Strain identifier

BacDive ID: 13713

Type strain: Yes

Species: Paracoccus aminovorans

Strain Designation: DM-82

Strain history: CIP <- 1999, JCM <- T. Urakami: strain DM-82

NCBI tax ID(s): 34004 (species)

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

@ref: 3238

BacDive-ID: 13713

DSM-Number: 8537

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

description: Paracoccus aminovorans DM-82 is an obligate aerobe, mesophilic bacterium that was isolated from soil Niigata Factory of Mitsubishi Gas Chemical Company.

NCBI tax id

  • NCBI tax id: 34004
  • Matching level: species

strain history

@refhistory
3238<- JCM <- T. Urakami, DM-82
67770T. Urakami DM-82.
116338CIP <- 1999, JCM <- T. Urakami: strain DM-82

doi: 10.13145/bacdive13713.20230509.8.1

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 aminovorans
  • full scientific name: Paracoccus aminovorans Urakami et al. 1990

@ref: 3238

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus aminovorans

full scientific name: Paracoccus aminovorans Urakami et al. 1990

strain designation: DM-82

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.305
6948099.997negative
116338nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3238MEDIUM FOR PARACOCCUS AMINOPHILUS AND P. AMINOVORANS (DSMZ Medium 774)yeshttps://mediadive.dsmz.de/medium/774Name: MEDIUM FOR PARACOCCUS AMINOPHILUS AND P. AMINOVORANS (DSMZ Medium 774) Composition: Agar 20.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l Distilled water
40405MEDIUM 199 - for Clavibacter michiganense subsp. insidiosumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (5.000g);Yeast extract (5.000 g);Peptone (5.000 g)
116338CIP Medium 364yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=364
116338CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3238positivegrowth30mesophilic
40405positivegrowth30mesophilic
67770positivegrowth30mesophilic
116338positivegrowth25-37mesophilic
116338nogrowth5psychrophilic
116338nogrowth10psychrophilic
116338nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116338
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
116338NaClpositivegrowth0-6 %
116338NaClnogrowth8 %
116338NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11633816947citrate-carbon source
1163384853esculin+hydrolysis
11633817632nitrate+reduction
11633816301nitrite+reduction
11633817632nitrate+respiration

antibiotic resistance

  • @ref: 116338
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116338
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116338oxidase+
116338beta-galactosidase-3.2.1.23
116338gelatinase-
116338amylase-
116338DNase-
116338caseinase-3.4.21.50
116338catalase+1.11.1.6
116338tween esterase-
116338lecithinase-
116338lipase-
116338protease-
116338tryptophan deaminase-
116338urease-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
116338-+++-+-+--++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3238soil Niigata Factory of Mitsubishi Gas Chemical CompanyJapanJPNAsia
67770Soil
116338Environment, SoilJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4614.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_529;97_2307;98_3463;99_4614&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: LN832559
  • Sequence Identity:
  • Total samples: 664
  • soil counts: 38
  • aquatic counts: 110
  • animal counts: 513
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
32381Risk group (German classification)
1163381Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
3238Paracoccus aminovorans gene for 16S rRNA, strain: JCM 7685D322401385ena34004
3238Paracoccus aminovorans gene for 16S rRNA, partial sequence, strain: NBRC 16711AB6811121388ena34004
3238Paracoccus aminovorans isolate JCM7685 genome assembly, chromosome: ILN8325593108335ena34004

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus aminovorans JCM7685GCA_900005615completencbi34004
66792Paracoccus aminovorans DSM 8537GCA_900113565contigncbi34004
66792Paracoccus aminovorans strain DSM 853734004.15wgspatric34004
66792Paracoccus aminovorans strain JCM768534004.11plasmidpatric34004
66792Paracoccus aminovorans strain JCM768534004.12plasmidpatric34004
66792Paracoccus aminovorans strain JCM768534004.10plasmidpatric34004
66792Paracoccus aminovorans strain JCM768534004.9completepatric34004
66792Paracoccus aminovorans DSM 85372615840720draftimg34004
66792Paracoccus aminovorans JCM76852773857812completeimg34004

GC content

@refGC-contentmethod
323867.0high performance liquid chromatography (HPLC)
6777067high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileno74.324no
flagellatedno93.396no
gram-positiveno98.248no
anaerobicno97.737no
aerobicyes91.643no
halophileno84.919no
spore-formingno94.649no
glucose-fermentno90.546no
thermophileno95.061yes
glucose-utilyes89.465no

External links

@ref: 3238

culture collection no.: DSM 8537, ATCC 49632, IAM 14244, JCM 7685, BCRC 80946, CIP 106076, IFO 16711, LMG 23829, NBRC 16711, VKM B-2140

straininfo link

  • @ref: 82897
  • straininfo: 42592

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2397196Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov., which utilize N,N-dimethylformamide.Urakami T, Araki H, Oyanagi H, Suzuki K, Komagata KInt J Syst Bacteriol10.1099/00207713-40-3-2871990Base Composition, DNA, Bacterial/analysis, Dimethylformamide/*metabolism, Nucleic Acid Hybridization, Paracoccus/*classification/metabolismMetabolism
Phylogeny22753523Paracoccus huijuniae sp. nov., an amide pesticide-degrading bacterium isolated from activated sludge of a wastewater biotreatment system.Sun LN, Zhang J, Kwon SW, He J, Zhou SG, Li SPInt J Syst Evol Microbiol10.1099/ijs.0.044180-02012Amides/*metabolism, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Pesticides/*metabolism, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/analysis, Waste Water/microbiologyMetabolism
Phylogeny28809137Paracoccus mangrovi sp. nov., isolated from a mangrove.Chen WM, Li YS, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0019932017Avicennia/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/metabolism, Nucleic Acid Hybridization, Paracoccus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Polyesters/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryMetabolism
Metabolism28856785Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685.Czarnecki J, Dziewit L, Puzyna M, Prochwicz E, Tudek A, Wibberg D, Schluter A, Puhler A, Bartosik DEnviron Microbiol10.1111/1462-2920.139012017Carbon/*metabolism, Gene Expression Regulation, Bacterial/genetics, Gene Transfer, Horizontal/genetics, Genome, Bacterial/genetics, Paracoccus/*genetics/*metabolism, Plasmids/*genetics, Replicon/*geneticsGenetics
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

@idauthorscataloguedoi/urltitlejournalpubmed
3238Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8537)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8537
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
40405Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18165
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82897Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42592.1StrainInfo: A central database for resolving microbial strain identifiers
116338Curators of the CIPCollection of Institut Pasteur (CIP 106076)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106076