Strain identifier

BacDive ID: 346

Type strain: Yes

Species: Castellaniella defragrans

Strain Designation: 54Pin, 54 Pin

Strain history: CIP <- 1998, J. Harder, Max Planck Inst., Bremen, Germany: strain 54 Pin

NCBI tax ID(s): 75697 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4617

BacDive-ID: 346

DSM-Number: 12141

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Castellaniella defragrans 54Pin is an aerobe, mesophilic, motile bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 75697
  • Matching level: species

strain history

@refhistory
4617<- J. Harder; 54Pin
118873CIP <- 1998, J. Harder, Max Planck Inst., Bremen, Germany: strain 54 Pin

doi: 10.13145/bacdive346.20230509.8.1

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 defragrans
  • full scientific name: Castellaniella defragrans (Foss et al. 1998) Kämpfer et al. 2006
  • synonyms

    • @ref: 20215
    • synonym: Alcaligenes defragrans

@ref: 4617

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Castellaniella

species: Castellaniella defragrans

full scientific name: Castellaniella defragrans (Foss et al. 1998) Kämpfer et al. 2006

strain designation: 54Pin, 54 Pin

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.484
6948099.999negative
118873yesnegativerod-shaped

colony morphology

  • @ref: 118873
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4617ANAEROBIC THAUERA MEDIUM (DSMZ Medium 1315)yeshttps://mediadive.dsmz.de/medium/1315Name: ANAEROBIC THAUERA MEDIUM (DSMZ Medium 1315) Composition: NaHCO3 2.52 g/l Na2HPO4 x 2 H2O 1.45 g/l K-acetate 0.98 g/l KNO3 0.85 g/l MgSO4 x 7 H2O 0.5 g/l NH4Cl 0.3 g/l KH2PO4 0.25 g/l NaCl 0.05 g/l MnSO4 0.01 g/l CaCl2 0.01 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l NaOH 0.001 g/l alpha-lipoic acid 0.00025 g/l Riboflavin 0.00025 g/l Thiamine-HCl x 2 H2O 0.00025 g/l Vitamin B12 0.00025 g/l Pantothenic acid 0.00025 g/l p-Aminobenzoic acid 0.00025 g/l CoCl2 x 6 H2O 0.00019 g/l Nicotinic acid 0.000125 g/l Nicotine amide 0.000125 g/l Folic acid 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l Biotin 0.0001 g/l ZnCl2 7e-05 g/l Pyridoxamine hydrochloride 5e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2WO4 x 2 H2O 8e-06 g/l Na2SeO3 x 5 H2O 6e-06 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
4617REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38568MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118873CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4617positivegrowth30mesophilic
38568positivegrowth30mesophilic
54933positivegrowth25-42
118873positivegrowth15-41
118873nogrowth5psychrophilic
118873nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54933aerobe
118873obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

compound production

  • @ref: 4617

halophily

@refsaltgrowthtested relationconcentration
118873NaClpositivegrowth0-4 %
118873NaClnogrowth6 %
118873NaClnogrowth8 %
118873NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118873citrate+carbon source16947
118873esculin-hydrolysis4853
118873hippurate+hydrolysis606565
118873nitrate+builds gas from17632
118873nitrate+reduction17632
118873nitrite+builds gas from16301
118873nitrite+reduction16301
118873malonate-assimilation15792
118873nitrate+respiration17632

antibiotic resistance

  • @ref: 118873
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 118873
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11887315688acetoin-
11887317234glucose-

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
118873oxidase+
118873beta-galactosidase-3.2.1.23
118873alcohol dehydrogenase-1.1.1.1
118873gelatinase+
118873amylase-
118873DNase-
118873caseinase-3.4.21.50
118873catalase+1.11.1.6
118873tween esterase-
118873gamma-glutamyltransferase+2.3.2.2
118873lecithinase-
118873lipase-
118873lysine decarboxylase-4.1.1.18
118873ornithine decarboxylase-4.1.1.17
118873phenylalanine ammonia-lyase+4.3.1.24
118873protease-
118873tryptophan deaminase-
118873urease-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
118873--++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118873-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118873++-----------------------------+-----------------++--++++-+-+++++-++--+--+-+-----------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
4617activated sludgeGermanyDEUEurope
54933Activated sludgeGermanyDEUEurope1995
118873Environment, Activated sludgeGermanyDEUEuropeNorthern1995

