Strain identifier

BacDive ID: 13706

Type strain: Yes

Species: Paracoccus pantotrophus

Strain Designation: GB 17

Strain history: CIP <- 2000, ATCC <- L.A. Robertson: strain GB 17

NCBI tax ID(s): 82367 (species)

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General

@ref: 1255

BacDive-ID: 13706

DSM-Number: 2944

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

description: Paracoccus pantotrophus GB 17 is an obligate aerobe, Gram-negative, ovoid-shaped bacterium that was isolated from denitrifying, sulfide-oxidizing effluent-treatment plant.

NCBI tax id

  • NCBI tax id: 82367
  • Matching level: species

strain history

@refhistory
1255<- C. Friedrich <- J.G. Kuenen, GB 17 (Thiosphaera pantotropha)
67770IAM 15022 <-- NCCB 82005 <-- LMD 82.5 <-- L. A. Robertson GB 17.
121536CIP <- 2000, ATCC <- L.A. Robertson: strain GB 17

doi: 10.13145/bacdive13706.20240916.9.1

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 pantotrophus
  • full scientific name: Paracoccus pantotrophus (Robertson and Kuenen 1984) Rainey et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Thiosphaera pantotropha

@ref: 1255

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus pantotrophus

full scientific name: Paracoccus pantotrophus (Robertson and Kuenen 1984) Rainey et al. 1999

strain designation: GB 17

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121536negativeovoid-shapedno
69480negative98

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1255NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
34087MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121536CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
1255positivegrowth28
34087positivegrowth37
67770positivegrowth37
121536positivegrowth25-41
121536nogrowth5
121536nogrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 121536
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 91.59

halophily

@refsaltgrowthtested relationconcentration
121536NaClpositivegrowth0-6 %
121536NaClnogrowth8 %
121536NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1215364853esculin-hydrolysis
12153617632nitrate+reduction
12153616301nitrite+reduction
12153617632nitrate+respiration

metabolite production

  • @ref: 121536
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 121536
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
121536oxidase+
121536beta-galactosidase-3.2.1.23
121536alcohol dehydrogenase-1.1.1.1
121536gelatinase-
121536amylase-
121536DNase-
121536caseinase-3.4.21.50
121536catalase+1.11.1.6
121536tween esterase-
121536lecithinase-
121536lipase-
121536lysine decarboxylase-4.1.1.18
121536ornithine decarboxylase-4.1.1.17
121536protease-
121536urease-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
121536-+++-------+---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121536++-++--+-++--------+--+--++++--+++++++---+------++----+-++-++++++--+---+-+-+--++++++--+-++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1255denitrifying, sulfide-oxidizing effluent-treatment plantDelftNetherlandsNLDEurope
67770Waste treatment plantNetherlandsNLDEurope
121536Waste treatment plantNetherlandsNLDEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Plant (Factory)
#Engineered#Waste#Water treatment plant
#Condition#Sulfuric

taxonmaps

  • @ref: 69479
  • File name: preview.99_869.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_31;97_32;98_688;99_869&stattab=map
  • Last taxonomy: Paracoccus
  • 16S sequence: Y16933
  • Sequence Identity:
  • Total samples: 5189
  • soil counts: 932
  • aquatic counts: 2441
  • animal counts: 1611
  • plant counts: 205

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
12551Risk group (German classification)
1215361Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paracoccus pantotrophus 16S rRNA gene, strain ATCC 35512TY169331395nuccore82367
20218Paracoccus denitrificans partial 16S rRNA gene, strain DSM 2944AJ2881591297nuccore266
20218Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: NBRC 102493AB6818301388nuccore82367

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus pantotrophus DSM 2944GCA_008824185completencbi82367
66792Paracoccus pantotrophus strain DSM 294482367.27completepatric82367
66792Paracoccus pantotrophus strain DSM 294482367.24wgspatric82367
66792Paracoccus pantotrophus DSM 29442772190981draftimg82367
67770Paracoccus pantotrophus DSM 2944GCA_003633525contigncbi82367

GC content

  • @ref: 1255
  • GC-content: 65.8-66.0

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno89no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.664yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes78.292yes
69480spore-formingspore-formingAbility to form endo- or exosporesno91.59no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.071yes
69480flagellatedmotile2+Ability to perform flagellated movementno58.074no

