Strain identifier

BacDive ID: 24251

Type strain: Yes

Species: Nocardioides psychrotolerans

Strain Designation: RHLT2-1

Strain history: CGMCC 1.11156 <-- Q. Liu et al. RHLT2-1.

NCBI tax ID(s): 1005945 (species)

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General

@ref: 20684

BacDive-ID: 24251

DSM-Number: 27452

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive, rod-shaped

description: Nocardioides psychrotolerans RHLT2-1 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1005945
  • Matching level: species

strain history

@refhistory
20684<- NBRC <- CGMCC 1.11156 <- Q. Liu, Chinese Acad. Sci. (CAS), Beijing; RHLT2-1
67770CGMCC 1.11156 <-- Q. Liu et al. RHLT2-1.

doi: 10.13145/bacdive24251.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides psychrotolerans
  • full scientific name: Nocardioides psychrotolerans Liu et al. 2013

@ref: 20684

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides psychrotolerans

full scientific name: Nocardioides psychrotolerans Liu et al. 2013 emend. Nouioui et al. 2018

strain designation: RHLT2-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30526positive1.26 µm0.82 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 20684
  • incubation period: 3-7 days

pigmentation

  • @ref: 30526
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20684
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20684positivegrowth20psychrophilic
30526positivegrowth0-25
30526positiveoptimum20psychrophilic
67770positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
30526positivegrowth6.5-9alkaliphile
30526positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 30526
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30526no
69481no94
69480no99.856

halophily

  • @ref: 30526
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0.25 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3052617057cellobiose+carbon source
3052628757fructose+carbon source
3052617754glycerol+carbon source
3052629864mannitol+carbon source
3052616634raffinose+carbon source
3052626546rhamnose+carbon source
3052627082trehalose+carbon source
3052617632nitrate+reduction

enzymes

@refvalueactivityec
30526alkaline phosphatase+3.1.3.1
30526catalase+1.11.1.6
30526gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20684soilSzechwan province, Hailuogou glacierChinaCHNAsia
67770Soil at Hailuogou glacierSzechwan Province, south-western of ChinaChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 20684
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20684
  • description: Nocardioides psychrotolerans strain CGMCC 1.11156 16S ribosomal RNA gene, partial sequence
  • accession: JF750425
  • length: 1399
  • database: ena
  • NCBI tax ID: 1005945

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides psychrotolerans strain CGMCC 1.111561005945.5wgspatric1005945
66792Nocardioides psychrotolerans strain NBRC 1085631005945.6wgspatric1005945
66792Nocardioides psychrotolerans CGMCC 1.111562663762759draftimg1005945
67770Nocardioides psychrotolerans NBRC 108563GCA_007992415contigncbi1005945
67770Nocardioides psychrotolerans CGMCC 1.11156GCA_900113685scaffoldncbi1005945

GC content

@refGC-contentmethod
2068467.8
6777067.8thermal denaturation, midpoint method (Tm)
6777070.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
motileno75.345yes
flagellatedno95.243yes
gram-positiveyes92.339yes
anaerobicno98.383no
aerobicyes91.102yes
halophileno94.115yes
spore-formingno83.3yes
thermophileno99.007no
glucose-utilyes85.018no
glucose-fermentno91.035no

External links

@ref: 20684

culture collection no.: DSM 27452, CGMCC 1.11156, NBRC 108563, JCM 19668

straininfo link

  • @ref: 88193
  • straininfo: 406467

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22345140Nocardioides szechwanensis sp. nov. and Nocardioides psychrotolerans sp. nov., isolated from a glacier.Liu Q, Xin YH, Liu HC, Zhou YG, Wen YInt J Syst Evol Microbiol10.1099/ijs.0.038091-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny24699067Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment.Fan X, Qiao Y, Gao X, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.059873-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25893957Nocardioides solisilvae sp. nov., isolated from a forest soil.Sultanpuram VR, Mothe T, Mohammed FAntonie Van Leeuwenhoek10.1007/s10482-015-0455-x2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Forests, India, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
20684Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27452Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27452)
30526Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172685828776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
88193Reimer, 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-ID406467.1