Strain identifier

BacDive ID: 13404

Type strain: Yes

Species: Pseudonocardia tropica

Strain history: W.-J. Li YIM 61452.

NCBI tax ID(s): 681289 (species)

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General

@ref: 15711

BacDive-ID: 13404

DSM-Number: 45199

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

description: Pseudonocardia tropica DSM 45199 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from surface-sterilized stem of Maytenus austroyunnanensis collected from the tropical rainforest.

NCBI tax id

  • NCBI tax id: 681289
  • Matching level: species

strain history

@refhistory
15711<- S.-K. Tang, YIM; YIM 61452 <- S. Qin and et al.
67770W.-J. Li YIM 61452.

doi: 10.13145/bacdive13404.20230509.8.1

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 tropica
  • full scientific name: Pseudonocardia tropica Qin et al. 2010

@ref: 15711

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia tropica

full scientific name: Pseudonocardia tropica Qin et al. 2010

type strain: yes

Morphology

cell morphology

  • @ref: 29750
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
21391Clay brown (8003)10-14 daysISP 2
21391Clay brown (8003)10-14 daysISP 3
21391Beige brown (8024)10-14 daysISP 4
21391Clay brown (8003)10-14 daysISP 5
21391Ochre brown (8001)10-14 daysISP 7
21391Nut brown (8011)10-14 daysSuter with tyrosine
21391Fawn brown (8007)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
21391yesAerial MyceliumPure white (9010)ISP 2
21391yesAerial MyceliumCream (9001)ISP 3
21391yesAerial MyceliumTraffic white (9016)ISP 4
21391yesAerial MyceliumBeige (1001)ISP 5
21391noISP 7
21391yesAerial MyceliumOyster white (1013)Suter with tyrosine
21391yesAerial MyceliumLight grey (7035)Suter without tyrosine

pigmentation

  • @ref: 29750
  • production: yes

multimedia

  • @ref: 15711
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45199.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15711GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
21391ISP 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
21391ISP 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:
21391ISP 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
21391ISP 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
21391ISP 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
21391Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21391Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
15711positivegrowth28mesophilic
29750positivegrowth15-37
29750positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29750positivegrowth06-09alkaliphile
29750positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29750
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29750
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
21391NaClpositivemaximum5 %
29750NaClpositivegrowth0-10 %
29750NaClpositiveoptimum1 %

observation

@refobservation
29750aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2139117234glucose+
2139122599arabinose+
2139117992sucrose+
2139118222xylose+
2139117268myo-inositol+
2139137684mannose+
2139128757fructose+
2139126546rhamnose+
2139116634raffinose+
2139162968cellulose+
2975017057cellobiose+carbon source
2975028757fructose+carbon source
2975017234glucose+carbon source
2975017306maltose+carbon source
2975029864mannitol+carbon source
2975017992sucrose+carbon source
2975018222xylose+carbon source
2975017632nitrate+reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29750catalase+1.11.1.6
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68382alkaline phosphatase-3.1.3.1
68382lipase (C 14)-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACGLYG
21391---------+-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21391-+/-+/--+/-+/----+/------+/----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15711surface-sterilized stem of Maytenus austroyunnanensis collected from the tropical rainforestMaytenus austroyunnanensisYunnan Province, XishuangbannaChinaCHNAsia
67770Surface-sterilized stem of Maytenus austroyunnanensis from the tropical rainforestMaytenus austroyunnanensisXishuangbanna, Yunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Stem (Branch)
#Host Body-Site#Plant#Sterilized plant part
#Climate#Hot#Tropical

taxonmaps

  • @ref: 69479
  • File name: preview.99_250.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_175;97_189;98_212;99_250&stattab=map
  • Last taxonomy: Pseudonocardia
  • 16S sequence: GQ906587
  • Sequence Identity:
  • Total samples: 16902
  • soil counts: 7999
  • aquatic counts: 2199
  • animal counts: 3094
  • plant counts: 3610

Safety information

risk assessment

  • @ref: 15711
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15711
  • description: Pseudonocardia tropica strain YIM 61452 16S ribosomal RNA gene, partial sequence
  • accession: GQ906587
  • length: 1461
  • database: ena
  • NCBI tax ID: 681289

GC content

@refGC-contentmethod
1571172.4high performance liquid chromatography (HPLC)
2975072.4

External links

@ref: 15711

culture collection no.: DSM 45199, CCTCC AA 208018, YIM 61452, JCM 19149

straininfo link

  • @ref: 82602
  • straininfo: 399811

literature

  • topic: Phylogeny
  • Pubmed-ID: 19965996
  • title: Pseudonocardia tropica sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis.
  • authors: Qin S, Zhu WY, Jiang JH, Klenk HP, Li J, Zhao GZ, Xu LH, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.020099-0
  • year: 2009
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/metabolism, Maytenus/*microbiology/physiology, Molecular Sequence Data, Phylogeny, Plant Stems/microbiology/physiology, RNA, Ribosomal, 16S/genetics, Symbiosis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15711Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45199)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45199
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
21391Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45199.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29750Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2613228776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
82602Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399811.1StrainInfo: A central database for resolving microbial strain identifiers