Strain identifier

BacDive ID: 13707

Type strain: No

Species: Paracoccus denitrificans

Strain Designation: 381, Delft

Strain history: CIP <- 1998, DSM <- R.Y. Stanier: strain 381, Micrococcus denitrificans <- C.B van Niel <- Lab. Microbiol.: strain Delft

NCBI tax ID(s): 82367 (species)

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General

@ref: 2048

BacDive-ID: 13707

DSM-Number: 65

keywords: Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped

description: Paracoccus denitrificans 381 is an obligate aerobe, mesophilic, Gram-negative bacterium of the family Paracoccaceae.

NCBI tax id

  • NCBI tax id: 82367
  • Matching level: species

strain history

@refhistory
2048<- IMG (Micrococcus denitrificans) <- C.B. van Niel <- Lab. Microbiol., strain Delft
121535CIP <- 1998, DSM <- R.Y. Stanier: strain 381, Micrococcus denitrificans <- C.B van Niel <- Lab. Microbiol.: strain Delft

doi: 10.13145/bacdive13707.20230509.8.1

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 denitrificans
  • full scientific name: Paracoccus denitrificans (Beijerinck and Minkman 1910) Davis 1969 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Micrococcus denitrificans

@ref: 2048

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus pantotrophus

full scientific name: Paracoccus pantotrophus (Robertson and Kuenen 1984) Rainey et al. 1999

strain designation: 381, Delft

type strain: no

Morphology

cell morphology

  • @ref: 121535
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 121535

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2048MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yeshttps://mediadive.dsmz.de/medium/81Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
2048NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
41176MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121535CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
2048positivegrowth30mesophilic
41176positivegrowth30mesophilic
121535positivegrowth22-41
121535nogrowth10psychrophilic
121535nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121535
  • oxygen tolerance: obligate aerobe

compound production

  • @ref: 2048
  • compound: ribulose-1,5-bisphosphate carboxylase

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121535hippurate+hydrolysis606565
121535nitrate+reduction17632
121535nitrite+reduction16301
121535tributyrin-hydrolysis35020

antibiotic resistance

  • @ref: 121535
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121535
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 121535
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
121535oxidase+
121535beta-galactosidase-3.2.1.23
121535alcohol dehydrogenase-1.1.1.1
121535gelatinase-
121535amylase-
121535DNase-
121535caseinase-3.4.21.50
121535catalase+1.11.1.6
121535tween esterase-
121535gamma-glutamyltransferase+2.3.2.2
121535lecithinase-
121535lipase-
121535lysine decarboxylase-4.1.1.18
121535ornithine decarboxylase-4.1.1.17
121535phenylalanine ammonia-lyase-4.3.1.24
121535protease-
121535urease-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
121535-+++------++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121535------------+/------------+/---+/----------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121535++-++--+-++-----+--+--+--++++---++++++-------+--++------++--+++++------+-+-+--+++-+++-+-+++++++++--

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20481Risk group (German classification)
1215351Risk group (French classification)

Sequence information

GC content

  • @ref: 2048
  • GC-content: 66.3

External links

@ref: 2048

culture collection no.: DSM 65, ATCC 17741, CIP 105417, ICPB 3979, NCIB 11627, Stanier 381

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8494744Transfer of Thiosphaera pantotropha to Paracoccus denitrificans.Ludwig W, Mittenhuber G, Friedrich CGInt J Syst Bacteriol10.1099/00207713-43-2-3631993Bacteria/classification, Bacteria, Aerobic/*classification, Base Sequence, Genes, Bacterial/*genetics, Gram-Negative Chemolithotrophic Bacteria/*classification, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification, Phylogeny, RNA, Ribosomal, 16S/*genetics, Rhodobacter/classification, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Genetics12813068Identification and characterization of transposable elements of Paracoccus pantotrophus.Bartosik D, Sochacka M, Baj JJ Bacteriol10.1128/JB.185.13.3753-3763.20032003Amino Acid Sequence, Base Sequence, Chromosome Mapping, Chromosomes, Bacterial, *DNA Transposable Elements, Gene Dosage, Molecular Sequence Data, Paracoccus/*genetics/growth & development, Plasmids, Sequence Analysis, DNA, Soil Microbiology, Species SpecificityTranscriptome

Reference

@idauthorscataloguedoi/urltitle
2048Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 65)https://www.dsmz.de/collection/catalogue/details/culture/DSM-65
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
41176Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17435
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
121535Curators of the CIPCollection of Institut Pasteur (CIP 105417)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105417