Strain identifier

BacDive ID: 5952

Type strain: Yes

Species: Halorubrum aidingense

Strain Designation: 31-hong

Strain history: S. Liu 31-hong.

NCBI tax ID(s): 1230454 (strain), 368623 (species)

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General

@ref: 17239

BacDive-ID: 5952

DSM-Number: 23496

keywords: genome sequence, 16S sequence, Archaea, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Halorubrum aidingense 31-hong is an aerobe, mesophilic, Gram-negative archaeon that was isolated from salt lake.

NCBI tax id

NCBI tax idMatching level
368623species
1230454strain

strain history

@refhistory
17239<- JCM <- S. Liu, State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing; 31-hong
67770S. Liu 31-hong.

doi: 10.13145/bacdive5952.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Haloferacales
  • family: Halorubraceae
  • genus: Halorubrum
  • species: Halorubrum aidingense
  • full scientific name: Halorubrum aidingense Cui et al. 2006

@ref: 17239

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halorubraceae

genus: Halorubrum

species: Halorubrum aidingense

full scientific name: Halorubrum aidingense Cui et al. 2006

strain designation: 31-hong

type strain: yes

Morphology

cell morphology

  • @ref: 31797
  • gram stain: negative
  • cell length: 3.6-6.4 µm
  • cell width: 0.9-1 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 31797
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17239
  • name: HALOBACTERIA MEDIUM (DSMZ Medium 372)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/372
  • composition: Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17239positivegrowth37mesophilic
31797positivegrowth25-52
31797positiveoptimum40-42thermophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31797positivegrowth07-09alkaliphile
31797positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31797
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31797
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31797NaClpositivegrowth9.86-24.94 %
31797NaClpositiveoptimum15.08 %

observation

  • @ref: 31797
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3179728757fructose+carbon source
3179728260galactose+carbon source
3179717234glucose+carbon source
3179717306maltose+carbon source
3179729864mannitol+carbon source
3179737684mannose+carbon source
3179717992sucrose+carbon source
3179717632nitrate+reduction

metabolite production

  • @ref: 31797
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 31797
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31797catalase+1.11.1.6
31797cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17239salt lakeXin-Jiang, Aiding LakeChinaCHNAsia
67770Aiding salt lake in Xin-JiangChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_191029.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17655;96_68889;97_89538;98_124473;99_191029&stattab=map
  • Last taxonomy: Halorubrum aidingense
  • 16S sequence: AB663402
  • Sequence Identity:
  • Total samples: 12
  • aquatic counts: 12

Safety information

risk assessment

  • @ref: 17239
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halorubrum aidingense gene for 16S ribosomal RNA, partial sequence, strain: JCM 13560AB4779761430ena1230454
20218Halorubrum aidingense gene for 16S rRNA, complete sequence, strain: JCM 13560AB6634021470ena1230454
17239Halorubrum aidingense strain 31-hong 16S ribosomal RNA gene, complete sequenceDQ3558131470ena1230454

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halorubrum aidingense JCM 135602554235475draftimg1230454
67770Halorubrum aidingense JCM 13560GCA_000336995contigncbi1230454
66792Halorubrum aidingense JCM 135601230454.4wgspatric1230454

GC content

@refGC-contentmethod
1723964.2thermal denaturation, midpoint method (Tm)
3179764.2

External links

@ref: 17239

culture collection no.: DSM 23496, CGMCC 1.2670, JCM 13560, KCTC 4073

straininfo link

  • @ref: 75441
  • straininfo: 297205

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825640Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China.Cui HL, Tohty D, Zhou PJ, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.64305-02006Bacterial Typing Techniques, Base Composition, China, DNA, Archaeal/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Halobacteriaceae/*classification/genetics/*isolation & purification/physiology, Lipids/analysis/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Water MicrobiologyEnzymology
Phylogeny18768599Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake.Gutierrez MC, Castillo AM, Pagaling E, Heaphy S, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.65840-02008Base Composition, Carbohydrate Metabolism, China, DNA, Archaeal/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Halobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Hydrogen-Ion Concentration, Hypotonic Solutions/toxicity, Lipids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature, *Water MicrobiologyMetabolism
Phylogeny26374710Halorubrum yunnanense sp. nov., isolated from a subterranean salt mine.Chen S, Liu HC, Zhao D, Yang J, Zhou J, Xiang HInt J Syst Evol Microbiol10.1099/ijsem.0.0006052015Base Composition, China, DNA, Archaeal/genetics, Fatty Acids/genetics, Genes, Archaeal, Halorubrum/*classification/genetics/isolation & purification, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylglycerols/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium ChlorideGenetics
Phylogeny27001607Haloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae.Chen S, Liu HC, Zhou J, Xiang HInt J Syst Evol Microbiol10.1099/ijsem.0.0010332016Base Composition, China, DNA, Archaeal/genetics, Genes, Archaeal, Glycolipids/chemistry, Halobacteriaceae/*classification/genetics/isolation & purification, Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium ChlorideTranscriptome
Phylogeny28819743Halorubrum salsamenti sp. nov., a Novel Halophilic Archaeon Isolated from a Brine of Salt Mine.Chen S, He J, Zhang J, Xu Y, Huang J, Ke LXCurr Microbiol10.1007/s00284-017-1325-82017Base Composition, DNA, Archaeal, Halorubrum/chemistry/*classification/genetics/isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *SaltsPhenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
17239Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23496)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23496
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
31797Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128068
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/
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
75441Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297205.1StrainInfo: A central database for resolving microbial strain identifiers