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BacDive ID 13352
Type strain
Culture col. no. DSM 43281 ATCC 15104 NCIB 9436 VTT E-073031 VKM Ac-799 PCM 2249 NRRL B-16171 NCIMB 9436 NBRC 14498 KCTC 9692 KCTC 9301 IMSNU 22140 IMET 7645 IFO 14498 HUT 6554 CGMCC 4.1218 BCRC 13740 JCM 3392 13 more
NCBI tax ID(s) 76726
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

General

@ref: 10924

BacDive-ID: 13352

DSM-Number: 43281

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic

description: Pseudonocardia hydrocarbonoxydans DSM 43281 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from air contaminant.

NCBI tax id

  • NCBI tax id: 76726
  • Matching level: species

strain history

@refhistory
10924<- K. Kieslich, Schering 228 <- ATCC <- P. Hirsch, 70
67770DSM 43281 <-- Schering Corp.; 228 <-- ATCC 15104 <-- P. Hirsch 70.

doi: 10.13145/bacdive13352.20250331.9.3

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 hydrocarbonoxydans
  • full scientific name: Pseudonocardia hydrocarbonoxydans (Nolof and Hirsch 1962) Warwick et al. 1994

  • synonyms

    @refsynonym
    20215Amycolata hydrocarbonoxydans
    20215Nocardia hydrocarbonoxydans

@ref: 10924

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia hydrocarbonoxydans

full scientific name: Pseudonocardia hydrocarbonoxydans (Nolof and Hirsch 1962) Warwick et al. 1994

type strain: yes

Morphology

cell morphology

  • @ref: 125439
  • gram stain: positive
  • confidence: 99.5

colony morphology

@refcolony colorincubation periodmedium used
19564Signal yellow10-14 daysISP 2
19564Signal yellow10-14 daysISP 3
19564Yellow10-14 daysISP 4
19564Yellow10-14 daysISP 5
19564Yellow10-14 daysISP 6
19564Yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19564yesAerial MyceliumWhiteISP 2
19564yesAerial MyceliumWhiteISP 3
19564yesAerial MyceliumWhiteISP 4
19564yesAerial MyceliumWhiteISP 5
19564noISP 6
19564noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19564ISP 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
19564ISP 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:
19564ISP 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
19564ISP 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
19564ISP 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
19564ISP 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
10924GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65

culture temp

@refgrowthtypetemperature
19564positiveoptimum30
10924positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
125438aerobe91.066
125439obligate aerobe99.9

spore formation

  • @ref: 19564
  • spore description: Formation of spores, spore surface smooth, fragmentation
  • type of spore: spore
  • spore formation: yes

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-8(H2), MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1956417234glucose+
1956422599arabinose+
1956417992sucrose+
1956418222xylose+/-
1956417268myo-inositol-
1956429864mannitol-
1956428757fructose-
1956426546rhamnose+/-
1956416634raffinose+/-
1956462968cellulose+/-
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916024D-mannose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin+
6836835581indole-

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
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)-
68369gelatinase-
68369urease-3.5.1.5
68369beta-glucosidase+3.2.1.21
68369arginine dihydrolase-3.5.3.6
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19564+-+-+++++++++-++---
10924--+/--++/--+/--+/-----++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19564+++++-+--++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
10924+----+-++/-+/--+/---+/--+/-+/---

Isolation, sampling and environmental information

isolation

@refsample type
10924air contaminant
67770Air contaminant

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Contaminant
#Environmental#Air

taxonmaps

  • @ref: 69479
  • File name: preview.99_17769.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2672;97_3280;98_4128;99_17769&stattab=map
  • Last taxonomy: Pseudonocardia
  • 16S sequence: AJ252826
  • Sequence Identity:
  • Total samples: 1556
  • soil counts: 920
  • aquatic counts: 153
  • animal counts: 418
  • plant counts: 65

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
195641Risk group (German classification)
109241Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218A.hydrocarbonoxydans (DSM 43281) 16S ribosomal RNA (partial)X769551342nuccore76726
20218Pseudonocardia hydrocarbonoxydans 16S rRNA gene, strain IMSNU 22140TAJ2528261511nuccore76726
20218Pseudonocardia hydrocarbonoxydans 16S ribosomal RNA gene, partial sequenceGU0835691398nuccore76726

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia hydrocarbonoxydans strain NBRC 1449876726.4wgspatric76726
67770Pseudonocardia hydrocarbonoxydans NBRC 14498GCA_006539565contigncbi76726

GC content

  • @ref: 67770
  • GC-content: 69
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.33no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.448no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.066no
125438spore-formingspore-formingAbility to form endo- or exosporesyes68.357no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.95yes
125438motile2+flagellatedAbility to perform flagellated movementno87.1no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno53.2
125439BacteriaNetmotilityAbility to perform movementno72.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.9

External links

@ref: 10924

culture collection no.: DSM 43281, ATCC 15104, NCIB 9436, JCM 3392, BCRC 13740, CGMCC 4.1218, HUT 6554, IFO 14498, IMET 7645, IMSNU 22140, KCTC 9301, KCTC 9692, NBRC 14498, NCIMB 9436, NRRL B-16171, PCM 2249, VKM Ac-799, VTT E-073031

straininfo link

  • @ref: 82550
  • straininfo: 88653

literature

  • topic: Phylogeny
  • Pubmed-ID: 28151383
  • title: Pseudonocardia profundimaris sp. nov., isolated from marine sediment.
  • authors: Zhang G, Wang L, Li J, Zhou Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001849
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10924Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43281)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43281
19564Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43281.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
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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
82550Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88653.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1

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