Strain identifier
BacDive ID: 131307
Type strain:
Species: Rhizobium smilacinae
Strain Designation: PTYR-5
Strain history: <- KCTC <- Y. Wang <- L. Zhang; PTYR-5
NCBI tax ID(s): 1395944 (species)
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
- @ref: 22534
- history: <- KCTC <- Y. Wang <- L. Zhang; PTYR-5
doi: 10.13145/bacdive131307.20230509.8.1
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
synonyms
- @ref: 20215
- synonym: Alirhizobium smilacinae
@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
colony morphology
- @ref: 22534
- incubation period: 2-3 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
22534 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
22534 | RHIZOBIUM MEDIUM (DSMZ Medium 98) | yes | https://mediadive.dsmz.de/medium/98 | Name: 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
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | + | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
22534 | catalase | + | 1.11.1.6 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | + | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhizobium smilacinae PTYR-5 | GCA_006335145 | contig | ncbi | 1395944 |
66792 | Rhizobium smilacinae CCTCC AB 2013016 | 2738541321 | draft | img | 1395944 |
External links
@ref: 22534
culture collection no.: DSM 100675, CCTCC AB 2013016, KCTC 32300, LMG 27604
straininfo link
- @ref: 89749
- straininfo: 388551
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 25077951 | Rhizobium 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 Y | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0241-1 | 2014 | Bacterial 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, DNA | Enzymology |
Phylogeny | 30259064 | Rhizobium 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 DC | Arch Microbiol | 10.1007/s00203-018-1578-z | 2018 | Bacterial 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 Microbiology | Enzymology |
Phylogeny | 31820041 | Rhizobium 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 L | Curr Microbiol | 10.1007/s00284-019-01831-4 | 2019 | Bacterial 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 Microbiology | Transcriptome |
Phylogeny | 34935074 | A 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 GZ | Arch Microbiol | 10.1007/s00203-021-02706-8 | 2021 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids/analysis, Phylogeny, *Populus, RNA, Ribosomal, 16S/genetics, *Rhizobium/genetics, Rhizosphere, Sequence Analysis, DNA, Soil, Soil Microbiology | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
22534 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100675 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100675) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68369 | Automatically annotated from API 20NE | |||
89749 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID388551.1 |