Strain identifier

BacDive ID: 2929

Type strain: Yes

Species: Comamonas nitrativorans

Strain Designation: 23310

Strain history: CIP <- 2001, C. Etchebehere, Departamento de Microbiologia, Uruguay: strain 23310

NCBI tax ID(s): 1121350 (strain), 108437 (species)

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General

@ref: 4860

BacDive-ID: 2929

DSM-Number: 13191

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Comamonas nitrativorans 23310 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from lab. scale denitrifying reactor treating landfill leachate.

NCBI tax id

NCBI tax idMatching level
1121350strain
108437species

strain history

@refhistory
4860<- C. Etchebehere; 23310
398902001, C. Etchebehere, Departamento de Microbiologia, Uruguay: strain 23310
121308CIP <- 2001, C. Etchebehere, Departamento de Microbiologia, Uruguay: strain 23310

doi: 10.13145/bacdive2929.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Comamonas
  • species: Comamonas nitrativorans
  • full scientific name: Comamonas nitrativorans Etchebehere et al. 2001

@ref: 4860

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Comamonas

species: Comamonas nitrativorans

full scientific name: Comamonas nitrativorans Etchebehere et al. 2001

strain designation: 23310

type strain: yes

Morphology

cell morphology

  • @ref: 121308
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 121308
  • production: no
  • name: Pyocyanin

multimedia

  • @ref: 4860
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_13191.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4860NUTRIENT 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
4860BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215; with strain-specific modifications) Composition: Brain heart infusion 37.0 g/l KNO3 0.72 g/l Distilled water
39890MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121308CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4860positivegrowth30mesophilic
39890positivegrowth30mesophilic
121308positivegrowth25-41
121308nogrowth5psychrophilic
121308nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
4860aerobe
4860microaerophile
121308obligate aerobe

halophily

  • @ref: 121308
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12130816947citrate-carbon source
1213084853esculin-hydrolysis
12130817632nitrate+reduction
12130816301nitrite+reduction
12130817632nitrate+respiration

antibiotic resistance

  • @ref: 121308
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12130835581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121308oxidase+
121308beta-galactosidase-3.2.1.23
121308alcohol dehydrogenase-1.1.1.1
121308gelatinase-
121308amylase-
121308DNase-
121308caseinase-3.4.21.50
121308catalase+1.11.1.6
121308tween esterase-
121308lecithinase-
121308lipase-
121308lysine decarboxylase-4.1.1.18
121308ornithine decarboxylase-4.1.1.17
121308protease-
121308tryptophan deaminase-
121308urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    56922C12:08.712
    56922C14:05.614
    56922C16:014.216
    56922C10:0 3OH1011.423
    56922C16:1 ω7c50.815.819
    56922C18:1 ω7c /12t/9t10.717.824
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121308--+--+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4860+----------------+-++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121308-------------------------------------------------+-----------+++---------+-+---++--+----++++++---+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4860lab. scale denitrifying reactor treating landfill leachateMontevideoUruguayURYMiddle and South America
56922Landfill leachate,denitrifying reactor
121308Denitrifying reactor treating landfill leachateUruguayURYMiddle and South America1998

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste#Landfill
#Engineered#Waste#Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_124254.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_8818;97_10600;98_15307;99_124254&stattab=map
  • Last taxonomy: Comamonas nitrativorans subclade
  • 16S sequence: AJ251577
  • Sequence Identity:
  • Total samples: 216
  • soil counts: 14
  • aquatic counts: 131
  • animal counts: 64
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48601Risk group (German classification)
1213081Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Comamonas sp. 16S rRNA gene, strain 23310
  • accession: AJ251577
  • length: 1498
  • database: ena
  • NCBI tax ID: 108437

Genome sequences

  • @ref: 66792
  • description: Comamonas nitrativorans DSM 13191
  • accession: 2574180442
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1121350

External links

@ref: 4860

culture collection no.: DSM 13191, CCT 7062, NCCB 100007, CCUG 45781, CIP 107121

straininfo link

  • @ref: 72452
  • straininfo: 49433

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11411724Comamonas nitrativorans sp. nov., a novel denitrifier isolated from a denitrifying reactor treating landfill leachate.Etchebehere C, Errazquin MI, Dabert P, Moletta R, Muxi LInt J Syst Evol Microbiol10.1099/00207713-51-3-9772001Anaerobiosis, Carboxylic Acids/metabolism, Catalase/metabolism, Comamonas/*classification/genetics/isolation & purification/physiology, DNA, Ribosomal/genetics, Environmental Pollutants/metabolism, Molecular Sequence Data, Nitrates/metabolism, Oxidoreductases/metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, UruguayMetabolism
Phylogeny18758728Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant.Kim KH, Ten LN, Liu QM, Im WT, Lee STJ Microbiol10.1007/s12275-008-0019-02008Base Composition, Bioreactors/microbiology, Comamonas/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, *Industrial Waste, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiologyMetabolism
Phylogeny24633862Comamonas faecalis sp. nov., isolated from domestic pig feces.Kim D, Lee SSCurr Microbiol10.1007/s00284-014-0561-42014Animals, Base Composition, Base Sequence, Comamonas/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/*analysis, Feces/microbiology, Gram-Negative Bacterial Infections/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA/veterinary, Sus scrofa, Swine, Swine Diseases/*microbiology, Ubiquinone/*analysisGenetics
Phylogeny32170406Comamonas flocculans sp. nov., a Floc-Forming Bacterium Isolated from Livestock Wastewater.Kim DH, Han KI, Kwon HJ, Kim MG, Kim YG, Choi DH, Lee KC, Suh MK, Kim HS, Lee JS, Kim JGCurr Microbiol10.1007/s00284-020-01940-52020Animals, Bacterial Typing Techniques, Base Composition, Comamonas/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genome, Bacterial, Livestock/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, Waste Water/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4860Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13191)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13191
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
39890Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4522
56922Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45781)https://www.ccug.se/strain?id=45781
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)
68369Automatically annotated from API 20NE
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
72452Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49433.1StrainInfo: A central database for resolving microbial strain identifiers
121308Curators of the CIPCollection of Institut Pasteur (CIP 107121)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107121