Strain identifier

BacDive ID: 13356

Type strain: Yes

Species: Pseudonocardia petroleophila

Strain Designation: 78

Strain history: CIP <- 1995, IFO <- 1984, ATCC <- P. Hirsch: strain 78

NCBI tax ID(s): 37331 (species)

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General

@ref: 10857

BacDive-ID: 13356

DSM-Number: 43193

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

description: Pseudonocardia petroleophila 78 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 37331
  • Matching level: species

strain history

@refhistory
10857<- I. J. Bousfield, NCIB <- P. Hirsch, 78
67770IFM 0243 <-- IFO 14406 <-- ATCC 15777 <-- P. Hirsch 78.
121789CIP <- 1995, IFO <- 1984, ATCC <- P. Hirsch: strain 78

doi: 10.13145/bacdive13356.20230509.8.1

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 petroleophila
  • full scientific name: Pseudonocardia petroleophila (Hirsch and Engel 1956) Warwick et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Nocardia petroleophila

@ref: 10857

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia petroleophila

full scientific name: Pseudonocardia petroleophila (Hirsch and Engel 1956) Warwick et al. 1994

strain designation: 78

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.865
69480100positive
121789nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10857TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
10857MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yeshttps://mediadive.dsmz.de/medium/81Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
10857GLYCEROL-SOIL MEDIUM (DSMZ Medium 80)yeshttps://mediadive.dsmz.de/medium/80Name: GLYCEROL-SOIL MEDIUM (DSMZ Medium 80) Composition: Glycerol 20.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Beef extract 3.0 g/l Soil extract Distilled water
39024MEDIUM 129 - for Pseudonocardia, Nocardia, Skermania and Streptomyces seoulensis, Streptomyces stramineusyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (10.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
121789CIP Medium 129yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=129

culture temp

@refgrowthtypetemperaturerange
10857positivegrowth28mesophilic
39024positivegrowth25mesophilic
67770positivegrowth28mesophilic
121789positivegrowth25mesophilic
121789nogrowth10psychrophilic
121789nogrowth37mesophilic
121789nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121789
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 90.638

compound production

  • @ref: 10857
  • compound: hydrocarbons

halophily

@refsaltgrowthtested relationconcentration
18481NaClpositivemaximum2.5 %
121789NaClpositivegrowth0-6 %
121789NaClnogrowth8 %
121789NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1848117234glucose+
1848122599arabinose+
1848117992sucrose+
1848118222xylose+
1848117268myo-inositol+
1848129864mannitol-
1848128757fructose-
1848126546rhamnose+
1848116634raffinose+
1848162968cellulose+
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1217894853esculin+hydrolysis
121789606565hippurate-hydrolysis
12178917632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12178935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-
12178915688acetoin-

enzymes

@refvalueactivityec
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
121789oxidase-
121789beta-galactosidase-3.2.1.23
121789alcohol dehydrogenase-1.1.1.1
121789gelatinase-
121789amylase+
121789DNase+
121789caseinase-3.4.21.50
121789catalase+1.11.1.6
121789tween esterase-
121789lecithinase+
121789lipase-
121789lysine decarboxylase-4.1.1.18
121789ornithine decarboxylase-4.1.1.17
121789urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382acid phosphatase+3.1.3.2
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- FucosidaseControl
18481+++-++++++-++-++---
121789+++-+----++-+-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18481+++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121789---+/----------+/----------+/-+/-+/-+/-+/---------------------+/-

Isolation, sampling and environmental information

isolation

@refsample type
10857soil
67770Soil
121789Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_32457.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1626;97_13840;98_17064;99_32457&stattab=map
  • Last taxonomy: Pseudonocardia petroleophila
  • 16S sequence: AJ252828
  • Sequence Identity:
  • Total samples: 272
  • soil counts: 160
  • aquatic counts: 41
  • animal counts: 54
  • plant counts: 17

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
108571Risk group (German classification)
184811German classification
1217892Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudonocardia petroleophila 16S rRNA gene, strain ATCC 15777TX805961402ena37331
20218Amycolata petrophilea 16S ribosomal RNA, partX556081419ena37331
20218Pseudonocardia petroleophila 16S rRNA gene, strain IMSNU 22072TAJ2528281515ena37331
20218Pseudonocardia petroleophila 16S ribosomal RNA gene, partial sequenceGU0835701417ena37331

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia petroleophila CGMCC 4.1532GCA_014235185completencbi37331
66792Pseudonocardia sp. CGMCC 4.15322761535.3completepatric2761535

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes81no
flagellatedno98.364no
gram-positiveyes90.861no
anaerobicno99.034no
aerobicyes92.588no
halophileno93.746no
spore-formingyes67.749no
glucose-utilyes85.209yes
thermophileno99.587no
motileno92.822no
glucose-fermentno93.319no

External links

@ref: 10857

culture collection no.: DSM 43193, ATCC 15777, DSM 655, IFO 14406, IMET 7162, JCM 3378, JCM 3394, NBRC 14406, NCIB 9438, BCRC 13694, CGMCC 4.1532, CIP 104515, IFM 0243, IMSNU 22072, KCTC 1060, MTCC 273, NCIMB 9438, NRRL B-16301, NRRL B-3075, VKM Ac-865

straininfo link

  • @ref: 82554
  • straininfo: 88075

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21691777Pseudonocardia serianimatus sp. nov., a novel actinomycete isolated from the surface-sterilized leaves of Artemisia annua L.Zhao GZ, Zhu WY, Li J, Xie Q, Xu LH, Li WJAntonie Van Leeuwenhoek10.1007/s10482-011-9607-92011Actinomycetales/classification/genetics/*isolation & purification, Artemisia annua/*microbiology, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolismMetabolism
Phylogeny33528351Pseudonocardia broussonetiae sp. nov., an endophytic actinomycete isolated from the roots of Broussonetia papyrifera.Mo P, Zhao Y, Liu J, Xu Z, Gao JInt J Syst Evol Microbiol10.1099/ijsem.0.0046802021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10857Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43193)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43193
18481Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43193.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
39024Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16432
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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)
82554Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88075.1StrainInfo: A central database for resolving microbial strain identifiers
121789Curators of the CIPCollection of Institut Pasteur (CIP 104515)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104515