Strain identifier

BacDive ID: 348

Type strain: Yes

Species: Castellaniella denitrificans

Strain Designation: NKNTAU

Strain history: CIP <- 2006, CCUG <- 1998, K. Denger, Konstanz Univ., Konstanz, Germany: strain NKNTAU

NCBI tax ID(s): 56119 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4168

BacDive-ID: 348

DSM-Number: 11046

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

description: Castellaniella denitrificans NKNTAU is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from anaerobic sewage digester.

NCBI tax id

  • NCBI tax id: 56119
  • Matching level: species

strain history

@refhistory
4168<- K. Denger, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; NKNTAU (Alcaligenes sp.) <- K. Denger {1996}
118893CIP <- 2006, CCUG <- 1998, K. Denger, Konstanz Univ., Konstanz, Germany: strain NKNTAU

doi: 10.13145/bacdive348.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Castellaniella
  • species: Castellaniella denitrificans
  • full scientific name: Castellaniella denitrificans Kämpfer et al. 2006

@ref: 4168

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Castellaniella

species: Castellaniella denitrificans

full scientific name: Castellaniella denitrificans Kämpfer et al. 2006

strain designation: NKNTAU

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31661negative1.3-2 µm0.2-0.8 µmrod-shapedyes
118893negativerod-shapedyes

colony morphology

  • @ref: 118893

pigmentation

  • @ref: 31661
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4168ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)yeshttps://mediadive.dsmz.de/medium/503Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: NaNO3 1.69492 g/l Na2CO3 1.49551 g/l Taurine 1.24626 g/l NaCl 0.997008 g/l KCl 0.498505 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 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 Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-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 Distilled water
37484MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
118893CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
4168positivegrowth30mesophilic
31661positivegrowth25-42
31661positiveoptimum25-30mesophilic
37484positivegrowth30mesophilic
54834positivegrowth30-37mesophilic

culture pH

@refabilitytypepH
31661positivegrowth7
31661positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
4168anaerobe
31661facultative anaerobe
54834aerobe
118893obligate aerobe

spore formation

  • @ref: 31661
  • spore formation: no

observation

  • @ref: 31661
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3166130089acetate+carbon source
3166116449alanine+carbon source
3166135391aspartate+carbon source
3166124265gluconate+carbon source
3166124996lactate+carbon source
3166125017leucine+carbon source
3166125115malate+carbon source
3166118257ornithine+carbon source
3166126271proline+carbon source
3166117272propionate+carbon source
3166115361pyruvate+carbon source
3166117822serine+carbon source
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
11889317632nitrate+reduction
11889316301nitrite+reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11889335581indoleno

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
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
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)-
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
118893oxidase+
118893catalase+1.11.1.6
118893urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
54834-----+--------------
118893-++--+------+---+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
54834+-------------++-++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4168anaerobic sewage digesterGermanyDEUEurope
54834Anaerobic sewage digesterGermanyDEUEurope
118893Environment, Anaerobic sewage digesterGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Anaerobic digestor
#Engineered#Waste#Wastewater
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_17735.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_739;97_862;98_1006;99_17735&stattab=map
  • Last taxonomy: Castellaniella denitrificans
  • 16S sequence: U82826
  • Sequence Identity:
  • Total samples: 6820
  • soil counts: 1695
  • aquatic counts: 3384
  • animal counts: 1188
  • plant counts: 553

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
41681Risk group (German classification)
1188931Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4168
  • description: Castellaniella denitrificans strain NKNTAU 16S ribosomal RNA gene, complete sequence
  • accession: U82826
  • length: 1470
  • database: ena
  • NCBI tax ID: 56119

External links

@ref: 4168

culture collection no.: CIP 109221, DSM 11046, CCUG 39541

straininfo link

  • @ref: 70028
  • straininfo: 359321

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585701Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov.Kampfer P, Denger K, Cook AM, Lee ST, Jackel U, Denner EBM, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.63989-02006Alcaligenaceae/*classification/isolation & purification, Alcaligenes/*classification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/analysis/geneticsGenetics
Phylogeny18768620Castellaniella caeni sp. nov., a denitrifying bacterium isolated from sludge of a leachate treatment plant.Liu QM, Ten LN, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.65314-02008Alcaligenaceae/*classification/genetics/*isolation & purification/physiology, Anaerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Industrial Microbiology, Locomotion, Molecular Sequence Data, Nitrogen/metabolism, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Ubiquinone/analysisGenetics
Phylogeny19605728Castellaniella ginsengisoli sp. nov., a beta-glucosidase-producing bacterium.Kim MK, Srinivasan S, Kim YJ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.008300-02009Alcaligenaceae/*classification/enzymology/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysis, beta-Glucosidase/*biosynthesisEnzymology
Phylogeny19819992Castellaniella daejeonensis sp. nov., isolated from soil.Lee M, Jung HM, Woo SG, Yoo SA, Ten LNInt J Syst Evol Microbiol10.1099/ijs.0.018887-02009Alcaligenaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny22523161Castellaniella hirudinis sp. nov., isolated from the skin of Hirudo verbana.Glaeser SP, Galatis H, Martin K, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.041392-02012Alcaligenaceae/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Leeches/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Putrescine/analogs & derivatives/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
4168Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11046)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11046
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
31661Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2794228776041
37484Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6938
54834Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39541)https://www.ccug.se/strain?id=39541
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
70028Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID359321.1StrainInfo: A central database for resolving microbial strain identifiers
118893Curators of the CIPCollection of Institut Pasteur (CIP 109221)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109221