Strain identifier

BacDive ID: 5951

Type strain: Yes

Species: Halorubrum lipolyticum

Strain Designation: 9-3

Strain history: S. Liu 9-3.

NCBI tax ID(s): 1227482 (strain), 368624 (species)

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General

@ref: 16088

BacDive-ID: 5951

DSM-Number: 21995

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

description: Halorubrum lipolyticum 9-3 is an aerobe, mesophilic, Gram-negative archaeon that was isolated from sediments of Aibi salt lake.

NCBI tax id

NCBI tax idMatching level
368624species
1227482strain

strain history

@refhistory
16088<- JCM/RIKEN <- S. Liu, State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing; strain 9-3
67770S. Liu 9-3.

doi: 10.13145/bacdive5951.20230509.8.1

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 lipolyticum
  • full scientific name: Halorubrum lipolyticum Cui et al. 2006

@ref: 16088

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Halobacteriales

family: Halorubraceae

genus: Halorubrum

species: Halorubrum lipolyticum

full scientific name: Halorubrum lipolyticum Cui et al. 2006

strain designation: 9-3

type strain: yes

Morphology

cell morphology

  • @ref: 31797
  • gram stain: negative
  • cell length: 1.8-5.5 µm
  • cell width: 0.9-1.2 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 31797
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16088
  • 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
16088positivegrowth37mesophilic
31797positivegrowth25-58
31797positiveoptimum45-48thermophilic
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
31797NaClpositivegrowth9.86-27.84 %
31797NaClpositiveoptimum15 %

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
3179737684mannose+carbon source
3179717992sucrose+carbon source
3179717632nitrate+reduction

enzymes

@refvalueactivityec
31797catalase+1.11.1.6
31797gelatinase+
31797cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16088sediments of Aibi salt lakeXin-JiangChinaCHNAsia
67770Aibi salt lake in Xin-JiangChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_187329.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17655;96_68889;97_89538;98_121837;99_187329&stattab=map
  • Last taxonomy: Halorubrum
  • 16S sequence: AB663415
  • Sequence Identity:
  • Total samples: 21
  • soil counts: 3
  • aquatic counts: 18

Safety information

risk assessment

  • @ref: 16088
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halorubrum lipolyticum gene for 16S ribosomal RNA, partial sequence, strain: JCM 13559AB4779781430ena368624
20218Halorubrum lipolyticum gene for 16S rRNA, complete sequence, strain: JCM 13559AB6634151470ena368624
16088Halorubrum lipolyticum strain 9-3 16S ribosomal RNA gene, partial sequenceDQ3558141470ena368624

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halorubrum lipolyticum DSM 219952534682115draftimg1227482
67770Halorubrum lipolyticum DSM 21995GCA_000337375contigncbi1227482
66792Halorubrum lipolyticum DSM 219951227482.3wgspatric1227482

GC content

@refGC-contentmethod
1608865.9thermal denaturation, midpoint method (Tm)
3179765.9

External links

@ref: 16088

culture collection no.: DSM 21995, CGMCC 1.5332, JCM 13559, KCTC 4069

straininfo link

  • @ref: 75440
  • straininfo: 297208

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
Phylogeny24643450Halorubrum salinum sp. nov., isolated from a marine solar saltern.Zhang WJ, Cui HLArch Microbiol10.1007/s00203-014-0975-12014Anti-Bacterial Agents/pharmacology, China, Halorubrum/chemistry/*classification/drug effects/isolation & purification/*physiology, Hydrogen-Ion Concentration, Lipids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Species SpecificityGenetics
Phylogeny25870255Halorubrum gandharaense sp. nov., an alkaliphilic haloarchaeon from commercial rock salt.Kondo Y, Minegishi H, Echigo A, Shimane Y, Kamekura M, Itoh T, Ohkuma M, Takahashi-Ando N, Fukushima Y, Yoshida Y, Usami RInt J Syst Evol Microbiol10.1099/ijs.0.0002612015Base Composition, DNA, Archaeal/genetics, Halorubrum/*classification/genetics/isolation & purification, Molecular Sequence Data, Pakistan, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, TemperatureGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16088Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21995)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21995
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
75440Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297208.1StrainInfo: A central database for resolving microbial strain identifiers