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_1274.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_739;97_862;98_1006;99_1274&stattab=map
  • Last taxonomy: Castellaniella defragrans
  • 16S sequence: AJ005447
  • Sequence Identity:
  • Total samples: 4605
  • soil counts: 1788
  • aquatic counts: 1604
  • animal counts: 804
  • plant counts: 409

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
46171Risk group (German classification)
1188731Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Alcaligenes defragrans 16S rRNA gene, strain 54Pin
  • accession: AJ005447
  • length: 1484
  • database: ena
  • NCBI tax ID: 75697

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Castellaniella defragrans DSM 12141GCA_014203015scaffoldncbi75697
66792Castellaniella defragrans CCUG 39790GCA_008801975contigncbi75697
66792Castellaniella defragrans strain CCUG 3979075697.10wgspatric75697
66792Castellaniella defragrans strain DSM 1214175697.11wgspatric75697
66792Castellaniella defragrans DSM 121412861677110draftimg75697

GC content

  • @ref: 4617
  • GC-content: 66.9±0.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno65.279no
gram-positiveno97.814no
anaerobicno97.435yes
aerobicyes78.64no
halophileno90.079no
spore-formingno93.912no
glucose-utilno66.162no
thermophileno96.186yes
motileyes90.034no
glucose-fermentno89.786no

External links

@ref: 4617

culture collection no.: DSM 12141, CCUG 39790, CIP 105602, LMG 18538

straininfo link

  • @ref: 70026
  • straininfo: 12163

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9704110Alcaligenes defragrans sp. nov., description of four strains isolated on alkenoic monoterpenes ((+)-menthene, alpha-pinene, 2-carene, and alpha-phellandrene) and nitrate.Foss S, Heyen U, Harder JSyst Appl Microbiol10.1016/s0723-2020(98)80028-31998Alcaligenes/chemistry/growth & development/*isolation & purification, Ammonia/analysis, Base Sequence, Bicyclic Monoterpenes, Chromatography, High Pressure Liquid, Cyclohexane Monoterpenes, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Microscopy, Phase-Contrast, Molecular Sequence Data, *Monoterpenes, Nephelometry and Turbidimetry, Nitrates/analysis/*metabolism, Nitrites/analysis, Phylogeny, Polymerase Chain Reaction, Sequence Analysis, DNA, Terpenes/chemistry/*metabolismGenetics
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
Phylogeny16738107Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3'-dithiodipropionic acid.Wubbeler JH, Lutke-Eversloh T, Van Trappen S, Vandamme P, Steinbuchel AInt J Syst Evol Microbiol10.1099/ijs.0.64126-02006Alcaligenaceae/*classification/isolation & purification, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, Disulfides/metabolism, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsEnzymology
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
Phylogeny21717340Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field.Kim SJ, Yoo SH, Weon HY, Kim YS, Anandham R, Suh JS, Kwon SWJ Microbiol10.1007/s12275-011-0076-72011*Agriculture, Alcaligenaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis/genetics, Genes, rRNA, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityPhenotype
Phylogeny32369004Pusillimonas maritima sp. nov., isolated from surface seawater.Li J, Qi M, Lai Q, Dong C, Liu X, Wang G, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0042022020Alcaligenaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Indian Ocean, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*chemistry, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4617Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12141)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12141
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
38568Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17639
54933Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39790)https://www.ccug.se/strain?id=39790
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)
68371Automatically annotated from API 50CH acid
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
70026Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12163.1StrainInfo: A central database for resolving microbial strain identifiers
118873Curators of the CIPCollection of Institut Pasteur (CIP 105602)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105602