Strain identifier

BacDive ID: 357

Type strain: Yes

Species: Pigmentiphaga kullae

Strain Designation: K24

Strain history: CIP <- 2004, CCUG <- 2002, NCIMB <- S. Blümel, Stuttgart, Germany <- T. Leisinger, ETH, Zürich, Switzerland: strain K24

NCBI tax ID(s): 151784 (species)

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General

@ref: 5109

BacDive-ID: 357

DSM-Number: 13608

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

description: Pigmentiphaga kullae K24 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 151784
  • Matching level: species

strain history

@refhistory
5109<- A. Stolz, Univ. Stuttgart <- S. Blümel <- T. Leisinger, ETH Zuerich; K24
120509CIP <- 2004, CCUG <- 2002, NCIMB <- S. Blümel, Stuttgart, Germany <- T. Leisinger, ETH, Zürich, Switzerland: strain K24

doi: 10.13145/bacdive357.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Alcaligenaceae
  • genus: Pigmentiphaga
  • species: Pigmentiphaga kullae
  • full scientific name: Pigmentiphaga kullae Blümel et al. 2001

@ref: 5109

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Pigmentiphaga

species: Pigmentiphaga kullae

full scientific name: Pigmentiphaga kullae Blümel et al. 2001

strain designation: K24

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23273negative1.3-4 µm0.7-1.2 µmrod-shapedyes
120509negativerod-shapedyes

colony morphology

@refcolony sizeincubation periodmedium usedcolony colorcolony shape
232731 mm3 daysLB agar
23273opaquecircular
120509

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5109REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
5109REACTIVATION 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
23273LB (Luria-Bertani) MEDIUMyes
33215MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120509CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120509CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
120509CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
120509CIP Medium 464yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=464

culture temp

@refgrowthtypetemperaturerange
5109positivegrowth30mesophilic
23273positivegrowth30mesophilic
23273positivegrowth37mesophilic
23273positivegrowth42thermophilic
23273nogrowth4psychrophilic
33215positivegrowth30mesophilic
120509positivegrowth15-37
120509nogrowth5psychrophilic
120509nogrowth41thermophilic
120509nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120509
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 23273
  • spore formation: no

compound production

  • @ref: 5109
  • compound: azoreductase

halophily

@refsaltgrowthtested relationconcentration
120509NaClpositivegrowth0-4 %
120509NaClnogrowth6 %
120509NaClnogrowth8 %
120509NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2327315963ribitol-builds acid from
2327317057cellobiose-builds acid from
2327318333D-arabitol-builds acid from
2327316899D-mannitol-builds acid from
2327316024D-mannose-builds acid from
2327365327D-xylose-builds acid from
2327316813galactitol-builds acid from
2327317113erythritol-builds acid from
2327317234glucose-builds acid from
2327317268myo-inositol-builds acid from
2327330849L-arabinose-builds acid from
2327317716lactose-builds acid from
2327317306maltose-builds acid from
2327328053melibiose-builds acid from
23273320061methyl alpha-D-glucopyranoside-builds acid from
2327316634raffinose-builds acid from
2327326546rhamnose-builds acid from
2327317814salicin-builds acid from
2327330911sorbitol-builds acid from
2327317992sucrose-builds acid from
2327327082trehalose-builds acid from
2327316865gamma-aminobutyric acid-carbon source
2327315963ribitol-carbon source
2327318305arbutin-carbon source
2327317057cellobiose-carbon source
2327315824D-fructose-carbon source
2327312936D-galactose-carbon source
2327317634D-glucose-carbon source
2327317306maltose-carbon source
2327316899D-mannitol-carbon source
2327316024D-mannose-carbon source
2327328053melibiose-carbon source
2327316988D-ribose-carbon source
2327317924D-sorbitol-carbon source
2327316551D-trehalose-carbon source
2327365327D-xylose-carbon source
2327324265gluconate-carbon source
2327316977L-alanine-carbon source
2327330849L-arabinose-carbon source
2327315971L-histidine-carbon source
2327315603L-leucine-carbon source
2327315729L-ornithine-carbon source
2327317295L-phenylalanine-carbon source
2327362345L-rhamnose-carbon source
2327317115L-serine-carbon source
2327316828L-tryptophan-carbon source
2327368428maltitol-carbon source
2327317268myo-inositol-carbon source
2327328037N-acetylgalactosamine-carbon source
23273506227N-acetylglucosamine-carbon source
2327318401phenylacetate-carbon source
2327317148putrescine-carbon source
2327317814salicin-carbon source
2327317992sucrose-carbon source
23273911224-nitrophenyl alpha-D-glucopyranoside-hydrolysis
232733557154-nitrophenyl beta-D-galactopyranoside-hydrolysis
23273902594-nitrophenyl beta-D-glucopyranoside-hydrolysis
23273901464-nitrophenyl beta-D-glucuronide-hydrolysis
23273901484-nitrophenyl beta-D-xylopyranoside-hydrolysis
232733122bis-4-nitrophenyl phosphate-hydrolysis
2327391050bis-4-nitrophenyl-phenyl phosphonate-hydrolysis
2327355394bis-4-nitrophenyl-phosphorylcholine-hydrolysis
23273gamma-L-glutamate-4-nitroanilide-hydrolysis
23273L-aniline-4-nitroanilide-hydrolysis
23273L-proline-4-nitroanilide-hydrolysis
23273309162-oxoglutarate+carbon source
23273161933-hydroxybenzoate+carbon source
23273370543-hydroxybutyrate+carbon source
23273178794-hydroxybenzoate+carbon source
2327330089acetate+carbon source
2327317128adipate+carbon source
2327378208azelaate+carbon source
2327316383cis-aconitate+carbon source
2327316947citrate+carbon source
2327329806fumarate+carbon source
2327317859glutaric acid+carbon source
2327317240itaconate+carbon source
2327329991L-aspartate+carbon source
2327324996lactate+carbon source
2327336986mesaconate+carbon source
2327317272propionate+carbon source
2327315361pyruvate+carbon source
232739300suberic acid+carbon source
2327315708trans-aconitate+carbon source
23273L-alanine 4-nitroanilide+hydrolysis
12050916947citrate+carbon source
1205094853esculin-hydrolysis
120509606565hippurate-hydrolysis
12050917632nitrate+reduction
12050916301nitrite-reduction
12050915792malonate+assimilation
12050917632nitrate-respiration

