Strain identifier

BacDive ID: 11367

Type strain: Yes

Species: Herbaspirillum rhizosphaerae

Strain Designation: UMS-37

Strain history: CIP <- 2005, J.H. Yoon, KRIBB, Taejon, South Korea: strain UMS-37

NCBI tax ID(s): 346179 (species)

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General

@ref: 16019

BacDive-ID: 11367

DSM-Number: 21885

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

description: Herbaspirillum rhizosphaerae UMS-37 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere soil of Allium victorialis var. platyphyllum.

NCBI tax id

  • NCBI tax id: 346179
  • Matching level: species

strain history

@refhistory
16019<- CIP <- J. H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; UMS-37
67771<- JH Yoon, KRIBB
122208CIP <- 2005, J.H. Yoon, KRIBB, Taejon, South Korea: strain UMS-37

doi: 10.13145/bacdive11367.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Herbaspirillum
  • species: Herbaspirillum rhizosphaerae
  • full scientific name: Herbaspirillum rhizosphaerae Jung et al. 2007

@ref: 16019

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herbaspirillum

species: Herbaspirillum rhizosphaerae

full scientific name: Herbaspirillum rhizosphaerae Jung et al. 2007

strain designation: UMS-37

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31928negative2 µm0.35 µmrod-shapedyes
67771negative

pigmentation

  • @ref: 31928
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16019NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
34977MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
122208CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
16019positivegrowth25-30mesophilic
31928positivegrowth04-34
31928positiveoptimum27.5mesophilic
34977positivegrowth25mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
31928positivegrowth5.0-7.5
31928positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
31928NaClpositivegrowth0-3 %
31928NaClpositiveoptimum1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3192830089acetate+carbon source
3192816947citrate+carbon source
3192817754glycerol+carbon source
3192825115malate+carbon source
3192815361pyruvate+carbon source
3192833942ribose+carbon source
3192830031succinate+carbon source
3192818222xylose+carbon source

enzymes

@refvalueactivityec
31928catalase+1.11.1.6
31928urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
16019rhizosphere soil of Allium victorialis var. platyphyllumAllium victorialis var. platyphyllumUlleung islandRepublic of KoreaKORAsia
67771From rhizospheric soil of `Allium victorialis` var. `platyphyllumRepublic of KoreaKORAsia
122208Environment, Rhizospheric soil of Allium victorialis var. platyphyllumUlleung IslandRepublic of KoreaKORAsia2004

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_5030.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_128;97_137;98_3761;99_5030&stattab=map
  • Last taxonomy: Herbaspirillum rhizosphaerae
  • 16S sequence: DQ188986
  • Sequence Identity:
  • Total samples: 147
  • soil counts: 9
  • aquatic counts: 90
  • animal counts: 30
  • plant counts: 18

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
160191Risk group (German classification)
1222081Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16019
  • description: Herbaspirillum rhizosphaerae strain UMS-37 16S ribosomal RNA gene, partial sequence
  • accession: DQ188986
  • length: 1488
  • database: ena
  • NCBI tax ID: 346179

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Herbaspirillum rhizosphaerae UMS-37GCA_001189965contigncbi346179
66792Herbaspirillum rhizosphaerae UMS-372654587705draftimg346179

GC content

@refGC-content
1601960.0
3192859.8

External links

@ref: 16019

culture collection no.: DSM 21885, CIP 108917, KCTC 12558

straininfo link

  • @ref: 80598
  • straininfo: 310992

literature

  • topic: Phylogeny
  • Pubmed-ID: 17911298
  • title: Herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of Allium victorialis var. platyphyllum.
  • authors: Jung SY, Lee MH, Oh TK, Yoon JH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64666-0
  • year: 2007
  • mesh: Allium/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Herbaspirillum/chemistry/*classification/genetics/*isolation & purification, Korea, Locomotion/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, Plant Roots/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16019Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21885)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21885
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
31928Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2818528776041
34977Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6600
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
80598Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310992.1StrainInfo: A central database for resolving microbial strain identifiers
122208Curators of the CIPCollection of Institut Pasteur (CIP 108917)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108917