Strain identifier

BacDive ID: 13412

Type strain: Yes

Species: Pseudonocardia xishanensis

Strain history: <- S-K Tang, Yunnan Inst., China

NCBI tax ID(s): 630995 (species)

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General

@ref: 17967

BacDive-ID: 13412

DSM-Number: 45635

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

description: Pseudonocardia xishanensis DSM 45635 is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from surface-sterilized roots of Artemisia annua L..

NCBI tax id

  • NCBI tax id: 630995
  • Matching level: species

strain history

@refhistory
17967<- S.-K. Tang, YIM; YIM 63638 <- G.-Z. Zhao
67770S.-K. Tang YIM 63638.
67771<- S-K Tang, Yunnan Inst., China

doi: 10.13145/bacdive13412.20230509.8.1

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 xishanensis
  • full scientific name: Pseudonocardia xishanensis Zhao et al. 2012

@ref: 17967

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia xishanensis

full scientific name: Pseudonocardia xishanensis Zhao et al. 2012

type strain: yes

Morphology

cell morphology

@refgram stainmotility
30479positiveno
67771positive

colony morphology

@refcolony colormedium used
69413Beige (1001)ISP 6
69413Ivory (1014)ISP 4
69413Light ivory (1015)ISP 3
69413Sand yellow (1002)suter without tyrosine
69413Sand yellow (1002), golden yellow (1004)ISP 2

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
69413yesAerial myceliumISP 2
69413yesAerial myceliumISP 3Cream (9001)
69413yesAerial myceliumISP 4
69413yesAerial myceliumISP 5Pure white (6010), brown beige (1011)
69413yesAerial myceliumISP 6
69413yesAerial myceliumISP 7Light ivory (1015), beige (1001)
69413yesAerial myceliumsuter with tyrosineBeige (1001), cream (9001)
69413yesAerial myceliumsuter without tyrosineCream (1002)

pigmentation

@refproductioncolorname
30479yes
69413yesSand yellow (1002)soluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69413DSM_45635_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69413DSM_45635_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 17967
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
17967positivegrowth28mesophilic
30479positivegrowth10-42
30479positiveoptimum28.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30479positivegrowth05-09alkaliphile
30479positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30479aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
30479NaClpositivegrowth0-7 %
30479NaClpositiveoptimum1.5 %
69413NaClpositivegrowth0-5 %

observation

@refobservation
67770quinones: MK-8(H4)
67771quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3047922599arabinose+carbon source
3047917057cellobiose+carbon source
3047928757fructose+carbon source
3047928260galactose+carbon source
3047917234glucose+carbon source
3047917754glycerol+carbon source
3047917716lactose+carbon source
3047917306maltose+carbon source
3047929864mannitol+carbon source
3047937684mannose+carbon source
3047917268myo-inositol+carbon source
3047926546rhamnose+carbon source
3047930911sorbitol+carbon source
3047917992sucrose+carbon source
3047918222xylose+carbon source
6941322599arabinose-growth
6941362968cellulose-growth
6941328757fructose+/-growth
6941317234glucose+growth
6941317268inositol+/-growth
6941337684mannose+/-growth
6941316634raffinose-growth
6941326546rhamnose-growth
6941317992sucrose+growth
6941318222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
30479catalase+1.11.1.6
30479urease+3.5.1.5
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
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69413--+/-+--+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69413+++-+++/---++---+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
17967surface-sterilized roots of Artemisia annua L.Artemisia annuaYunnan province, Kunming City, Xishan MountainChinaCHNAsia
67770Surface-sterilized roots of Artemisia annua from Xishan MountainArtemisia annuaKunming City, Yunnan Province, south-west ChinaChinaCHNAsia
67771From plantYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_99558.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2672;97_3280;98_12070;99_99558&stattab=map
  • Last taxonomy: Pseudonocardia xishanensis
  • 16S sequence: FJ817397
  • Sequence Identity:
  • Total samples: 75
  • soil counts: 42
  • aquatic counts: 13
  • animal counts: 12
  • plant counts: 8

Safety information

risk assessment

  • @ref: 17967
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17967
  • description: Pseudonocardia xishanensis strain YIM 63638 16S ribosomal RNA gene, partial sequence
  • accession: FJ817397
  • length: 1521
  • database: ena
  • NCBI tax ID: 630995

GC content

@refGC-contentmethod
1796772.1high performance liquid chromatography (HPLC)
6777172.1

External links

@ref: 17967

culture collection no.: DSM 45635, JCM 17906, KCTC 29005, YIM 63638, BCRC 16943

straininfo link

  • @ref: 82609
  • straininfo: 403372

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22140165Pseudonocardia xishanensis sp. nov., an endophytic actinomycete isolated from the roots of Artemisia annua L.Zhao GZ, Li J, Zhu WY, Wei DQ, Zhang JL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.037028-02011Actinomycetales/*classification/genetics/isolation & purification, Artemisia annua/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny28853680Pseudonocardia thailandensis sp. nov., an actinomycete isolated from a subterranean termite nest.Sujarit K, Sujada N, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong SInt J Syst Evol Microbiol10.1099/ijsem.0.0020172017Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Isoptera/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33890128Pseudonocardia pini sp. nov., an endophytic actinobacterium isolated from roots of the pine tree Callitris preissii.Kaewkla O, Franco CMMArch Microbiol10.1007/s00203-021-02309-32021*Cupressaceae/microbiology, Fatty Acids/analysis, Nucleic Acid Hybridization, Phylogeny, *Plant Roots/microbiology, *Pseudonocardia/classification/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17967Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45635)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45635
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
30479Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2681328776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69413Wink, J.https://cdn.dsmz.de/wink/DSM%2045635.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
82609Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403372.1StrainInfo: A central database for resolving microbial strain identifiers