antibiotic resistance

  • @ref: 120509
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120509
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12050915688acetoin-
12050917234glucose-

enzymes

@refvalueactivityec
23273catalase+1.11.1.6
23273cytochrome oxidase+1.9.3.1
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
120509oxidase+
120509beta-galactosidase-3.2.1.23
120509alcohol dehydrogenase-1.1.1.1
120509gelatinase-
120509amylase-
120509DNase-
120509caseinase-3.4.21.50
120509catalase+1.11.1.6
120509tween esterase-
120509gamma-glutamyltransferase-2.3.2.2
120509lecithinase-
120509lipase-
120509lysine decarboxylase-4.1.1.18
120509ornithine decarboxylase-4.1.1.17
120509phenylalanine ammonia-lyase-4.3.1.24
120509protease-
120509tryptophan deaminase-
120509urease-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
120509--+--+---+-+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120509-------------------------------------------+--+-++++++--------++-++--------+---+++-----++++-------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
5109soilSwitzerlandCHEEurope
57611Soil,enrichment with 1-(4'-carboxy-phenylazo)-4-n.SwitzerlandCHEEuropeZürich ?
120509Environment, SoilSwitzerlandCHEEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_40308.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_1835;97_16214;98_20090;99_40308&stattab=map
  • Last taxonomy: Pigmentiphaga
  • 16S sequence: AF282916
  • Sequence Identity:
  • Total samples: 7339
  • soil counts: 1825
  • aquatic counts: 3532
  • animal counts: 1092
  • plant counts: 890

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51091Risk group (German classification)
1205091Risk group (French classification)

Sequence information

16S sequences

  • @ref: 23273
  • description: Pigmentiphaga kullae strain K24 16S ribosomal RNA gene, partial sequence
  • accession: AF282916
  • length: 1482
  • database: nuccore
  • NCBI tax ID: 151784

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pigmentiphaga kullae K24GCA_004216695contigncbi151784
66792Pigmentiphaga kullae strain K24151784.3wgspatric151784
66792Pigmentiphaga kullae DSM 136082795386136draftimg151784

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.168yes
gram-positiveno98.544yes
anaerobicno99.068no
aerobicyes92.555no
halophileno91.718no
spore-formingno95.811yes
glucose-utilno74.635no
flagellatedno70.783no
thermophileno99.139no
glucose-fermentno92.497no

External links

@ref: 5109

culture collection no.: CCUG 47266, CIP 108234, DSM 13608, NCIMB 13708

straininfo link

  • @ref: 70037
  • straininfo: 49495

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19671719Parapusillimonas granuli gen. nov., sp. nov., isolated from granules from a wastewater-treatment bioreactor.Kim YJ, Kim MK, Im WT, Srinivasan S, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.009720-02009Alcaligenaceae/classification/*genetics/isolation & purification, Base Sequence, Carboxylic Acids/metabolism, Cell Size, DNA, Bacterial/genetics, Enzymes/metabolism, Glucose/metabolism, Molecular Sequence Data, Phylogeny, Quinones/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsMetabolism
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5109Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13608)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13608
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
23273S Blümel, B Mark, H J Busse, P Kämpfer, A Stolz10.1099/00207713-51-5-1867Pigmentiphaga kullae gen. nov., sp. nov., a novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically.IJSEM 51: 1867-1871 200111594620
33215Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5834
57611Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47266)https://www.ccug.se/strain?id=47266
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)
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
70037Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49495.1StrainInfo: A central database for resolving microbial strain identifiers
120509Curators of the CIPCollection of Institut Pasteur (CIP 108234)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108234