Strain identifier

BacDive ID: 13712

Type strain: Yes

Species: Paracoccus kocurii

Strain Designation: B

Strain history: CIP <- 1999, JCM <- Y. Katayama: strain B

NCBI tax ID(s): 1122932 (strain), 34005 (species)

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General

@ref: 3237

BacDive-ID: 13712

DSM-Number: 8536

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

description: Paracoccus kocurii B is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from activated sludge for the treatment of tetramethylammonium.

NCBI tax id

NCBI tax idMatching level
34005species
1122932strain

strain history

@refhistory
3237<- JCM <- Y. Katayama, strain B
67770Y. Katayama strain B.
120456CIP <- 1999, JCM <- Y. Katayama: strain B

doi: 10.13145/bacdive13712.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Paracoccus
  • species: Paracoccus kocurii
  • full scientific name: Paracoccus kocurii Ohara et al. 1990

@ref: 3237

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus kocurii

full scientific name: Paracoccus kocurii Ohara et al. 1990

strain designation: B

type strain: yes

Morphology

cell morphology

  • @ref: 120456
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3237PARACOCCUS KOCURII MEDIUM (DSMZ Medium 773)yeshttps://mediadive.dsmz.de/medium/773Name: PARACOCCUS KOCURII MEDIUM (DSMZ Medium 773) Composition: NaH2PO4 x 2 H2O 1.71 g/l K2HPO4 1.41 g/l Tetramethyl ammonium chloride 1.0 g/l (NH4)2SO4 1.0 g/l MgSO4 x 7 H2O 0.594 g/l Nitrilotriacetic acid 0.2 g/l CaCl2 x 2 H2O 0.0667 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Thiamine-HCl x 2 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Distilled water
32935MEDIUM 312 - for Paracoccus kocuriiyesSolution 1 - M0626 (980.000 ml)
3237OXOID NUTRIENT BROTH (DSMZ Medium 948)yeshttps://mediadive.dsmz.de/medium/948Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water
120456CIP Medium 312yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=312

culture temp

@refgrowthtypetemperaturerange
3237positivegrowth28mesophilic
32935positivegrowth30mesophilic
67770positivegrowth30mesophilic
120456positivegrowth30-37mesophilic
120456nogrowth5psychrophilic
120456nogrowth10psychrophilic
120456nogrowth25mesophilic
120456nogrowth41thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
120456NaClpositivegrowth0 %
120456NaClnogrowth2 %
120456NaClnogrowth4 %
120456NaClnogrowth6 %
120456NaClnogrowth8 %
120456NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12045616947citrate-carbon source
1204564853esculin-hydrolysis
12045617632nitrate+reduction
12045616301nitrite+reduction
12045617632nitrate+respiration

metabolite production

  • @ref: 120456
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 120456
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
120456oxidase+
120456beta-galactosidase-3.2.1.23
120456alcohol dehydrogenase-1.1.1.1
120456gelatinase-
120456amylase-
120456DNase-
120456caseinase-3.4.21.50
120456catalase+1.11.1.6
120456tween esterase-
120456lysine decarboxylase-4.1.1.18
120456ornithine decarboxylase-4.1.1.17
120456tryptophan deaminase-
120456urease-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
120456--++----------------

Isolation, sampling and environmental information

isolation

@refsample type
3237activated sludge for the treatment of tetramethylammonium
67770Activated sludge for the treatment of tetramethylammonium
120456Environment, Activated sludge

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_10105.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_4950;97_5994;98_7507;99_10105&stattab=map
  • Last taxonomy: Paracoccus kocurii subclade
  • 16S sequence: AB681114
  • Sequence Identity:
  • Total samples: 343
  • soil counts: 34
  • aquatic counts: 187
  • animal counts: 107
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32371Risk group (German classification)
1204561Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paracoccus kocurii gene for 16S rRNA, strain: JCM 7684D322411387ena34005
20218Paracoccus kocurii gene for 16S rRNA, partial sequence, strain: NBRC 16713AB6811141390ena34005

GC content

  • @ref: 3237
  • GC-content: 71
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 3237

culture collection no.: DSM 8536, ATCC 49631, CCM 4333, IAM 14243, JCM 7684, CIP 106074, IFO 16713, NBRC 16713, NCIMB 13628, VKM B-2139

straininfo link

  • @ref: 82896
  • straininfo: 42591

literature

  • topic: Phylogeny
  • Pubmed-ID: 2397197
  • title: Paracoccus kocurii sp. nov., a tetramethylammonium-assimilating bacterium.
  • authors: Ohara M, Katayama Y, Tsuzaki M, Nakamoto S, Kuraishi H
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-40-3-292
  • year: 1990
  • mesh: *Benzoquinones, DNA, Bacterial/analysis, Fatty Acids/analysis, Nucleic Acid Hybridization, Paracoccus/classification/isolation & purification/*metabolism/ultrastructure, Quaternary Ammonium Compounds/*metabolism, Quinones/analysis
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3237Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8536)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8536
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
32935Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18163
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
82896Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42591.1StrainInfo: A central database for resolving microbial strain identifiers
120456Curators of the CIPCollection of Institut Pasteur (CIP 106074)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106074