Strain identifier

BacDive ID: 13393

Type strain: Yes

Species: Pseudonocardia ammonioxydans

Strain Designation: H9, CMGCC 4.1877

Strain history: CIP <- 2006, JCM <- CGMCC 4.1877 <- Z.-H. Liu H9

NCBI tax ID(s): 260086 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 12211

BacDive-ID: 13393

DSM-Number: 44958

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

description: Pseudonocardia ammonioxydans H9 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from coastal sediment.

NCBI tax id

  • NCBI tax id: 260086
  • Matching level: species

strain history

@refhistory
12211<- Z. Liu, CGMCC
67770CGMCC 4.1877 <-- Z.-H. Liu H9.
116342CIP <- 2006, JCM <- CGMCC 4.1877 <- Z.-H. Liu H9

doi: 10.13145/bacdive13393.20230509.8.1

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 ammonioxydans
  • full scientific name: Pseudonocardia ammonioxydans Liu et al. 2006

@ref: 12211

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia ammonioxydans

full scientific name: Pseudonocardia ammonioxydans Liu et al. 2006 emend. Nouioui et al. 2018

strain designation: H9, CMGCC 4.1877

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidencemotility
31603positiverod-shaped
69480positive100
116342positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20144Brown beige (1011)10-14 daysISP 2
20144Brown beige (1011)10-14 daysISP 3
20144Beige (1001)10-14 daysISP 4
20144Beige (1001)10-14 daysISP 5
20144Beige (1001)10-14 daysISP 6
20144Beige (1001)10-14 daysISP 7
116342

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20144yesAerial MyceliumCreamISP 2
20144yesAerial MyceliumCreamISP 3
20144noISP 4
20144noISP 5
20144yesAerial MyceliumCreamISP 6
20144noISP 7

pigmentation

  • @ref: 31603
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12211LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
20144ISP 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
20144ISP 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:
20144ISP 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
20144ISP 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
20144ISP 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
20144ISP 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
12211GYM 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
116342CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
116342CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368

culture temp

@refgrowthtypetemperaturerange
12211positivegrowth28mesophilic
20144positiveoptimum28mesophilic
31603positivegrowth10-40
31603positiveoptimum10-40
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31603positivegrowth7
31603positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
12211aerobe
31603aerobe
116342obligate aerobe

spore formation

@refspore formationconfidence
31603yes
69481yes100
116342no

halophily

@refsaltgrowthtested relationconcentration
31603NaClpositivegrowth0-8 %
31603NaClpositiveoptimum3.5 %

observation

@refobservation
31603aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2014417234glucose+
2014422599arabinose-
2014417992sucrose+
2014418222xylose-
2014417268myo-inositol-
2014429864mannitol+
2014428757fructose+
2014426546rhamnose-
2014416634raffinose+
2014462968cellulose+
3160315963ribitol+carbon source
3160322599arabinose+carbon source
3160328260galactose+carbon source
3160317306maltose+carbon source
3160337684mannose+carbon source
3160317632nitrate+reduction
11634217632nitrate+reduction
11634216301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3160316136hydrogen sulfideyes
11634235581indoleno

enzymes

@refvalueactivityec
31603catalase+1.11.1.6
31603urease+3.5.1.5
116342oxidase-
116342catalase+1.11.1.6
116342urease+3.5.1.5
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
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
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
20144+++-++------+-+----
116342-++-++---++-+++-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12211coastal sedimentJiao-Dong peninsula, Tsingdao cityChinaCHNAsia
67770Coastal sedimentJiao-Dong Peninsula near Tsingdao City, Shandong ProvinceChinaCHNAsia
116342Environment, Coastal sedimentJiao Dong peninsulaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122111Risk group (German classification)
201441German classification
1163421Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12211
  • description: Pseudonocardia ammonioxydans strain H9 16S ribosomal RNA gene, partial sequence
  • accession: AY500143
  • length: 1430
  • database: ena
  • NCBI tax ID: 260086

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia ammonioxydans strain CGMCC 4.1877260086.4wgspatric260086
66792Pseudonocardia ammonioxydans CGMCC 4.18772671180038draftimg260086
67770Pseudonocardia ammonioxydans CGMCC 4.1877GCA_900115005scaffoldncbi260086

GC content

@refGC-contentmethod
1221169.6
6777069.6thermal denaturation, midpoint method (Tm)
6777073.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.358no
gram-positiveyes89.375yes
anaerobicno98.983yes
aerobicyes92.332no
halophileno74.171no
spore-formingyes74.689yes
glucose-utilyes87.595yes
flagellatedno98.176no
thermophileno98.7yes
glucose-fermentno93.132no

External links

@ref: 12211

culture collection no.: DSM 44958, CGMCC 4.1877, JCM 12462, CIP 109186, CGMCC 4.11877

straininfo link

  • @ref: 82590
  • straininfo: 290997

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16514026Pseudonocardia ammonioxydans sp. nov., isolated from coastal sediment.Liu ZP, Wu JF, Liu ZH, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.63878-02006Actinomycetales/*classification/genetics/isolation & purification/physiology, Base Composition, China, DNA, Ribosomal/chemistry, Geologic Sediments/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny30536164Pseudonocardia tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.).Song J, Qiu S, Zhao J, Han C, Wang Y, Sun X, Jiang S, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-018-01210-22018Actinobacteria/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Soil/chemistry, *Soil Microbiology, Triticum/growth & developmentMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12211Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44958)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44958
20144Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44958.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
31603Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2789128776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
82590Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290997.1StrainInfo: A central database for resolving microbial strain identifiers
116342Curators of the CIPCollection of Institut Pasteur (CIP 109186)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109186