Strain identifier

BacDive ID: 13715

Type strain: Yes

Species: Paracoccus solventivorans

Strain Designation: L1

Strain history: CIP <- 1997, J. Winter, Karlsruhe Univ., Karlsruhe, Germany: strain L1 <- R. Morenweiser

NCBI tax ID(s): 53463 (species)

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General

@ref: 2642

BacDive-ID: 13715

DSM-Number: 6637

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative

description: Paracoccus solventivorans L1 is a facultative anaerobe, Gram-negative bacterium that was isolated from soil near natural gas distribution station.

NCBI tax id

  • NCBI tax id: 53463
  • Matching level: species

strain history

@refhistory
2642<- J. Winter, L1
122674CIP <- 1997, J. Winter, Karlsruhe Univ., Karlsruhe, Germany: strain L1 <- R. Morenweiser

doi: 10.13145/bacdive13715.20240916.9.1

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 solventivorans
  • full scientific name: Paracoccus solventivorans Siller et al. 1996

@ref: 2642

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus solventivorans

full scientific name: Paracoccus solventivorans Siller et al. 1996 emend. Lipski et al. 1998

strain designation: L1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122674negativerod-shapedno
69480negative97.091

colony morphology

  • @ref: 2642
  • incubation period: 8-14 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2642DESULFOBACTER MEDIUM (DSMZ Medium 193)yeshttps://mediadive.dsmz.de/medium/193Name: DESULFOBACTER MEDIUM (DSMZ Medium 193; with strain-specific modifications) Composition: NaCl 6.97906 g/l Na-pyruvate 4.98504 g/l KNO3 3.38983 g/l Na2SO4 2.99102 g/l Na2CO3 1.49551 g/l MgCl2 x 6 H2O 1.29611 g/l None 0.578265 g/l KCl 0.498505 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299102 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
38530MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2642NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
122674CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122674CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
2642positivegrowth30
38530positivegrowth30
2642positivegrowth28
122674positivegrowth10-37
122674nogrowth5

Physiology and metabolism

oxygen tolerance

  • @ref: 2642
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69480no90.929
69481no92

halophily

@refsaltgrowthtested relationconcentration
122674NaClpositivegrowth0-6 %
122674NaClnogrowth8 %
122674NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12267416947citrate-carbon source
1226744853esculin-hydrolysis
12267417632nitrate+reduction
12267416301nitrite+reduction
12267417632nitrate+respiration

antibiotic resistance

  • @ref: 122674
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122674
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
122674oxidase+
122674beta-galactosidase-3.2.1.23
122674alcohol dehydrogenase+1.1.1.1
122674gelatinase-
122674amylase-
122674DNase-
122674caseinase-3.4.21.50
122674catalase+1.11.1.6
122674tween esterase-
122674lecithinase-
122674lipase-
122674lysine decarboxylase-4.1.1.18
122674ornithine decarboxylase-4.1.1.17
122674tryptophan deaminase-
122674urease-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
122674-+++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
2642soil near natural gas distribution stationGermanyDEUEurope
122674Environment, Soil sample of a defunct natural gas companyGermanyDEUEuropeLandshut1991

isolation source categories

Cat1Cat2Cat3
#Engineered
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4260.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_2589;98_3209;99_4260&stattab=map
  • Last taxonomy: Paracoccus solventivorans
  • 16S sequence: AY014175
  • Sequence Identity:
  • Total samples: 1143
  • soil counts: 153
  • aquatic counts: 406
  • animal counts: 523
  • plant counts: 61

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
26421Risk group (German classification)
1226741Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
2642Paracoccus solventivorans 16S ribosomal RNA gene, partial sequenceAY0141751450nuccore53463
124043P.solventivorans 16S rRNA geneY077051405nuccore53463

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus solventivorans DSM 6637GCA_900142875contigncbi53463
66792Paracoccus solventivorans strain DSM 663753463.8wgspatric53463
66792Paracoccus solventivorans DSM 66372695420926draftimg53463

GC content

  • @ref: 2642
  • GC-content: 70
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno92no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.091no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no90.838yes
69480spore-formingspore-formingAbility to form endo- or exosporesno90.929no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.282yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes69.791yes
69480flagellatedmotile2+Ability to perform flagellated movementno62.19no

External links

@ref: 2642

culture collection no.: DSM 6637, CIP 105051

straininfo link

  • @ref: 82899
  • straininfo: 13500

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8863446Isolation and characterization of a new gram-negative, acetone-degrading, nitrate-reducing bacterium from soil, Paracoccus solventivorans sp. nov.Siller H, Rainey FA, Stackebrandt E, Winter JInt J Syst Bacteriol10.1099/00207713-46-4-11251996Acetone/*metabolism, Base Sequence, Carbon Dioxide/metabolism, Molecular Sequence Data, Nitrates/*metabolism, Oxidation-Reduction, Paracoccus/classification/*isolation & purification/metabolism, Phylogeny, *Soil MicrobiologyMetabolism
Phylogeny30489238Description of Paracoccus endophyticus sp. nov., isolated from Gastrodia elata Blume.Zhang H, Li YQ, Xiao M, Fang BZ, Alkhalifah DHM, Hozzein WN, Rao MPN, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0031422018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrodia/*microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Tubers/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2642Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6637)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6637
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
38530Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17027
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
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
82899Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13500.1StrainInfo: A central database for resolving microbial strain identifiers
122674Curators of the CIPCollection of Institut Pasteur (CIP 105051)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105051
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy