Strain identifier

BacDive ID: 13388

Type strain: Yes

Species: Pseudonocardia antarctica

Strain Designation: DVS-5a1

Strain history: CIP <- 2004, MTCC <- DSMZ <- S. Shivaji, CCMB, Hyderabad, India: strain DVS 5a1

NCBI tax ID(s): 237656 (species)

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General

@ref: 12058

BacDive-ID: 13388

DSM-Number: 44749

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic

description: Pseudonocardia antarctica DVS-5a1 is an obligate aerobe, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 237656
  • Matching level: species

strain history

@refhistory
12058<- S. Shivaji; DVS-5a1
67770S. Shivaji DVS 5a1.
116402CIP <- 2004, MTCC <- DSMZ <- S. Shivaji, CCMB, Hyderabad, India: strain DVS 5a1

doi: 10.13145/bacdive13388.20230509.8.1

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 antarctica
  • full scientific name: Pseudonocardia antarctica Prabahar et al. 2004

@ref: 12058

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia antarctica

full scientific name: Pseudonocardia antarctica Prabahar et al. 2004

strain designation: DVS-5a1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.121
69480100positive
116402nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19701Copper brown10-14 daysISP 2
19701White10-14 daysISP 3
1970110-14 daysISP 4
1970110-14 daysISP 5
19701Pale orange10-14 daysISP 6
19701Copper brown10-14 daysISP 7
116402

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19701yesAerial MyceliumCreamISP 2
19701yesAerial MyceliumCreamISP 3
19701noISP 4
19701noISP 5
19701yesAerial MyceliumCreamISP 6
19701yesAerial MyceliumIvoryISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12058GYM 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
19701ISP 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
19701ISP 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:
19701ISP 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
19701ISP 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
19701ISP 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
19701ISP 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
33256MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
116402CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12058positivegrowth28mesophilic
19701positiveoptimum28mesophilic
33256positivegrowth25mesophilic
67770positivegrowth28mesophilic
116402positivegrowth25-37mesophilic
116402nogrowth10psychrophilic
116402nogrowth41thermophilic
116402nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116402
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116402NaClpositivegrowth0-8 %
116402NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1970117234glucose+
1970122599arabinose+
1970117992sucrose+
1970118222xylose+
1970117268myo-inositol-
1970129864mannitol+
1970126546rhamnose+
1970116634raffinose-
1970162968cellulose+
11640216947citrate-carbon source
1164024853esculin+hydrolysis
116402606565hippurate+hydrolysis
11640217632nitrate-reduction
11640216301nitrite-reduction
11640217632nitrate-respiration

antibiotic resistance

  • @ref: 116402
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116402
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11640215688acetoin-
11640217234glucose-

enzymes

@refvalueactivityec
116402oxidase-
116402beta-galactosidase+3.2.1.23
116402alcohol dehydrogenase-1.1.1.1
116402gelatinase-
116402amylase+
116402DNase-
116402caseinase-3.4.21.50
116402catalase+1.11.1.6
116402tween esterase-
116402gamma-glutamyltransferase+2.3.2.2
116402lecithinase-
116402lipase-
116402lysine decarboxylase-4.1.1.18
116402ornithine decarboxylase-4.1.1.17
116402phenylalanine ammonia-lyase+4.3.1.24
116402protease-
116402tryptophan deaminase-
116402urease+3.5.1.5
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
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- FucosidaseControl
19701+++-+++--+--+-++---
116402+++-++---++-+-++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
12058soilMcMurdo Dry ValleyAustralia and Oceania
67770Moraine sampleMcMurdo Dry ValleysAntarcticaAntarcticaATA
116402Moraine sampleMcMurdo dry valleysAntarcticaAntarcticaATA

isolation source categories

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

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: AJ576010
  • Sequence Identity:
  • Total samples: 16902
  • soil counts: 7999
  • aquatic counts: 2199
  • animal counts: 3094
  • plant counts: 3610

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120581Risk group (German classification)
197011Risk group (German classification)
1164022Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Pseudonocardia antarctica partial 16S rRNA gene, type strain DVS 5a1T
  • accession: AJ576010
  • length: 1479
  • database: ena
  • NCBI tax ID: 237656

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia antarctica strain DSM 44749237656.4wgspatric237656
66792Pseudonocardia antarctica DSM 447492852158739draftimg237656
67770Pseudonocardia antarctica DSM 44749GCA_013408715contigncbi237656

GC content

  • @ref: 12058
  • GC-content: 71

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes62no
motileno92.752no
gram-positiveyes90.502no
anaerobicno99.115no
aerobicyes94.294no
halophileno82.78no
spore-formingyes61.674no
glucose-utilyes88.696yes
flagellatedno97.727no
thermophileno99.259no
glucose-fermentno93.189no

External links

@ref: 12058

culture collection no.: DSM 44749, MTCC 4297, JCM 12172, CIP 108584, DVS 5a1

straininfo link

  • @ref: 82585
  • straininfo: 132798

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12058Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44749)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44749
19701Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44749.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
33256Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6229
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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)
82585Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132798.1StrainInfo: A central database for resolving microbial strain identifiers
116402Curators of the CIPCollection of Institut Pasteur (CIP 108584)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108584