Strain identifier

BacDive ID: 13139

Type strain: Yes

Species: Pseudomonas reinekei

Strain Designation: MT1

Strain history: CIP <- 2007, CCUG <- 2006, B. Camara & D.H. Pieper, HZI, Braunschweig, Germany: strain MT1

NCBI tax ID(s): 395598 (species)

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General

@ref: 7436

BacDive-ID: 13139

DSM-Number: 18361

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative

description: Pseudomonas reinekei MT1 is an aerobe, Gram-negative bacterium that was isolated from aerobic zone of Elbe sediment enriched with 4-chlorosalicylate.

NCBI tax id

  • NCBI tax id: 395598
  • Matching level: species

strain history

@refhistory
7436<- D. Pieper, GBF; MT1 <- U. Faude
122152CIP <- 2007, CCUG <- 2006, B. Camara & D.H. Pieper, HZI, Braunschweig, Germany: strain MT1

doi: 10.13145/bacdive13139.20240916.9.1

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 reinekei
  • full scientific name: Pseudomonas reinekei Cámara et al. 2007

@ref: 7436

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas reinekei

full scientific name: Pseudomonas reinekei Cámara et al. 2007

strain designation: MT1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31953negative
122152negativerod-shapedyes
69480negative99
69480yes93.134

pigmentation

  • @ref: 31953
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7436MINERAL MEDIUM PH 7.25 (DSMZ Medium 465)yeshttps://mediadive.dsmz.de/medium/465Name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l None 0.8 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 Na2-EDTA 0.0005 g/l H3BO3 0.0003 g/l FeSO4 x 7 H2O 0.0002 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
7436TRYPTICASE 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
37791MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122152CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
7436positivegrowth30
37791positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31953aerobe
122152obligate aerobe
69480aerobe90.942

spore formation

@refspore formationconfidence
31953no
69481no100

halophily

  • @ref: 31953
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3195316000ethanolamine+carbon source
3195330089acetate+carbon source
3195321217L-alaninamide+carbon source
3195316449alanine+carbon source
3195322599arabinose+carbon source
3195318403L-arabitol+carbon source
3195322653asparagine+carbon source
3195335391aspartate+carbon source
3195317126DL-carnitine+carbon source
3195316947citrate+carbon source
3195315740formate+carbon source
3195328260galactose+carbon source
3195324175galacturonate+carbon source
3195324265gluconate+carbon source
3195317234glucose+carbon source
3195329987glutamate+carbon source
3195317754glycerol+carbon source
3195324996lactate+carbon source
3195315792malonate+carbon source
3195351850methyl pyruvate+carbon source
3195350048phenylethylamine+carbon source
3195326271proline+carbon source
3195317272propionate+carbon source
3195326490quinate+carbon source
3195317822serine+carbon source
3195330031succinate+carbon source
3195327248urocanic acid+carbon source
12215217632nitrate-reduction
12215216301nitrite-reduction

metabolite production

  • @ref: 122152
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31953cytochrome oxidase+1.9.3.1
122152oxidase+
122152catalase+1.11.1.6
122152urease-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
122152-+++-+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7436aerobic zone of Elbe sediment enriched with 4-chlorosalicylateSachsen Anhalt, BitterfeldGermanyDEUEurope
122152Continuous enrichment on 4-chlorosalicylateBitterfeld, Elbe RiverGermanyDEUEurope1993

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_185.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_185&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AM293565
  • Sequence Identity:
  • Total samples: 2464
  • soil counts: 833
  • aquatic counts: 448
  • animal counts: 521
  • plant counts: 662

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74361Risk group (German classification)
1221521Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas reinekei strain MT1 16S ribosomal RNA gene, partial sequenceJQ178342421nuccore395598
31953Pseudomonas reinekei partial 16S rRNA gene, type strain MT1TAM2935651492nuccore395598

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas reinekei MT1GCA_001945365contigncbi395598
66792Pseudomonas reinekei CCUG 53116GCA_008801455contigncbi395598
66792Pseudomonas reinekei strain CCUG 53116395598.13wgspatric395598
66792Pseudomonas reinekei DSM 183612639762506draftimg395598
66792Pseudomonas reinekei MT12582581646draftimg395598
66792Pseudomonas reinekei DSM 18361GCA_900104125chromosomencbi395598

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.361yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.942no
69480spore-formingspore-formingAbility to form endo- or exosporesno83.659yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98yes
69480flagellatedmotile2+Ability to perform flagellated movementyes93.134no

External links

@ref: 7436

culture collection no.: DSM 18361, CCM 7743, CCUG 53116, CIP 109621

straininfo link

  • @ref: 82347
  • straininfo: 354058

literature

  • topic: Phylogeny
  • Pubmed-ID: 17473234
  • title: Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid.
  • authors: Camara B, Strompl C, Verbarg S, Sproer C, Pieper DH, Tindall BJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64703-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Carboxylic Acids/*metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenanthrenes/*metabolism, Phylogeny, Pseudomonas/chemistry/*classification/isolation & purification/*physiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Salicylates/*metabolism, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7436Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18361)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18361
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
31953Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128209
37791Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7385
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)
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
82347Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID354058.1StrainInfo: A central database for resolving microbial strain identifiers
122152Curators of the CIPCollection of Institut Pasteur (CIP 109621)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109621