Strain identifier

BacDive ID: 11153

Type strain: Yes

Species: Nocardioides alpinus

Strain Designation: Cr7-14

Strain history: LMG 26053 <-- R. Margesin Cr7-14.

NCBI tax ID(s): 748909 (species)

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General

@ref: 16795

BacDive-ID: 11153

DSM-Number: 23325

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

description: Nocardioides alpinus Cr7-14 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from alpine glacier cryoconite.

NCBI tax id

  • NCBI tax id: 748909
  • Matching level: species

strain history

@refhistory
16795<- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; Cr7-14
67770LMG 26053 <-- R. Margesin Cr7-14.

doi: 10.13145/bacdive11153.20230509.8.1

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 alpinus
  • full scientific name: Nocardioides alpinus Zhang et al. 2012

@ref: 16795

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides alpinus

full scientific name: Nocardioides alpinus Zhang et al. 2012

strain designation: Cr7-14

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30220positive1.5-3.0 µm0.4-0.5 µmrod-shapedno
69480no95.346
69480positive100

pigmentation

  • @ref: 30220
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16795
  • 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
30220positivegrowth1-25
30220positiveoptimum25mesophilic
67770positivegrowth20psychrophilic
16795positivegrowth20psychrophilic

culture pH

  • @ref: 30220
  • ability: positive
  • type: growth
  • pH: 07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 30220
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.532

halophily

  • @ref: 30220
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3022022599arabinose+carbon source
3022024265gluconate+carbon source
3022017234glucose+carbon source
3022025115malate+carbon source
3022017306maltose+carbon source
3022029864mannitol+carbon source
3022037684mannose+carbon source
3022053426tween 80+carbon source
3022017632nitrate+reduction

enzymes

@refvalueactivityec
30220acid phosphatase+3.1.3.2
30220alkaline phosphatase+3.1.3.1
30220catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16795alpine glacier cryoconiteÖtztaler AlpsAustriaAUTEurope
67770Alpine glacier cryoconite in the Ötztaler AlpsAustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Condition#Psychrophilic (<10°C)
#Climate#Cold#Alpine
#Environmental#Terrestrial#Geologic

Safety information

risk assessment

  • @ref: 16795
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16795
  • description: Nocardioides alpinus strain Cr7-14 16S ribosomal RNA gene, partial sequence
  • accession: GU784866
  • length: 1507
  • database: ena
  • NCBI tax ID: 748909

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides alpinus strain CGMCC 1.10697748909.6wgspatric748909
66792Nocardioides alpinus strain DSM 23325748909.8wgspatric748909
66792Nocardioides alpinus CGMCC 1.106972663762717draftimg748909
66792Nocardioides alpinus Cr7-142802429337draftimg748909
67770Nocardioides alpinus CGMCC 1.10697GCA_900112035scaffoldncbi748909
67770Nocardioides alpinus DSM 23325GCA_002836395contigncbi748909
66792Nocardioides alpinus JCM 18960GCA_021083255scaffoldncbi748909

GC content

@refGC-contentmethod
1679571.9thermal denaturation, midpoint method (Tm)
3022071.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.732yes
flagellatedno98.201yes
gram-positiveyes93.061yes
anaerobicno99.391yes
aerobicyes95.135no
halophileno96.44no
spore-formingno83.765no
thermophileno99.167yes
glucose-utilyes84.877no
glucose-fermentno91.486no

External links

@ref: 16795

culture collection no.: DSM 23325, CGMCC 1.10697, LMG 26053, JCM 18960

straininfo link

  • @ref: 80402
  • straininfo: 370922

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21460134Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite.Zhang DC, Schumann P, Redzic M, Zhou YG, Liu HC, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.031047-02011Actinomycetales/chemistry/*classification/genetics/*isolation & purification, *Altitude, Austria, Bacterial Typing Techniques, Base Composition, *Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Ice Cover/*microbiology, Lipids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Vitamin K 2/analysisGenetics
Phylogeny27654931Nocardioides flavus sp. nov., isolated from marine sediment.Wang S, Zhou Y, Zhang GInt J Syst Evol Microbiol10.1099/ijsem.0.0015072016Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryEnzymology
Phylogeny27902315Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave.Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0016762017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28771135Nocardioides sonneratiae sp. nov., an endophytic actinomycete isolated from a branch of Sonneratia apetala.Li F, Tuo L, Su ZW, Wei XQ, Zhang XY, Gao CH, Huang RMInt J Syst Evol Microbiol10.1099/ijsem.0.0019792017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lythraceae/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29372423Nocardioides astragali sp. nov., isolated from a nodule of wild Astragalus chrysopterus in northwestern China.Xu L, Zhang Y, Li C, Wang X, Liu J, Friman VPAntonie Van Leeuwenhoek10.1007/s10482-018-1020-12018Actinobacteria/classification/genetics/*isolation & purification/metabolism, Astragalus Plant/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry/metabolism, China, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Soil MicrobiologyMetabolism
Phylogeny34542392Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula.Chhetri G, Kim I, Kang M, Kim J, So Y, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0050122021*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nocardioides, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *TagetesTranscriptome
Phylogeny34846610Nocardioides lacusdianchii sp. nov., an attached bacterium of Microcystis aeruginosa.Xiao Y, Wang L, Wang X, Chen M, Chen J, Tian BY, Zhang BHAntonie Van Leeuwenhoek10.1007/s10482-021-01690-92021DNA, Bacterial/genetics, *Microcystis/genetics, Nocardioides, Phylogeny, RNA, Ribosomal, 16S/genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16795Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23325)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23325
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
30220Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2656328776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic 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 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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80402Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370922.1StrainInfo: A central database for resolving microbial strain identifiers