External links

@ref: 1255

culture collection no.: DSM 2944, DSM 3967, LMD 82.5, JCM 21485, ATCC 35512, CIP 106514, IAM 15022, NBRC 102493, NCCB 82005

straininfo link

  • @ref: 82891
  • straininfo: 41128

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology8606159Cytochrome cb-type nitric oxide reductase with cytochrome c oxidase activity from Paracoccus denitrificans ATCC 35512.Fujiwara T, Fukumori YJ Bacteriol10.1128/jb.178.7.1866-1871.19961996Catalysis, Electron Transport, Electron Transport Complex IV/chemistry/isolation & purification/*metabolism, Molecular Structure, Nitric Oxide/metabolism, Oxidoreductases/chemistry/isolation & purification/*metabolism, Paracoccus denitrificans/*enzymology, SpectrophotometryMetabolism
Metabolism11298242Comparison of aerobic denitrification under high oxygen atmosphere by Thiosphaera pantotropha ATCC 35512 and Pseudomonas stutzeri SU2 newly isolated from the activated sludge of a piggery wastewater treatment system.Su JJ, Liu BY, Liu CYJ Appl Microbiol10.1046/j.1365-2672.2001.01265.x2001Aerobiosis, Animal Husbandry, Culture Media, Gram-Negative Chemolithotrophic Bacteria/growth & development/*metabolism, Industrial Waste, Nitrates/*metabolism, Oxygen/*pharmacology, Pseudomonas/growth & development/isolation & purification/*metabolism, Sewage/*microbiology, Waste Disposal, FluidCultivation
Genetics12813068Identification and characterization of transposable elements of Paracoccus pantotrophus.Bartosik D, Sochacka M, Baj JJ Bacteriol10.1128/JB.185.13.3753-3763.20032003Amino Acid Sequence, Base Sequence, Chromosome Mapping, Chromosomes, Bacterial, *DNA Transposable Elements, Gene Dosage, Molecular Sequence Data, Paracoccus/*genetics/growth & development, Plasmids, Sequence Analysis, DNA, Soil Microbiology, Species SpecificityTranscriptome
Metabolism15366931Paracoccus pantotrophus pseudoazurin is an electron donor to cytochrome c peroxidase.Pauleta SR, Guerlesquin F, Goodhew CF, Devreese B, Van Beeumen J, Pereira AS, Moura I, Pettigrew GWBiochemistry10.1021/bi04911442004Azurin/*analogs & derivatives/biosynthesis/genetics/*metabolism, Copper/chemistry/metabolism, Cytochrome-c Peroxidase/chemistry/*metabolism, Dimerization, Electron Transport, Gene Expression Regulation, Bacterial, Hydrophobic and Hydrophilic Interactions, Kinetics, Lysine/metabolism, Magnetic Resonance Spectroscopy, Metalloproteins/chemistry/metabolism, Models, Molecular, Oxidation-Reduction, Paracoccus pantotrophus/*enzymology, Peptide Mapping, Protein Binding, Static Electricity, Substrate SpecificityEnzymology
Metabolism26269005Sulphate production by Paracoccus pantotrophus ATCC 35512 from different sulphur substrates: sodium thiosulphate, sulphite and sulphide.Meyer DD, Andrino FG, Possedente de Lira S, Fornaro A, Corcao G, Brandelli AEnviron Technol10.1080/09593330.2015.10814112015Paracoccus pantotrophus/*metabolism, Sulfates/*metabolism, Sulfides/*metabolism, Sulfites/*metabolism, Thiosulfates/*metabolismBiotechnology
Genetics31896641Complete Genome Sequence and Annotation of the Paracoccus pantotrophus Type Strain DSM 2944.Bockwoldt JA, Zimmermann M, Tiso T, Blank LMMicrobiol Resour Announc10.1128/MRA.01290-192020
Metabolism32174525Eco-friendly decolorization and degradation of reactive yellow 145 textile dye by Pseudomonas aeruginosa and Thiosphaera pantotropha.Garg N, Garg A, Mukherji SJ Environ Manage10.1016/j.jenvman.2020.1103832020Azo Compounds, Biodegradation, Environmental, Coloring Agents, *Paracoccus pantotrophus, Pseudomonas aeruginosa, Textile Industry, Textiles

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1255Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2944)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2944
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
34087Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18653
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/
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
82891Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41128.1StrainInfo: A central database for resolving microbial strain identifiers
121536Curators of the CIPCollection of Institut Pasteur (CIP 106514)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106514