Strain identifier

BacDive ID: 13360

Type strain: Yes

Species: Pseudonocardia halophobica

Strain Designation: SS1/1 (as Nocardia sp.), SS1/1 (as Nocardia sp.)

Strain history: DSM 43089 <-- R. E. Gordon IMRU 1300 <-- M. P. Lechevalier SS1/1.

NCBI tax ID(s): 471802 (strain), 29401 (species)

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General

@ref: 10752

BacDive-ID: 13360

DSM-Number: 43089

keywords: 16S sequence, Bacteria, spore-forming, mesophilic

description: Pseudonocardia halophobica SS1/1 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
471802strain
29401species

strain history

@refhistory
10752<- R.E. Gordon, IMRU (Streptomyces autothrophicus) <- M.P. Lechevalier, SS1/1 (Nocardia sp.)
67770DSM 43089 <-- R. E. Gordon IMRU 1300 <-- M. P. Lechevalier SS1/1.

doi: 10.13145/bacdive13360.20230509.8.1

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 halophobica
  • full scientific name: Pseudonocardia halophobica (Akimov et al. 1989) McVeigh et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Pseudoamycolata halophobica

@ref: 10752

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia halophobica

full scientific name: Pseudonocardia halophobica (Akimov et al. 1989) McVeigh et al. 1994

strain designation: SS1/1 (as Nocardia sp.), SS1/1 (as Nocardia sp.)

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19937Melony yellow (1028)10-14 daysISP 2
19937Colorless10-14 daysISP 3
19937Colorless10-14 daysISP 4
19937Melony yellow (1028)10-14 daysISP 5
19937Melony yellow (1028)10-14 daysISP 6
19937Melony yellow (1028)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19937yesAerial MyceliumDusty grey (7037)ISP 2
19937yesAerial MyceliumDusty grey (7037)ISP 3
19937yesAerial MyceliumDusty grey (7037)ISP 4
19937yesAerial MyceliumDusty grey (7037)ISP 5
19937noISP 6
19937yesAerial MyceliumDusty grey (7037)ISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10752GYM 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
19937ISP 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
19937ISP 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
19937ISP 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
19937ISP 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
19937ISP 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
19937ISP 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:

culture temp

@refgrowthtypetemperaturerange
19937positiveoptimum28mesophilic
10752positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 19937
  • spore description: Formation of spore chains, spore surface smooth
  • spore formation: yes

halophily

  • @ref: 19937
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1993762968cellulose-
1993716634raffinose-
1993726546rhamnose-
1993728757fructose-
1993729864mannitol+
1993717268myo-inositol-
1993718222xylose-
1993717992sucrose-
1993722599arabinose+
1993717234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

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
68382alkaline phosphatase+3.1.3.1
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
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19937+++-++-+-++-+-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19937------+--++

Isolation, sampling and environmental information

isolation

@refsample type
10752soil
67770Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
107521Risk group (German classification)
199371German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218P.halophobica 16S rRNA geneY085341455ena29401
20218P.halophobica 16S ribosomal RNA (partial)Z141111438ena29401
20218Pseudonocardia halophobica 16S rRNA gene, strain IMSNU 21327TAJ2528271512ena29401
20218Pseudonocardia halophobica 16S ribosomal RNA gene, partial sequenceEU1395761384ena29401

GC content

  • @ref: 67770
  • GC-content: 72
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 10752

culture collection no.: DSM 43089, ATCC 51535, DSM 656, IMRU 1300, JCM 9421, NRRL B-16064, VKM Ac-1069, CGMCC 4.1288, IFO 15048, IMSNU 21327, KCTC 9296, NBRC 15048, NCIMB 13212, NRRL B-16514

straininfo link

  • @ref: 82558
  • straininfo: 88631

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8186094The phylogenetic position of Pseudoamycolata halophobica (Akimov et al. 1989) and a proposal to reclassify it as Pseudonocardia halophobica.McVeigh HP, Munro J, Embley TMInt J Syst Bacteriol10.1099/00207713-44-2-3001994Actinomycetales/*classification/genetics, DNA, Ribosomal/*genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*geneticsGenetics
Phylogeny18768609Pseudonocardia ailaonensis sp. nov., isolated from soil in China.Qin S, Su YY, Zhang YQ, Wang HB, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.65721-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
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
Phylogeny22200780Pseudonocardia yuanmoensis sp. nov., a novel actinobacterium isolated from soil in Yunnan, south-west China.Nie GX, Ming H, Wei DQ, Zhou EM, Tang X, Cheng J, Tang SK, Li WJAntonie Van Leeuwenhoek10.1007/s10482-011-9689-42011Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Trees, Vitamin K 2/analysisGenetics
Phylogeny29683415Pseudonocardia lutea sp. nov., a novel actinobacterium isolated from soil in Chad.Gao Y, Piao C, Wang H, Shi L, Guo X, Song J, Xiang W, Zhao J, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0027802018Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Chad, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/analysis, Geologic Sediments/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10752Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43089)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43089
19937Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43089.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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
82558Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88631.1StrainInfo: A central database for resolving microbial strain identifiers