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Strain identifier

BacDive ID: 131307

Type strain: Yes

Species: Rhizobium smilacinae

Strain Designation: PTYR-5

Strain history: <- KCTC <- Y. Wang <- L. Zhang; PTYR-5

NCBI tax ID(s): 1395944 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 22534

BacDive-ID: 131307

DSM-Number: 100675

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Rhizobium smilacinae PTYR-5 is a mesophilic bacterium that was isolated from surface-sterilized leaf of Smilacina japonica A. Gray.

NCBI tax id

  • NCBI tax id: 1395944
  • Matching level: species

strain history: <- KCTC <- Y. Wang <- L. Zhang; PTYR-5

doi: 10.13145/bacdive131307.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Rhizobium
  • species: Rhizobium smilacinae
  • full scientific name: Rhizobium smilacinae Zhang et al. 2015

@ref: 22534

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium smilacinae

full scientific name: Rhizobium smilacinae Zhang et al. 2015

strain designation: PTYR-5

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 98.604

colony morphology

  • @ref: 22534
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22534NUTRIENT 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
22534RHIZOBIUM MEDIUM (DSMZ Medium 98)yeshttps://mediadive.dsmz.de/medium/98Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water

culture temp

  • @ref: 22534
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 97.959

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 96.864

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
22534catalase+1.11.1.6
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
22534--+/--++-++++++-+--+--

Isolation, sampling and environmental information

isolation

  • @ref: 22534
  • sample type: surface-sterilized leaf of Smilacina japonica A. Gray
  • host species: Smilacina japonica
  • geographic location: Taibai Mountain, Shaanxi Province
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

  • @ref: 22534
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22534
  • description: Rhizobium smilacinae strain PTYR-5 16S ribosomal RNA gene, partial sequence
  • accession: KF551141
  • length: 1336
  • database: ena
  • NCBI tax ID: 1395944

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium smilacinae PTYR-5GCA_006335145contigncbi1395944
66792Rhizobium smilacinae CCTCC AB 20130162738541321draftimg1395944

External links

@ref: 22534

culture collection no.: DSM 100675, CCTCC AB 2013016, KCTC 32300, LMG 27604

straininfo link

@refpassport
20218http://www.straininfo.net/strains/902670
20218http://www.straininfo.net/strains/902671
20218http://www.straininfo.net/strains/887189

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25077951Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica.Zhang L, Shi X, Si M, Li C, Zhu L, Zhao L, Shen X, Wang YAntonie Van Leeuwenhoek10.1007/s10482-014-0241-12014Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/classification/genetics/isolation & purification/physiology, Genes, Bacterial, Genes, Essential, Maianthemum/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNAEnzymology
Phylogeny30259064Rhizobium panacihumi sp. nov., an isolate from ginseng-cultivated soil, as a potential plant growth promoting bacterium.Kang JP, Huo Y, Kim YJ, Ahn JC, Hurh J, Yang DU, Yang DCArch Microbiol10.1007/s00203-018-1578-z2018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Essential/genetics, Nucleic Acid Hybridization, Oxidoreductases/genetics, Panax/*microbiology, Phylogeny, Plant Development/*physiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizobium/*classification/genetics/*isolation & purification, Sequence Analysis, DNA, Soil, Soil MicrobiologyEnzymology
Phylogeny31820041Rhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China.Liu L, Liang L, Xu L, Chi M, Zhang X, Li LCurr Microbiol10.1007/s00284-019-01831-42019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/isolation & purification, Sand/microbiology, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny34935074A non-symbiotic novel species, Rhizobium populisoli sp. nov., isolated from rhizosphere soil of Populus popularis.Shen L, Liu JJ, Liu PX, An MM, He XW, Zhao GZArch Microbiol10.1007/s00203-021-02706-82021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids/analysis, Phylogeny, *Populus, RNA, Ribosomal, 16S/genetics, *Rhizobium/genetics, Rhizosphere, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
22534Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100675Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100675)
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
68369Automatically annotated from API 20NE
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