Strain identifier

BacDive ID: 13693

Type strain: Yes

Species: Paracoccus denitrificans

Strain history: IAM 15021 <-- NCCB 22021 <-- LMD 22.21 <-- M. W. Beijerinck.

NCBI tax ID(s): 1302247 (strain), 266 (species)

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

@ref: 186

BacDive-ID: 13693

DSM-Number: 413

keywords: aerobe, Bacteria, 16S sequence, genome sequence, mesophilic

description: Paracoccus denitrificans CCUG 30144 is an aerobe, mesophilic bacterium that was isolated from Soil,garden.

NCBI tax id

NCBI tax idMatching level
266species
1302247strain

strain history

doi: 10.13145/bacdive13693.20220920.7

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Rhodobacteraceae
  • 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: 186

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus denitrificans

full scientific name: Paracoccus denitrificans (Beijerinck and Minkman 1910) Davis 1969 emend. Rainey et al. 1999

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35203MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
37731MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
186NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://bacmedia.dsmz.de/medium/1
186MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yesName: 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 waterhttps://bacmedia.dsmz.de/medium/81

culture temp

@refgrowthtypetemperaturerange
35203positivegrowth30mesophilic
37731positivegrowth30mesophilic
49937positivegrowth26mesophilic
186positivegrowth30mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 49937
  • oxygen tolerance: aerobe

observation

  • @ref: 20216
  • observation: Degradation of creatine

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    49937C16:013.216
    49937C17:00.917
    49937C18:04.518
    49937C10:0 3OH2.711.423
    49937C14:0 3OH/C16:1 ISO I1.215.485
    49937C18:1 ω7c /12t/9t72.317.824
    49937C19:0 CYCLO ω8c1.918.9
    49937Unidentified1.616.297
    49937unknown 11.7982.511.798
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
49937Soil,garden
67770Garden soil, DelftNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Garden
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 186
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paracoccus denitrificans strain ATCC 17741 clone ControlA04 16S ribosomal RNA gene, partial sequenceJF508186661ena266
20218Paracoccus denitrificans strain ATCC 17741 clone ControlB11 16S ribosomal RNA gene, partial sequenceJF508203673ena266
20218Paracoccus denitrificans 16S rRNA gene, strain ATCC 17741TY169271395ena266
20218Paracoccus denitrificans 16S rRNA gene, strain DSM 413Y169291395ena266
20218Paracoccus pantotrophus 16S rRNA gene, strain DSM 65Y169351395ena82367
20218Paracoccus denitrificans strain JCM6892 16S rRNA geneY175111418ena266
20218P.denitrificans 16S rRNAX691591458ena266
20218Paracoccus pantotrophus 16S rRNA gene, strain LMG 4218Y169361395ena82367
20218Paracoccus denitrificans gene for 16S rRNA, partial sequence, strain: NBRC 102528AB6818621388ena266
20218Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: NBRC 16712AB6811131388ena82367
20218Paracoccus denitrificans 16S rRNA gene, strain ATCC 19367Y169301395ena266

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus denitrificans ATCC 19367GCA_004063735completencbi266
66792Paracoccus denitrificans DSM 413GCA_900100045scaffoldncbi266
66792Paracoccus denitrificans NBRC 102528GCA_007989485contigncbi266
66792Paracoccus denitrificans JCM 21484 JCM 21484GCA_001313145contigncbi1302247
66792Paracoccus denitrificans JCM 214841302247.4wgspatric1302247
66792Paracoccus denitrificans strain ATCC 19367266.34completepatric266
66792Paracoccus denitrificans strain DSM 413266.10wgspatric266
66792Paracoccus denitrificans strain NBRC 102528266.43wgspatric266
66792Paracoccus denitrificans ATCC 193672841597668completeimg266
66792Paracoccus denitrificans JCM 214842734481933draftimg1302247
66792Paracoccus denitrificans DSM 4132597490357draftimg266

