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, mesophilic, Gram-negative

description: Paracoccus pantotrophus GB 17 is an obligate aerobe, mesophilic, Gram-negative 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/bacdive13706.20230509.8.1

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 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 stainconfidencecell shapemotility
69480negative99.999
121536negativeovoid-shapedno

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

@refgrowthtypetemperaturerange
1255positivegrowth28mesophilic
34087positivegrowth37mesophilic
67770positivegrowth37mesophilic
121536positivegrowth25-41
121536nogrowth5psychrophilic
121536nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121536
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.977

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 35512TY169331395ena82367
20218Paracoccus denitrificans partial 16S rRNA gene, strain DSM 2944AJ2881591297ena266
20218Paracoccus pantotrophus gene for 16S rRNA, partial sequence, strain: NBRC 102493AB6818301388ena82367

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

traitpredictionconfidencetraining_data
spore-formingno89no
motileno64.257no
flagellatedno85.81no
gram-positiveno99.005no
anaerobicno96.978no
aerobicyes89.009no
halophileno80.341no
spore-formingno96.947no
thermophileno90.516yes
glucose-utilyes88.72no
glucose-fermentno86.056no

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)
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