Strain identifier

BacDive ID: 133607

Type strain: Yes

Species: Halogeometricum rufum

Strain Designation: RO1-4

Strain history: H.-L. Cui RO1-4.

NCBI tax ID(s): 553469 (species)

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General

@ref: 29723

BacDive-ID: 133607

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

description: Halogeometricum rufum RO1-4 is an aerobe, Gram-negative, motile archaeon that was isolated from marine solar saltern.

NCBI tax id

  • NCBI tax id: 553469
  • Matching level: species

strain history

  • @ref: 67770
  • history: H.-L. Cui RO1-4.

doi: 10.13145/bacdive133607.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/methanobacteriota
  • domain: Archaea
  • phylum: Methanobacteriota
  • class: Halobacteria
  • order: Haloferacales
  • family: Haloferacaceae
  • genus: Halogeometricum
  • species: Halogeometricum rufum
  • full scientific name: Halogeometricum rufum Cui et al. 2010

@ref: 29723

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Haloferacales

family: Haloferacaceae

genus: Halogeometricum

species: Halogeometricum rufum

strain designation: RO1-4

type strain: yes

Morphology

cell morphology

  • @ref: 29723
  • gram stain: negative
  • cell shape: ovoid-shaped
  • motility: yes

pigmentation

  • @ref: 29723
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29723positivegrowth25-55
29723positiveoptimum40-42thermophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
29723positivegrowth6-8.5alkaliphile
29723positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29723
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
29723NaClpositivegrowth11-27 %
29723NaClpositiveoptimum21 %

observation

  • @ref: 29723
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2972330089acetate+carbon source
2972316449alanine+carbon source
2972329016arginine+carbon source
2972335391aspartate+carbon source
2972328260galactose+carbon source
2972317234glucose+carbon source
2972329987glutamate+carbon source
2972317754glycerol+carbon source
2972324996lactate+carbon source
2972317716lactose+carbon source
2972325115malate+carbon source
2972317306maltose+carbon source
2972329864mannitol+carbon source
2972337684mannose+carbon source
2972318257ornithine+carbon source
2972315361pyruvate+carbon source
2972330911sorbitol+carbon source
2972330031succinate+carbon source

metabolite production

@refChebi-IDmetaboliteproduction
2972316136hydrogen sulfideyes
2972335581indoleyes

metabolite tests

  • @ref: 29723
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29723catalase+1.11.1.6
29723cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
29723marine solar saltern
67770Marine solar saltern in JiangsuChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Condition#Saline
#Engineered#Industrial#Industrial production
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_188815.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17828;96_68944;97_89600;98_121893;99_188815&stattab=map
  • Last taxonomy: Halogeometricum rufum
  • 16S sequence: EU887286
  • Sequence Identity:
  • Total samples: 1
  • aquatic counts: 1

Sequence information

16S sequences

  • @ref: 29723
  • description: Halogeometricum rufum strain RO1-4 16S ribosomal RNA gene, complete sequence
  • accession: EU887286
  • length: 1472
  • database: nuccore
  • NCBI tax ID: 553469

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halogeometricum rufum CGMCC 1.77362617270920draftimg553469
67770Halogeometricum rufum CGMCC 1.7736GCA_900112175contigncbi553469
66792Halogeometricum rufum strain CGMCC 1.7736553469.3wgspatric553469

GC content

@refGC-contentmethod
2972364.9
6777064.9high performance liquid chromatography (HPLC)

External links

@ref: 29723

culture collection no.: CGMCC 1.7736, JCM 15770

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20023063Halogeometricum rufum sp. nov., a halophilic archaeon from a marine solar saltern, and emended description of the genus Halogeometricum.Cui HL, Yang X, Gao X, Li XY, Xu XW, Zhou YG, Liu HC, Zhou PJInt J Syst Evol Microbiol10.1099/ijs.0.019463-02009DNA, Archaeal/genetics, Halobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sodium Chloride/*metabolismMetabolism
Phylogeny24097833Taxonomic study of the genera Halogeometricum and Halosarcina: transfer of Halosarcina limi and Halosarcina pallida to the genus Halogeometricum as Halogeometricum limi comb. nov. and Halogeometricum pallidum comb. nov., respectively.Qiu XX, Zhao ML, Han D, Zhang WJ, Dyall-Smith ML, Cui HLInt J Syst Evol Microbiol10.1099/ijs.0.055038-02013DNA, Archaeal/genetics, Genes, Archaeal, Halobacteriaceae/*classification/genetics, Lipids/analysis, Molecular Sequence Data, Peptide Elongation Factor 2/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
29723Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172610628776041
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/