Strain identifier

BacDive ID: 134312

Type strain: Yes

Species: Halogeometricum pallidum

Strain Designation: BZ256

Strain history: <- Kristen N Savage, Univ. of Oklahoma, USA

NCBI tax ID(s): 1227487 (strain), 411361 (species)

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General

@ref: 32375

BacDive-ID: 134312

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

description: Halogeometricum pallidum BZ256 is an aerobe, Gram-negative, coccus-shaped archaeon that was isolated from freshwater .

NCBI tax id

NCBI tax idMatching level
411361species
1227487strain

strain history

@refhistory
67770K. N. Savage BZ256.
67771<- Kristen N Savage, Univ. of Oklahoma, USA

doi: 10.13145/bacdive134312.20230509.8.1

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 pallidum
  • full scientific name: Halogeometricum pallidum (Savage et al. 2008) Qiu et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Halosarcina pallida

@ref: 32375

domain: Archaea

phylum: Euryarchaeota

class: Halobacteria

order: Haloferacales

family: Haloferacaceae

genus: Halogeometricum

species: Halogeometricum pallidum

strain designation: BZ256

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
32375negative0.9 µmcoccus-shapedno
67771coccus-shapedno

pigmentation

  • @ref: 32375
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32375positivegrowth25-45
32375positiveoptimum30mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
32375positivegrowth5-8.5alkaliphile
32375positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32375aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
32375NaClpositivegrowth9.86-24.94 %
32375NaClpositiveoptimum17.98 %

observation

  • @ref: 32375
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3237530089acetate+carbon source
3237535391aspartate+carbon source
3237528757fructose+carbon source
3237528260galactose+carbon source
3237517234glucose+carbon source
3237529987glutamate+carbon source
3237517754glycerol+carbon source
3237515428glycine+carbon source
3237527570histidine+carbon source
3237524996lactate+carbon source
3237517716lactose+carbon source
3237525115malate+carbon source
3237528044phenylalanine+carbon source
3237515361pyruvate+carbon source
3237517814salicin+carbon source
3237530911sorbitol+carbon source
3237530031succinate+carbon source
3237517992sucrose+carbon source
3237527082trehalose+carbon source
3237517632nitrate+reduction

metabolite production

  • @ref: 32375
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 32375
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32375catalase+1.11.1.6
32375cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
32375freshwater (river, lake, pond)
67770Zodletone Spring, a sulfide- and sulfur-rich springsouth-west OklahomaUSAUSANorth America
67771From Zodletone Spring, a sulfide- and sulfur-rich spring in south-western OklahomaUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Pond (small)
#Environmental#Aquatic#River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_187370.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17828;96_68944;97_89600;98_121901;99_187370&stattab=map
  • Last taxonomy: Halogeometricum pallidum subclade
  • 16S sequence: HM185493
  • Sequence Identity:
  • Total samples: 9
  • soil counts: 3
  • aquatic counts: 3
  • animal counts: 3

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
32375Halosarcina pallida strain BZ256 16S ribosomal RNA gene, partial sequenceEF0554541351nuccore1227487
67770Halosarcina pallida gene for 16S ribosomal RNA, partial sequence, strain: JCM 14848AB4779801433ena1227487
67770Halosarcina pallida strain BZ256 16S ribosomal RNA gene, partial sequenceHM1854931473ena1227487
67771Halosarcina pallida gene for 16S rRNA, complete sequence, strain: JCM 14848AB6634291473ena1227487

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halogeometricum pallidum JCM 148482554235507draftimg1227487
67771Halogeometricum pallidum JCM 14848GCA_000337095contigncbi1227487
66792Halosarcina pallida JCM 148481227487.5wgspatric1227487

GC content

  • @ref: 32375
  • GC-content: 65.4

External links

@ref: 32375

culture collection no.: KCTC 4017, JCM 14848

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18398182Halosarcina pallida gen. nov., sp. nov., a halophilic archaeon from a low-salt, sulfide-rich spring.Savage KN, Krumholz LR, Oren A, Elshahed MSInt J Syst Evol Microbiol10.1099/ijs.0.65398-02008Base Composition, DNA, Archaeal/chemistry/genetics, Fresh Water/microbiology, Genes, Archaeal, Halobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Microscopy, Electron, Scanning, Molecular Sequence Data, Oklahoma, Phenotype, Phospholipids/metabolism, Phylogeny, RNA, Archaeal/genetics, RNA, Ribosomal, 16S/genetics, Salinity, Species Specificity, Sulfides/metabolismMetabolism
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_referencepubmedjournal
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
32375Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172860328776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/