Strain identifier

BacDive ID: 133645

Type strain: Yes

Species: Halomonas xianhensis

Strain Designation: A-1

Strain history: B. Zhao A-1.

NCBI tax ID(s): 442341 (species)

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General

@ref: 29905

BacDive-ID: 133645

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Halomonas xianhensis A-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 442341
  • Matching level: species

strain history

  • @ref: 67770
  • history: B. Zhao A-1.

doi: 10.13145/bacdive133645.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas xianhensis
  • full scientific name: Halomonas xianhensis Zhao et al. 2012

  • synonyms

    • @ref: 20215
    • synonym: Modicisalibacter xianhensis

@ref: 29905

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas xianhensis

strain designation: A-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29905negative1.2-1.4 µm0.5-0.6 µmrod-shapedno
69480negative100

pigmentation

  • @ref: 29905
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperature
29905positivegrowth10-42
29905positiveoptimum30
67770positivegrowth30

culture pH

@refabilitytypepHPH range
29905positivegrowth5.5-9.0alkaliphile
29905positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

  • @ref: 29905
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2990516449alanine+carbon source
2990522599arabinose+carbon source
2990517057cellobiose+carbon source
2990528757fructose+carbon source
2990528260galactose+carbon source
2990517234glucose+carbon source
2990517754glycerol+carbon source
2990517716lactose+carbon source
2990515792malonate+carbon source
2990529864mannitol+carbon source
2990537684mannose+carbon source
2990526271proline+carbon source
2990516634raffinose+carbon source
2990533942ribose+carbon source
2990530911sorbitol+carbon source
299054853esculin+hydrolysis
2990517632nitrate+reduction

enzymes

@refvalueactivityec
29905acid phosphatase+3.1.3.2
29905alkaline phosphatase+3.1.3.1
29905catalase+1.11.1.6
29905cytochrome oxidase+1.9.3.1
29905urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
29905soil
67770Oil-polluted saline soil from XianheShangdong ProvinceChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_20287.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_1984;97_2385;98_15344;99_20287&stattab=map
  • Last taxonomy: Halomonas xianhensis subclade
  • 16S sequence: EF421176
  • Sequence Identity:
  • Total samples: 629
  • soil counts: 74
  • aquatic counts: 343
  • animal counts: 201
  • plant counts: 11

Sequence information

16S sequences

  • @ref: 29905
  • description: Halomonas xianhensis strain A-1 16S ribosomal RNA gene, partial sequence
  • accession: EF421176
  • length: 1499
  • database: nuccore
  • NCBI tax ID: 442341

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas xianhensis CGMCC 1.6848GCA_900113605scaffoldncbi442341
66792Halomonas xianhensis strain CGMCC 1.6848442341.9wgspatric442341
66792Halomonas xianhensis CGMCC 1.68482617270878draftimg442341

GC content

@refGC-contentmethod
2990567.1
6777067.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno100yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.615yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes78.791no
69480spore-formingspore-formingAbility to form endo- or exosporesno87.603no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.978yes
69480flagellatedmotile2+Ability to perform flagellated movementyes84.405no

External links

@ref: 29905

culture collection no.: CGMCC 1.6848, JCM 14849

literature

  • topic: Phylogeny
  • Pubmed-ID: 21378136
  • title: Halomonas xianhensis sp. nov., a moderately halophilic bacterium isolated from a saline soil contaminated with crude oil.
  • authors: Zhao B, Wang H, Mao X, Li R, Zhang YJ, Tang S, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.025627-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Halomonas/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Petroleum, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Temperature
  • topic2: Genetics

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
29905Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172627728776041
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/
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1