Strain identifier

BacDive ID: 7625

Type strain: Yes

Species: Arthrobacter alpinus

Strain Designation: S6-3

Strain history: CGMCC 1.8950 <-- R. Margesin S6-3.

NCBI tax ID(s): 656366 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16249

BacDive-ID: 7625

DSM-Number: 22274

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

description: Arthrobacter alpinus S6-3 is an aerobe, Gram-positive, ovoid-shaped bacterium that was isolated from alpine soil, north slope, 2300 m above sea level.

NCBI tax id

  • NCBI tax id: 656366
  • Matching level: species

strain history

@refhistory
16249<- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; S6-3
67770CGMCC 1.8950 <-- R. Margesin S6-3.

doi: 10.13145/bacdive7625.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Arthrobacter
  • species: Arthrobacter alpinus
  • full scientific name: Arthrobacter alpinus Zhang et al. 2010

@ref: 16249

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter alpinus

full scientific name: Arthrobacter alpinus Zhang et al. 2010 emend. Nouioui et al. 2018

strain designation: S6-3

type strain: yes

Morphology

cell morphology

  • @ref: 29621
  • gram stain: positive
  • cell length: 1.3-1.9 µm
  • cell width: 0.8-1 µm
  • cell shape: ovoid-shaped
  • motility: no

pigmentation

  • @ref: 29621
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16249R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
16249NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16249positivegrowth15-25
29621positivegrowth01-25
29621positiveoptimum20-25
67770positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
29621positivegrowth06-09alkaliphile
29621positiveoptimum7-7.2

Physiology and metabolism

oxygen tolerance

  • @ref: 29621
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
29621NaClpositivegrowth0-5 %
29621NaClpositiveoptimum0-5 %

murein

  • @ref: 16249
  • murein short key: A11.28
  • type: A3alpha L-Lys-L-Thr-L-Ala3

observation

@refobservation
29621aggregates in chains
67770quinones: MK-9(H2), MK-8(H2), MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2962122599arabinose+carbon source
2962117234glucose+carbon source
2962117716lactose+carbon source
2962117306maltose+carbon source
2962129864mannitol+carbon source
2962137684mannose+carbon source
296214853esculin+hydrolysis

enzymes

  • @ref: 29621
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16249alpine soil, north slope, 2300 m above sea levelHohe Tauern, Grossglockner area, FuschertörlAustriaAUTEurope
67770Alpine soil in FuschertörlHohe TauernAustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Climate#Cold#Alpine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1334.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_773;97_901;98_1057;99_1334&stattab=map
  • Last taxonomy: Arthrobacter
  • 16S sequence: GQ227413
  • Sequence Identity:
  • Total samples: 3496
  • soil counts: 1504
  • aquatic counts: 494
  • animal counts: 1120
  • plant counts: 378

Safety information

risk assessment

  • @ref: 16249
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16249
  • description: Arthrobacter alpinus strain S6-3 16S ribosomal RNA gene, partial sequence
  • accession: GQ227413
  • length: 1530
  • database: ena
  • NCBI tax ID: 656366

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter alpinus strain DSM 22274656366.8wgspatric656366
66792Arthrobacter alpinus DSM 222742634166197draftimg656366
67770Arthrobacter alpinus DSM 22274GCA_900105965contigncbi656366

GC content

@refGC-contentmethod
1624961.9thermal denaturation, midpoint method (Tm)
2962161.9
6777060.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes93.707no
anaerobicno99.741yes
halophileno84.146no
spore-formingno86.367no
glucose-utilyes88.976yes
thermophileno99.52yes
flagellatedno95.992yes
motileno94.013no
aerobicyes96.316yes
glucose-fermentno77.352no

External links

@ref: 16249

culture collection no.: DSM 22274, CGMCC 1.8950, JCM 17736

straininfo link

  • @ref: 77069
  • straininfo: 370639

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19880631Arthrobacter alpinus sp. nov., a psychrophilic bacterium isolated from alpine soil.Zhang DC, Schumann P, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin RInt J Syst Evol Microbiol10.1099/ijs.0.017178-02009Arthrobacter/*classification/genetics/*isolation & purification/metabolism, Cold Temperature, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny30482657Genetic diversity of glacier-inhabiting Cryobacterium bacteria in China and description of Cryobacterium zongtaii sp. nov. and Arthrobacter glacialis sp. nov.Liu Q, Liu HC, Zhou YG, Xin YHSyst Appl Microbiol10.1016/j.syapm.2018.10.0052018Actinomycetales/*classification/isolation & purification, Arthrobacter/*classification/isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial, Fatty Acids/chemistry, Genes, Bacterial, Genetic Variation, Ice Cover/*microbiology, Multilocus Sequence Typing, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Vitamin K 2/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16249Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22274)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22274
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
29621Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2601128776041
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/
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
77069Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370639.1StrainInfo: A central database for resolving microbial strain identifiers