappingEnzymology
Metabolism9493393Natural genetic transformation of Pseudomonas stutzeri in a non-sterile soil.Sikorski J, Graupner S, Lorenz MG, Wackernagel WMicrobiology (Reading)10.1099/00221287-144-2-5691998DNA, Bacterial/analysis/*genetics/metabolism, Deoxyribonuclease I/pharmacology, Deoxyribonucleases/metabolism, Histidine/genetics, Molecular Sequence Data, Plasmids/analysis/*genetics/metabolism, Pseudomonas/*genetics, Soil Microbiology, *Transformation, GeneticGenetics
Genetics10735861Type IV pilus genes pilA and pilC of Pseudomonas stutzeri are required for natural genetic transformation, and pilA can be replaced by corresponding genes from nontransformable species.Graupner S, Frey V, Hashemi R, Lorenz MG, Brandes G, Wackernagel WJ Bacteriol10.1128/JB.182.8.2184-2190.20002000Bacterial Proteins/*genetics, Biological Transport, DNA, Bacterial/metabolism, DNA-Binding Proteins/*genetics, *Endopeptidases, Fimbriae Proteins, Genes, Bacterial, Genetic Complementation Test, Membrane Proteins/genetics, Molecular Sequence Data, Mutation, Open Reading Frames, *Oxidoreductases, Pili, Sex/*genetics, Pseudomonas/*genetics, *Transformation, BacterialMetabolism
Genetics11101666The potential for intraspecific horizontal gene exchange by natural genetic transformation: sexual isolation among genomovars of Pseudomonas stutzeri.Lorenz MG, Sikorski JMicrobiology (Reading)10.1099/00221287-146-12-30812000*Conjugation, Genetic/genetics, DNA, Bacterial/analysis/genetics, DNA-Directed RNA Polymerases/*genetics, *Gene Transfer, Horizontal, Genotype, Humans, Molecular Sequence Data, Phylogeny, Pseudomonas/classification/*genetics/physiology, Sequence Analysis, DNA, *Transformation, BacterialPhylogeny
Enzymology11790331Cyclohexadienyl dehydrogenase from Pseudomonas stutzeri exemplifies a widespread type of tyrosine-pathway dehydrogenase in the TyrA protein family.Xie G, Bonner CA, Jensen RAComp Biochem Physiol C Toxicol Pharmacol10.1016/s0742-8413(99)00090-02000Amino Acid Sequence, Bacterial Proteins/genetics/*metabolism, Base Sequence, Catalysis, Chromatography, DEAE-Cellulose, Chromatography, Ion Exchange, Cloning, Molecular, Culture Media, DNA, Bacterial/genetics, Durapatite, Electrophoresis, Polyacrylamide Gel, Molecular Sequence Data, Molecular Weight, *Multienzyme Complexes, Plasmids/genetics, Prephenate Dehydrogenase/genetics/*metabolism, Pseudomonas/*enzymology/geneticsMetabolism
Metabolism12686632DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300.Berndt C, Meier P, Wackernagel WMicrobiology (Reading)10.1099/mic.0.26033-02003DNA Restriction-Modification Enzymes/genetics/*metabolism, DNA, Bacterial/metabolism, DNA, Single-Stranded/metabolism, Electroporation, Escherichia coli/genetics, Genetic Vectors, Humans, Mutation, Plasmids, Pseudomonas/enzymology/*genetics, Recombination, Genetic, Restriction Mapping, *Transformation, BacterialEnzymology
15601698Impact of mutS inactivation on foreign DNA acquisition by natural transformation in Pseudomonas stutzeri.Meier P, Wackernagel WJ Bacteriol10.1128/JB.187.1.143-154.20052005Adenosine Triphosphatases/chemistry/*physiology, Bacterial Proteins/chemistry/*physiology, *Base Pair Mismatch, *DNA Repair, DNA-Binding Proteins/chemistry/*physiology, Escherichia coli Proteins, MutS DNA Mismatch-Binding Protein, Plasmids, Pseudomonas stutzeri/*genetics, Recombination, Genetic, *Transformation, Bacterial
Metabolism15635461Posttranslational modification of myxobacterial carrier protein domains in Pseudomonas sp. by an intrinsic phosphopantetheinyl transferase.Gross F, Gottschalk D, Muller RAppl Microbiol Biotechnol10.1007/s00253-004-1836-72005Amino Acid Sequence, Bacterial Proteins/chemistry/*metabolism, Carrier Proteins/*metabolism, Fatty Acid Synthases/metabolism, Molecular Sequence Data, Myxococcales/*metabolism, Peptide Synthases/metabolism, Polyketide Synthases/metabolism, *Protein Processing, Post-Translational, Pseudomonas/*enzymology, Recombinant Proteins/metabolism, Sequence Alignment, Sequence Homology, Amino Acid, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Transferases (Other Substituted Phosphate Groups)/chemistry/*metabolismGenetics
Genetics22965097Genome sequence of Pseudomonas stutzeri strain JM300 (DSM 10701), a soil isolate and model organism for natural transformation.Busquets A, Pena A, Gomila M, Bosch R, Nogales B, Garcia-Valdes E, Lalucat J, Bennasar AJ Bacteriol10.1128/JB.01257-122012*Genome, Bacterial, Molecular Sequence Data, Pseudomonas stutzeri/*genetics, *Soil Microbiology, *Transformation, Genetic
Metabolism29752987Expression of nirK and nirS genes in two strains of Pseudomonas stutzeri harbouring both types of NO-forming nitrite reductases.Wittorf L, Jones CM, Bonilla-Rosso G, Hallin SRes Microbiol10.1016/j.resmic.2018.04.0102018Cytochromes/*genetics/*metabolism, Denitrification/genetics/*physiology, Gene Expression Regulation/*genetics, Nitrates/chemistry, Nitric Oxide/*biosynthesis, Nitrite Reductases/*genetics/*metabolism, Nitrites/chemistry, Oxidation-Reduction, Oxygen/chemistry, Pseudomonas stutzeri/*genetics/*metabolism, Trans-Activators/genetics/metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4044Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10701)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10701
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
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
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)