Strain identifier

BacDive ID: 13387

Type strain: Yes

Species: Pseudonocardia benzenivorans

Strain Designation: B5

Strain history: CIP 107928 <-- P. Kämpfer B5 <-- A. Prieger-Kraft.

NCBI tax ID(s): 228005 (species)

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General

@ref: 11894

BacDive-ID: 13387

DSM-Number: 44703

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Pseudonocardia benzenivorans B5 is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from enrichment culture from soil.

NCBI tax id

  • NCBI tax id: 228005
  • Matching level: species

strain history

@refhistory
11894<- P. Kämpfer; B5 <- A. Prieger-Kraft
67770CIP 107928 <-- P. Kämpfer B5 <-- A. Prieger-Kraft.

doi: 10.13145/bacdive13387.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia benzenivorans
  • full scientific name: Pseudonocardia benzenivorans Kämpfer and Kroppenstedt 2004

@ref: 11894

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia benzenivorans

full scientific name: Pseudonocardia benzenivorans Kämpfer and Kroppenstedt 2004

strain designation: B5

type strain: yes

Morphology

cell morphology

  • @ref: 30010
  • gram stain: positive
  • cell shape: rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20097Sand yellow (1002)10-14 daysISP 2
20097Sand yellow (1002)10-14 daysISP 3
20097Beige (1001)10-14 daysISP 4
20097Beige (1001)10-14 daysISP 5
2009710-14 daysISP 6
20097Rose (3017)10-14 daysISP 7
584425-12 days

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20097yesAerial MyceliumWhiteISP 2
20097yesAerial MyceliumWhiteISP 3
20097yesAerial MyceliumWhiteISP 4
20097yesAerial MyceliumWhiteISP 5
20097noISP 6
20097yesAerial MyceliumWhiteISP 7

pigmentation

  • @ref: 30010
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11894GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
11894GYM+S MEDIUM (DSMZ Medium 214)yeshttps://mediadive.dsmz.de/medium/214Name: GYM+S MEDIUM (DSMZ Medium 214) Composition: Starch 20.0 g/l Agar 12.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
20097ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20097ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20097ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20097ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20097ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
20097ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
11894positivegrowth28mesophilic
20097positiveoptimum28
30010positivegrowth25-30
30010positiveoptimum27.5
58442positivegrowth30
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30010aerobe
58442aerobe

spore formation

  • @ref: 30010
  • spore formation: no

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2009717234glucose+
2009722599arabinose-
2009717992sucrose-
2009718222xylose+
2009717268myo-inositol+
2009729864mannitol-
2009728757fructose-
2009726546rhamnose+
2009716634raffinose+
2009762968cellulose+
30010178794-hydroxybenzoate+carbon source
3001017240itaconate+carbon source
3001024996lactate+carbon source
3001037684mannose+carbon source
3001028044phenylalanine+carbon source
3001033942ribose+carbon source
3001017822serine+carbon source
3001027082trehalose+carbon source
3001018222xylose+carbon source

enzymes

@refvalueactivityec
30010cytochrome oxidase+1.9.3.1
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20097-++-+---------+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11894enrichment culture from soilSachsen, BitterfeldGermanyDEUEurope
67770Enrichment culture from soilBitterfeldGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5531.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2672;97_3280;98_4128;99_5531&stattab=map
  • Last taxonomy: Pseudonocardia
  • 16S sequence: AJ556156
  • Sequence Identity:
  • Total samples: 1848
  • soil counts: 1233
  • aquatic counts: 241
  • animal counts: 242
  • plant counts: 132

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118941Risk group (German classification)
200971German classification

Sequence information

16S sequences

  • @ref: 11894
  • description: Pseudonocardia benzenivorans partial 16S rRNA gene, type strain B5
  • accession: AJ556156
  • length: 1494
  • database: ena
  • NCBI tax ID: 228005

External links

@ref: 11894

culture collection no.: DSM 44703, CIP 107928, CCUG 49018, JCM 12694

straininfo link

  • @ref: 82584
  • straininfo: 132027

literature

  • topic: Phylogeny
  • Pubmed-ID: 15143019
  • title: Pseudonocardia benzenivorans sp. nov.
  • authors: Kampfer P, Kroppenstedt RM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02825-0
  • year: 2004
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/metabolism, Chlorobenzenes/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
11894Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44703)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44703
20097Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44703.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
30010Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2637428776041
58442Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49018)https://www.ccug.se/strain?id=49018
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
82584Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132027.1StrainInfo: A central database for resolving microbial strain identifiers