Strain identifier

BacDive ID: 135951

Type strain: Yes

Species: Paracoccus thiocyanatus

Strain history: CIP <- 1999, IFO <- IAM <- Y. Fujimura & H. Kuraishi <- H. Murooka

NCBI tax ID(s): 34006 (species)

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

@ref: 35239

BacDive-ID: 135951

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

description: Paracoccus thiocyanatus CIP 106060 is an obligate aerobe, mesophilic bacterium that was isolated from Activated sludge.

NCBI tax id

  • NCBI tax id: 34006
  • Matching level: species

strain history

@refhistory
67770IAM 12816 <-- Y. Katayama THI 011 <-- H. Murooka 1-8A.
35239CIP <- 1999, IFO <- IAM <- Y. Fujimura & H. Kuraishi <- H. Murooka

doi: 10.13145/bacdive135951.20230509.8.1

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 thiocyanatus
  • full scientific name: Paracoccus thiocyanatus Katayama et al. 1996

@ref: 35239

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus thiocyanatus

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.032
6948099.998negative
35239nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35239MEDIUM 127 - for Streptomyces scabiei and Thiobacillus novellusyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.100 g);Agar (15.000 g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (1.500 g);Ammonium chloride (0.300 g);Sodium thiosulphate pentahydrate (5.000 g);Di Sodium hydrogen
35239CIP Medium 127yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=127

culture temp

@refgrowthtypetemperaturerange
35239positivegrowth30mesophilic
67770positivegrowth30mesophilic
35239positivegrowth25-37mesophilic
35239nogrowth5psychrophilic
35239nogrowth10psychrophilic
35239nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 35239
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.985

halophily

@refsaltgrowthtested relationconcentration
35239NaClpositivegrowth0-4 %
35239NaClnogrowth6 %
35239NaClnogrowth8 %
35239NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
352394853esculin-hydrolysis
3523917632nitrate+reduction
3523916301nitrite+reduction

antibiotic resistance

  • @ref: 35239
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 35239
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
35239oxidase+
35239beta-galactosidase-3.2.1.23
35239alcohol dehydrogenase-1.1.1.1
35239gelatinase-
35239amylase-
35239DNase-
35239caseinase-3.4.21.50
35239catalase+1.11.1.6
35239tween esterase-
35239lecithinase-
35239lipase-
35239lysine decarboxylase-4.1.1.18
35239ornithine decarboxylase-4.1.1.17
35239protease-
35239tryptophan deaminase-
35239urease-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
35239-+++-+----++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
35239--+-----------------+-----+++----+--++------------------------++--+----+-+-+--+--++-----+-++----+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
67770Activated sludgeJapanJPNAsia
35239Environment, Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_62297.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_2307;98_44138;99_62297&stattab=map
  • Last taxonomy: Paracoccus thiocyanatus subclade
  • 16S sequence: D32242
  • Sequence Identity:
  • Total samples: 45
  • soil counts: 5
  • aquatic counts: 22
  • animal counts: 9
  • plant counts: 9

Safety information

risk assessment

  • @ref: 35239
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Paracoccus thiocyanatus gene for 16S rRNA, partial sequence, strain: NBRC 14569AB6806351388ena34006
67770Paracoccus thiocyanatus gene for 16S rRNA, strain: THI 011D322421384ena34006

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus thiocyanatus ATCC 700171GCA_900156255scaffoldncbi34006
66792Paracoccus thiocyanatus strain ATCC 70017134006.7wgspatric34006
66792Paracoccus thiocyanatus ATCC 7001712681812813draftimg34006

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno64.639no
flagellatedno91.857no
gram-positiveno98.619no
anaerobicno96.198no
aerobicyes86.651no
halophileno75.088no
spore-formingno96.437no
thermophileno82.81no
glucose-utilyes83.273no
glucose-fermentno88.95no

External links

@ref: 35239

culture collection no.: CIP 106060, IAM 12816, IFO 14569, JCM 20756, ATCC 700171, NBRC 14569, NCIMB 13627, VKM B-2162

straininfo link

  • @ref: 93210
  • straininfo: 46218

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics11882723Characterization of the replicator region of megaplasmid pTAV3 of Paracoccus versutus and search for plasmid-encoded traits.Bartosik D, Baj J, Bartosik AA, Wlodarczyk MMicrobiology (Reading)10.1099/00221287-148-3-8712002Amino Acid Sequence, Base Sequence, Gene Deletion, Molecular Sequence Data, Paracoccus/*genetics/growth & development, Plasmids/*genetics, Replication Origin, Replicon/*genetics, Sequence Analysis, DNATranscriptome
Metabolism32291967Involvement of membrane vesicles in long-chain-AHL delivery in Paracoccus species.Morinaga K, Nagakubo T, Nomura N, Toyofuku MEnviron Microbiol Rep10.1111/1758-2229.128432020Acyl-Butyrolactones/*metabolism, Biological Transport, *Extracellular Vesicles, Microbial Interactions, Paracoccus/*metabolism, Paracoccus denitrificans/metabolism, *Quorum Sensing

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
35239Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106060Collection of Institut Pasteur (CIP 106060)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
93210Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID46218.1