Strain identifier
BacDive ID: 13636
Type strain:
Species: Rhizobium pisi
Strain history: IAM 12609 <-- ATCC (as ATCC 10004) <-- L. W. Erdman (as strain 3HOq18).
NCBI tax ID(s): 574561 (species)
General
@ref: 9153
BacDive-ID: 13636
DSM-Number: 30132
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Rhizobium pisi DSM 30132 is a mesophilic bacterium that was isolated from effective nodules Pisum sativum.
NCBI tax id
- NCBI tax id: 574561
- Matching level: species
strain history
@ref | history |
---|---|
9153 | <- ATCC <- L.W. Erdman, 3HOq18 |
67770 | IAM 12609 <-- ATCC (as ATCC 10004) <-- L. W. Erdman (as strain 3HOq18). |
doi: 10.13145/bacdive13636.20230509.8.1
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 pisi
- full scientific name: Rhizobium pisi Ramírez-Bahena et al. 2008
synonyms
- @ref: 20215
- synonym: Rhizobium fabae
@ref: 9153
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Rhizobium
species: Rhizobium pisi
full scientific name: Rhizobium pisi Ramírez-Bahena et al. 2008
type strain: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9153 | 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 |
9153 | 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 | growth | type | temperature | range |
---|---|---|---|---|
9153 | positive | growth | 26 | mesophilic |
67770 | positive | growth | 25 | 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 | 17634 | D-glucose | - | fermentation |
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 |
---|---|---|---|
68369 | cytochrome oxidase | + | 1.9.3.1 |
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 | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9153 | - | - | - | - | + | + | - | + | + | + | + | + | + | + | - | - | - | + | +/- | - | + |
9153 | - | - | - | - | + | + | - | + | + | + | + | + | + | + | - | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species |
---|---|---|
9153 | effective nodules Pisum sativum | Pisum sativum |
67770 | Effective nodules of Pisum sativum | Pisum sativum |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root nodule |
taxonmaps
- @ref: 69479
- File name: preview.99_77.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_62;97_65;98_70;99_77&stattab=map
- Last taxonomy: Rhizobium
- 16S sequence: AY509899
- Sequence Identity:
- Total samples: 333
- soil counts: 50
- aquatic counts: 32
- animal counts: 28
- plant counts: 223
Safety information
risk assessment
- @ref: 9153
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 9153
- description: Rhizobium pisi strain DSM 30132 16S ribosomal RNA gene, partial sequence
- accession: AY509899
- length: 1475
- database: ena
- NCBI tax ID: 574561
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhizobium pisi DSM 30132 | GCA_003938655 | contig | ncbi | 574561 |
66792 | Rhizobium pisi strain DSM 30132 | 574561.3 | wgs | patric | 574561 |
66792 | Rhizobium pisi DSM 30132 | 2738541312 | draft | img | 574561 |
GC content
- @ref: 9153
- GC-content: 61.5
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 97.752 | no |
anaerobic | no | 98.391 | no |
halophile | no | 94.24 | no |
spore-forming | no | 93.857 | no |
glucose-util | yes | 84.051 | yes |
thermophile | no | 99.571 | yes |
motile | yes | 85.428 | no |
flagellated | no | 85.038 | no |
aerobic | yes | 92.85 | no |
glucose-ferment | no | 89.184 | yes |
External links
@ref: 9153
culture collection no.: DSM 30132, NCIB 11478, NCIMB 11478, JCM 20680, IAM 12609, NBRC 14778
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18984681 | Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov. | Ramirez-Bahena MH, Garcia-Fraile P, Peix A, Valverde A, Rivas R, Igual JM, Mateos PF, Martinez-Molina E, Velazquez E | Int J Syst Evol Microbiol | 10.1099/ijs.0.65621-0 | 2008 | Bacterial Proteins/genetics, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Rhizobium/*classification/genetics/physiology, Rhizobium leguminosarum/*classification/genetics/physiology, Sequence Analysis, DNA, Species Specificity | Genetics |
Phylogeny | 23507586 | Rhizobium pisi sv. trifolii K3.22 harboring nod genes of the Rhizobium leguminosarum sv. trifolii cluster. | Marek-Kozaczuk M, Leszcz A, Wielbo J, Wdowiak-Wrobel S, Skorupska A | Syst Appl Microbiol | 10.1016/j.syapm.2013.01.005 | 2013 | Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, Bacterial, Host Specificity, Medicago/microbiology, Molecular Sequence Data, Molecular Typing, Phylogeny, Plant Root Nodulation, Plasmids, RNA, Ribosomal, 16S/genetics, Rhizobium leguminosarum/*classification/*genetics/isolation & purification/physiology, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
9153 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30132) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-30132 | |
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68369 | Automatically annotated from API 20NE | |||
69479 | João 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 |