External links

@ref: 186

culture collection no.: CCUG 30144, LMG 4049, LMG 4219, IFO 13301, DSM 413, ATCC 17741, ATCC 19367, CCM 982, LMD 22.21, NCIB 8944, JCM 21484, IAM 15021, NBRC 102528, NCCB 22021

straininfo link

@refpassport
20218http://www.straininfo.net/strains/16103
20218http://www.straininfo.net/strains/16114
20218http://www.straininfo.net/strains/16100
20218http://www.straininfo.net/strains/16101
20218http://www.straininfo.net/strains/235066
20218http://www.straininfo.net/strains/16110

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology1653018Cytochrome c' of Paracoccus denitrificans.Gilmour R, Goodhew CF, Pettigrew GWBiochim Biophys Acta10.1016/s0005-2728(05)80208-71991Amino Acid Sequence, Amino Acids/analysis, Chromatium/enzymology, Chromatography, Gel, Cytochrome c Group/*isolation & purification, Molecular Sequence Data, Paracoccus denitrificans/*enzymology, Protein Conformation, Rhodobacter capsulatus/enzymology, Rhodospirillum rubrum/enzymologyGenetics
Enzymology7002036The regulation of hydrogenase formation as a differentiating character of strains of Paracoccus denitrificans.Nokhal TH, Schlegel HGAntonie Van Leeuwenhoek10.1007/BF004440691980Aerobiosis, Anaerobiosis, Cell Membrane/enzymology, Cell-Free System, Culture Media, Enzyme Induction, Hydrogenase, Oxidoreductases/*biosynthesis/metabolism, Paracoccus denitrificans/*classification/enzymology/growth & developmentCultivation
Genetics7642505Integration of heterologous DNA into the genome of Paracoccus denitrificans is mediated by a family of IS1248-related elements and a second type of integrative recombination event.Van Spanning RJ, Reijnders WN, Stouthamer AHJ Bacteriol10.1128/jb.177.16.4772-4778.19951995Base Sequence, Blotting, Southern, DNA Transposable Elements/*genetics, DNA, Bacterial/*genetics, Genetic Vectors, Genome, Bacterial, Gram-Negative Chemolithotrophic Bacteria/genetics, Molecular Sequence Data, Paracoccus denitrificans/classification/*genetics, *Recombination, Genetic, Restriction Mapping, Sequence Analysis, DNA, Thiobacillus/geneticsTranscriptome
Metabolism9874223The surface-charge asymmetry and dimerisation of cytochrome c550 from Paracoccus denitrificans--implications for the interaction with cytochrome c peroxidase.Pettigrew GW, Gilmour R, Goodhew CF, Hunter DJ, Devreese B, Van Beeumen J, Costa C, Prazeres S, Krippahl L, Palma PN, Moura I, Moura JJEur J Biochem10.1046/j.1432-1327.1998.2580559.x1998Amino Acid Sequence, Bacterial Proteins/chemistry, Carbodiimides/metabolism, Computer Simulation, Cross-Linking Reagents/metabolism, Cytochrome c Group/*chemistry, Cytochrome-c Peroxidase/*metabolism, Dimerization, Electron Transport/physiology, Kinetics, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Osmolar Concentration, Oxidation-Reduction, Paracoccus denitrificans/*chemistry, Protein Binding, Sequence AnalysisEnzymology
Phylogeny10319488A re-evaluation of the taxonomy of Paracoccus denitrificans and a proposal for the combination Paracoccus pantotrophus comb. nov.Rainey FA, Kelly DP, Stackebrandt E, Burghardt J, Hiraishi A, Katayama Y, Wood APInt J Syst Bacteriol10.1099/00207713-49-2-6451999Cytochrome c Group/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/physiology, Paracoccus denitrificans/*classification/genetics/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Biotechnology12501289Production of ubiquinone-10 using bacteria.Yoshida H, Kotani Y, Ochiai K, Araki KJ Gen Appl Microbiol10.2323/jgam.44.191998
Phylogeny12624070Paracoccus yeeii sp. nov. (formerly CDC group EO-2), a novel bacterial species associated with human infection.Daneshvar MI, Hollis DG, Weyant RS, Steigerwalt AG, Whitney AM, Douglas MP, Macgregor JP, Jordan JG, Mayer LW, Rassouli SM, Barchet W, Munro C, Shuttleworth L, Bernard KJ Clin Microbiol10.1128/JCM.41.3.1289-1294.20032003DNA, Bacterial/analysis, Gram-Negative Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, Paracoccus/*classification/genetics, Phenotype, Phylogeny, RNA, Ribosomal, 16S/*analysis/geneticsPathogenicity
