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): 266 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 6 (current version):
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 6 (current version)

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 Proteobacterium that was isolated from Soil,garden.

NCBI tax id

  • NCBI tax id: 266
  • Matching level: species

strain history

doi: 10.13145/bacdive13693.20211221.6

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/proteobacteria
  • 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 (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 16S rRNAD134801286ena266
20218Paracoccus denitrificans strain IAM12479 16S rRNA geneY175121424ena266
20218Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: JCM 6892AB5987451385ena82367
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

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
20215D.Gleim, M.Kracht, N.Weiss et. al.http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.htmlProkaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
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/