Strain identifier

BacDive ID: 160626

Type strain: Yes

Species: Pseudonocardia abyssalis

Strain Designation: KRD168

Strain history: <- J. Parra, University of Strathclyde; KRD168 <- N. Millan-Aguinaga, University of Strathclyde; KRD168

NCBI tax ID(s): 2792008 (species)

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General

@ref: 67534

BacDive-ID: 160626

DSM-Number: 111918

keywords: genome sequence, 16S sequence, Bacteria

description: Pseudonocardia abyssalis KRD168 is a bacterium that was isolated from Sediment core, depth 4539 m.

NCBI tax id

  • NCBI tax id: 2792008
  • Matching level: species

strain history

  • @ref: 67534
  • history: <- J. Parra, University of Strathclyde; KRD168 <- N. Millan-Aguinaga, University of Strathclyde; KRD168

doi: 10.13145/bacdive160626.20240916.9.1

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 abyssalis
  • full scientific name: Pseudonocardia abyssalis Parra et al. 2021

@ref: 67534

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Pseudonocardiales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia abyssalis

full scientific name: Pseudonocardia abyssalis Parra J, Soldatou S, Rooney LM, Duncan KR, 2021

strain designation: KRD168

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 67534
  • 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

  • @ref: 67534
  • growth: positive
  • type: growth
  • temperature: 28

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase-3.1.3.1
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
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
67534--+/-+/--+----------+/----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
67534-----++/-++++++++-++--

Isolation, sampling and environmental information

isolation

  • @ref: 67534
  • sample type: Sediment core, depth 4539 m
  • geographic location: Weddell Sea (62° 57' 33.6'' S, 27° 53' 13.8'' W)
  • country: International waters
  • latitude: -62.9593
  • longitude: -27.8872

Sequence information

16S sequences

  • @ref: 67534
  • description: Pseudonocardia abyssalis strain KRD168 16S ribosomal RNA gene, partial sequence
  • accession: MH725312
  • length: 1348
  • database: nuccore
  • NCBI tax ID: 2792008

Genome sequences

  • @ref: 66792
  • description: Pseudonocardia abyssalis KRD168
  • accession: GCA_019263705
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2792008

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes88no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes86.735no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.532no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.306no
69480spore-formingspore-formingAbility to form endo- or exosporesyes67.278no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.95no
69480flagellatedmotile2+Ability to perform flagellated movementno85no

External links

@ref: 67534

culture collection no.: DSM 111918, NCIMB 15270

straininfo link

  • @ref: 112864
  • straininfo: 407667

literature

  • topic: Phylogeny
  • Pubmed-ID: 34582326
  • title: Pseudonocardia abyssalis sp. nov. and Pseudonocardia oceani sp. nov., two novel actinomycetes isolated from the deep Southern Ocean.
  • authors: Parra J, Soldatou S, Rooney LM, Duncan KR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.005032
  • year: 2021
  • mesh: *Actinobacteria/genetics, Actinomyces, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Oceans and Seas, Phylogeny, Pseudonocardia, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67534Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-111918Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 111918)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
112864Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID407667.1