Strain identifier

BacDive ID: 13711

Type strain: Yes

Species: Paracoccus alcaliphilus

Strain Designation: TK 1015

Strain history: CIP <- 1999, JCM <- T. Urakami: strain TK 1015

NCBI tax ID(s): 34002 (species)

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General

@ref: 3293

BacDive-ID: 13711

DSM-Number: 8512

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, oval-shaped

description: Paracoccus alcaliphilus TK 1015 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 34002
  • Matching level: species

strain history

@refhistory
3293<- JCM <- T. Urakami, TK 1015
67770T. Urakami TK 1015.
116208CIP <- 1999, JCM <- T. Urakami: strain TK 1015

doi: 10.13145/bacdive13711.20230509.8.1

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 alcaliphilus
  • full scientific name: Paracoccus alcaliphilus Urakami et al. 1989

@ref: 3293

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus alcaliphilus

full scientific name: Paracoccus alcaliphilus Urakami et al. 1989

strain designation: TK 1015

type strain: yes

Morphology

cell morphology

  • @ref: 116208
  • gram stain: negative
  • cell shape: oval-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3293PARACOCCUS ALCALIPHILUS MEDIUM (DSMZ Medium 772)yeshttps://mediadive.dsmz.de/medium/772Name: PARACOCCUS ALCALIPHILUS MEDIUM (DSMZ Medium 772) Composition: Methanol 7.92 g/l (NH4)2SO4 3.0 g/l Na2HPO4 3.0 g/l KH2PO4 1.4 g/l MgSO4 x 7 H2O 0.2 g/l Fe(III) citrate 0.03 g/l CaCl2 x 2 H2O 0.03 g/l MnCl2 x 4 H2O 0.005 g/l ZnSO4 x 7 H2O 0.005 g/l CuSO4 x 2 H2O 0.0005 g/l Thiamine-HCl x 2 H2O 0.0004 g/l Distilled water
32934MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116208CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
116208CIP Medium 229yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=229

culture temp

@refgrowthtypetemperaturerange
3293positivegrowth30mesophilic
32934positivegrowth30mesophilic
67770positivegrowth30mesophilic
116208positivegrowth25-30mesophilic
116208nogrowth5psychrophilic
116208nogrowth10psychrophilic
116208nogrowth37mesophilic
116208nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116208
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116208NaClpositivegrowth0-6 %
116208NaClnogrowth8 %
116208NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11620816947citrate-carbon source
1162084853esculin-hydrolysis
11620817632nitrate+reduction
11620816301nitrite-reduction
11620817632nitrate-respiration

antibiotic resistance

  • @ref: 116208
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116208
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116208oxidase+
116208beta-galactosidase-3.2.1.23
116208alcohol dehydrogenase-1.1.1.1
116208gelatinase-
116208amylase-
116208DNase-
116208caseinase-3.4.21.50
116208catalase-1.11.1.6
116208tween esterase-
116208lecithinase-
116208lipase-
116208lysine decarboxylase-4.1.1.18
116208ornithine decarboxylase-4.1.1.17
116208protease-
116208tryptophan deaminase-
116208urease-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
116208-+++-+++--++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116208+++-+--------------+-+----++---+-+---------++-------+-++--------+--+---+-++-------------+++--------

Isolation, sampling and environmental information

isolation

@refsample type
3293soil
67770Soil
116208Environment, Soil

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_48905.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_12974;98_28523;99_48905&stattab=map
  • Last taxonomy: Paracoccus alcaliphilus
  • 16S sequence: D32238
  • Sequence Identity:
  • Total samples: 817
  • soil counts: 133
  • aquatic counts: 254
  • animal counts: 406
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32931Risk group (German classification)
1162081Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paracoccus alcaliphilus 16S ribosomal RNA gene, partial sequenceAY0141771456ena34002
20218Paracoccus alcaliphilus gene for 16S rRNA, strain: JCM 7364D322381385ena34002

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus alcaliphilus strain DSM 851234002.8wgspatric34002
66792Paracoccus alcaliphilus DSM 85122636415977draftimg34002
67770Paracoccus alcaliphilus DSM 8512GCA_900110285scaffoldncbi34002
66792Paracoccus alcaliphilus TK 1015 = DSM 8512GCA_028553725completencbi34002

GC content

  • @ref: 3293
  • GC-content: 64.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno79.38no
flagellatedno93.794no
gram-positiveno97.954no
anaerobicno98.405no
aerobicyes91.183no
halophileno69.5no
spore-formingno95.896no
glucose-fermentno84.388no
thermophileno96.584yes
glucose-utilyes86.975no

External links

@ref: 3293

culture collection no.: DSM 8512, ATCC 51199, JCM 7364, NCIMB 13180, BCRC 80157, CIP 106073, IAM 14749, IFO 16719, LMG 24023, NBRC 16719, VKM B-2138

straininfo link

  • @ref: 82895
  • straininfo: 45274

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics11407917Characterization and sequence analysis of the replicator region of the novel plasmid pALC1 from Paracoccus alcaliphilus.Bartosik D, Witkowska M, Baj J, Wlodarczyk MPlasmid10.1006/plas.2000.15052001Amino Acid Sequence, Bacterial Proteins/genetics, Base Sequence, *DNA Replication, Molecular Sequence Data, Paracoccus/*genetics, Plasmids/*genetics, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Transcription Factors/geneticsTranscriptome
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
Phylogeny20851920Paracoccus caeni sp. nov., isolated from sludge.Lee M, Woo SG, Park G, Kim MKInt J Syst Evol Microbiol10.1099/ijs.0.017897-02010DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Paracoccus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiologyMetabolism
Phylogeny20935084Paracoccus stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata.Sheu SY, Jiang SR, Chen CA, Wang JT, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.028035-02010Aerobiosis, Anaerobiosis, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Taiwan, TemperatureGenetics
Phylogeny21960015Paracoccus oceanense sp. nov., isolated from the West Pacific.Fu Y, Li Q, Liu K, Xu Y, Wang Y, Jiao NCurr Microbiol10.1007/s00284-011-0015-12011Base Sequence, DNA, Bacterial/chemistry/genetics, Microbial Sensitivity Tests, Microscopy, Electron, Transmission, Molecular Sequence Data, Pacific Ocean, Paracoccus/chemistry/genetics/*isolation & purification/ultrastructure, Polymerase Chain Reaction, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNAGenetics
Phylogeny23546859Paracoccus siganidrum sp. nov., isolated from fish gastrointestinal tract.Liu Y, Xie QY, Hong K, Li L, Zhao YM, Tang YL, An JY, Zhu PP, Xu CHAntonie Van Leeuwenhoek10.1007/s10482-013-9894-42013Animals, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fishes/*microbiology, Gastrointestinal Tract/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3293Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8512)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8512
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
32934Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18162
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
82895Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45274.1StrainInfo: A central database for resolving microbial strain identifiers
116208Curators of the CIPCollection of Institut Pasteur (CIP 106073)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106073