Strain identifier

BacDive ID: 13390

Type strain: Yes

Species: Pseudonocardia zijingensis

Strain Designation: 6330

Strain history: CIP <- 2002, JCM <- 2001, Z. Liu: strain 6330

NCBI tax ID(s): 153376 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12079

BacDive-ID: 13390

DSM-Number: 44774

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

description: Pseudonocardia zijingensis 6330 is a mesophilic, Gram-positive, rod-shaped bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 153376
  • Matching level: species

strain history

@refhistory
12079<- CGMCC <- Z. Liu; 6330
67770Z. Liu 6330.
124031CIP <- 2002, JCM <- 2001, Z. Liu: strain 6330

doi: 10.13145/bacdive13390.20230509.8.1

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 zijingensis
  • full scientific name: Pseudonocardia zijingensis Huang et al. 2002

@ref: 12079

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia zijingensis

full scientific name: Pseudonocardia zijingensis Huang et al. 2002

strain designation: 6330

type strain: yes

Morphology

cell morphology

  • @ref: 124031
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12079GYM 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
34377MEDIUM 275 - for Actinomadura rugatobispora and Actinomadura verrucososporayesDistilled water make up to (1000.000 ml);Sodium chloride (1.000 g);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Ammonium sulphate (2.000 g);Starch maize (10.000 g);Calcium carbonate (2.000 g);Trace salt solution - M00447 (1.000 ml)
124031CIP Medium 275yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=275

culture temp

@refgrowthtypetemperaturerange
12079positivegrowth28mesophilic
34377positivegrowth30mesophilic
67770positivegrowth28mesophilic
124031positivegrowth25-41
124031nogrowth10psychrophilic
124031nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
124031NaClpositivegrowth0 %
124031NaClnogrowth2 %
124031NaClnogrowth4 %
124031NaClnogrowth6 %
124031NaClnogrowth8 %
124031NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin-hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate+reduction17632
124031esculin-hydrolysis4853
124031hippurate-hydrolysis606565
124031nitrate-reduction17632
124031nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12403135581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12403115688acetoin-
12403117234glucose-

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
124031oxidase-
124031alcohol dehydrogenase-1.1.1.1
124031gelatinase-
124031catalase+1.11.1.6
124031gamma-glutamyltransferase-2.3.2.2
124031lysine decarboxylase-4.1.1.18
124031ornithine decarboxylase-4.1.1.17
124031phenylalanine ammonia-lyase-4.3.1.24
124031tryptophan deaminase-
124031urease-3.5.1.5
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
12079-++/-+/--++/-------+-+/-----
124031--++-+-+--++-+-+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
12079+----+-+-----+/-------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
124031---+/-+/----------+/---------+/------------------+/-------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12079soil sampleYunnan Province, Zijing MountainChinaCHNAsia
67770SoilZijing Mountain, Yunnan ProvinceChinaCHNAsia
124031Environment, SoilZijing moutain, YunnanChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120791Risk group (German classification)
1240312Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Pseudonocardia zijingensis 16S ribosomal RNA gene, partial sequence
  • accession: AF325725
  • length: 1422
  • database: ena
  • NCBI tax ID: 153376

GC content

  • @ref: 67770
  • GC-content: 70.9
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 12079

culture collection no.: DSM 44774, AS 4.1545, CIP 107621, JCM 11117, BCRC 16328, CGMCC 4.1545

straininfo link

  • @ref: 82587
  • straininfo: 100894

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12054266Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov..Huang Y, Wang L, Lu Z, Hong L, Liu Z, Tan GYA, Goodfellow MInt J Syst Evol Microbiol10.1099/00207713-52-3-9772002Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny20827574Pseudonocardia sichuanensis sp. nov., a novel endophytic actinomycete isolated from the root of Jatropha curcas L.Qin S, Xing K, Fei SM, Lin Q, Chen XM, Cao CL, Sun Y, Wang Y, Li WJ, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-010-9504-72010Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Cell Wall/chemistry, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Jatropha/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny20971834Pseudonocardia kunmingensis sp. nov., an actinobacterium isolated from surface-sterilized roots of Artemisia annua L.Zhao GZ, Li J, Huang HY, Zhu WY, Park DJ, Kim CJ, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.027607-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Artemisia annua/*microbiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12079Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44774)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44774
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
34377Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5077
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
82587Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100894.1StrainInfo: A central database for resolving microbial strain identifiers
124031Curators of the CIPCollection of Institut Pasteur (CIP 107621)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107621