Enzymology12835921A novel enzyme, D-3-hydroxyaspartate aldolase from Paracoccus denitrificans IFO 13301: purification, characterization, and gene cloning.Liu JQ, Dairi T, Itoh N, Kataoka M, Shimizu SAppl Microbiol Biotechnol10.1007/s00253-003-1238-22003Amino Acid Sequence, Aspartic Acid/analogs & derivatives/*metabolism, Base Sequence, Cloning, Molecular, Fructose-Bisphosphate Aldolase/*genetics/isolation & purification/*metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Molecular Weight, Paracoccus denitrificans/*enzymology, Substrate Specificity, TemperatureMetabolism
Enzymology12959522Growth and nitrite and nitrous oxide accumulation of Paracoccus denitrificans ATCC 19367 in the presence of selected pesticides.Saez F, Pozo C, Gomez MA, Rodelas B, Gonzalez-Lopez JEnviron Toxicol Chem10.1897/02-3512003Carbon Dioxide/analysis, Nitrates/*pharmacokinetics, Nitrous Oxide/*pharmacokinetics, Paracoccus denitrificans/*growth & development/physiology, Pesticides/*toxicity, Water Pollutants, Chemical/*toxicity
Metabolism24271182Potential role of nitrite for abiotic Fe(II) oxidation and cell encrustation during nitrate reduction by denitrifying bacteria.Klueglein N, Zeitvogel F, Stierhof YD, Floetenmeyer M, Konhauser KO, Kappler A, Obst MAppl Environ Microbiol10.1128/AEM.03277-132013Acetates/metabolism, Anaerobiosis, Betaproteobacteria/growth & development/*metabolism/ultrastructure, Comamonadaceae/growth & development/*metabolism/ultrastructure, *Denitrification, Ferrous Compounds/*metabolism, Microscopy, Electron, Minerals/metabolism, Nitrates/*metabolism, Nitrites/*metabolism, Oxidation-Reduction, Periplasm/metabolism
Enzymology25805905Molecular, Physiological and Phenotypic Characterization of Paracoccus denitrificans ATCC 19367 Mutant Strain P-87 Producing Improved Coenzyme Q10.Tokdar P, Sanakal A, Ranadive P, Khora SS, George S, Deshmukh SKIndian J Microbiol10.1007/s12088-014-0506-42014
Phylogeny30663955Paracoccus suum sp. nov., isolated from a pig farm dust collector.Heo J, Cho HY, Kim JS, Hong SB, Kwon SW, Kim SJInt J Syst Evol Microbiol10.1099/ijsem.0.0032262019Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Dust, Farms, Fatty Acids/chemistry, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Swine, Ubiquinone/chemistryTranscriptome
Genetics30897350Complete genome sequence of Paracoccus denitrificans ATCC 19367 and its denitrification characteristics.Si YY, Xu KH, Yu XY, Wang MF, Chen XHCan J Microbiol10.1139/cjm-2019-00372019Base Sequence, *Denitrification, Genome, Bacterial, Paracoccus denitrificans/*genetics/metabolism, *Whole Genome SequencingMetabolism
Metabolism33305820Temperature and oxygen level determine N2 O respiration activities of heterotrophic N2 O-reducing bacteria: Biokinetic study.Zhou Y, Suenaga T, Qi C, Riya S, Hosomi M, Terada ABiotechnol Bioeng10.1002/bit.276542020Nitrous Oxide/*metabolism, Paracoccus denitrificans/*metabolism, Pseudomonas stutzeri/*metabolism, Rhodocyclaceae/*metabolism, *Temperature

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
186Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 413)https://www.dsmz.de/collection/catalogue/details/culture/DSM-413
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
35203Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18421
37731Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10580
49937Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30144)https://www.ccug.se/strain?id=30144
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/