Strain identifier
BacDive ID: 13602
Type strain: 
Species: Rhizobium leguminosarum
Strain Designation: 3D1k22a
Strain history: IAM 12613 <-- ATCC 14480 <-- U. M. Means 3D1k22a.
NCBI tax ID(s): 384 (species)
version 8.1 (current version)
General
@ref: 9165
BacDive-ID: 13602
DSM-Number: 30141
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile
description: Rhizobium leguminosarum 3D1k22a is a mesophilic, motile bacterium of the family Rhizobiaceae.
NCBI tax id
- NCBI tax id: 384
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9165 | <- ATCC <- Ura Mae Means (USDA), 3D1k22a |
| 67770 | IAM 12613 <-- ATCC 14480 <-- U. M. Means 3D1k22a. |
doi: 10.13145/bacdive13602.20230509.8.1
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 leguminosarum
- full scientific name: Rhizobium leguminosarum (Frank 1879) Frank 1889 (Approved Lists 1980)
synonyms
@ref synonym 20215 Schinzia leguminosarum 20215 Rhizobium trifolii
@ref: 9165
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Rhizobium
species: Rhizobium leguminosarum
full scientific name: Rhizobium leguminosarum (Frank 1879) Frank 1889 emend. Ramírez-Bahena et al. 2008
strain designation: 3D1k22a
type strain: no
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 91.874 | |
| 69480 | 99.965 | negative |
Culture and growth conditions
culture medium
- @ref: 9165
- name: RHIZOBIUM MEDIUM (DSMZ Medium 98)
- growth: yes
- link: https://mediadive.dsmz.de/medium/98
- composition: 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 |
|---|---|---|---|---|
| 9165 | positive | growth | 26 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.988 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | + | assimilation |
| 68369 | 16899 | D-mannitol | - | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9165 | - | - | - | - | + | + | - | + | - | +/- | +/- | - | + | +/- | - | - | - | +/- | - | - | + |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_1406.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_62;97_65;98_70;99_1406&stattab=map
- Last taxonomy: Rhizobium
- 16S sequence: AY509900
- Sequence Identity:
- Total samples: 7647
- soil counts: 4296
- aquatic counts: 531
- animal counts: 942
- plant counts: 1878
Safety information
risk assessment
- @ref: 9165
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Rhizobium leguminosarum strain DSM 30141 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence | AF345272 | 1161 | ena | 384 |
| 9165 | Rhizobium leguminosarum strain ATCC 14480 16S ribosomal RNA gene, partial sequence | AY509900 | 1475 | ena | 384 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhizobium leguminosarum DSM 30141 | GCA_014138565 | scaffold | ncbi | 384 |
| 66792 | Rhizobium leguminosarum strain DSM 30141 | 384.400 | wgs | patric | 384 |
| 66792 | Rhizobium trifolii DSM 30141 | 2861129306 | draft | img | 384 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | no | 83.332 | no |
| gram-positive | no | 97.902 | no |
| anaerobic | no | 98.25 | no |
| aerobic | yes | 90.455 | no |
| halophile | no | 94.858 | no |
| spore-forming | no | 92.308 | no |
| glucose-util | yes | 84.07 | no |
| thermophile | no | 99.639 | no |
| motile | yes | 86.894 | no |
| glucose-ferment | no | 88.919 | yes |
External links
@ref: 9165
culture collection no.: DSM 30141, ATCC 14480, JCM 20684, IAM 12613, NBRC 14784
straininfo link
- @ref: 82789
- straininfo: 4783
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17985116 | Phylogenetic diversity based on rrs, atpD, recA genes and 16S-23S intergenic sequence analyses of rhizobial strains isolated from Vicia faba and Pisum sativum in Peru. | Santillana N, Ramirez-Bahena MH, Garcia-Fraile P, Velazquez E, Zuniga D | Arch Microbiol | 10.1007/s00203-007-0313-y | 2007 | Bacterial Proteins/genetics, *Biodiversity, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, Molecular Sequence Data, Peas/*microbiology, Peru, *Phylogeny, Plant Roots/microbiology, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Rhizobium/*classification/genetics/*isolation & purification, Sequence Analysis, DNA, Sequence Homology, Vicia faba/*microbiology | Genetics |
| 33255180 | Exogenous ACC Deaminase Is Key to Improving the Performance of Pasture Legume-Rhizobial Symbioses in the Presence of a High Manganese Concentration. | Paco A, da-Silva JR, Torres DP, Glick BR, Brigido C | Plants (Basel) | 10.3390/plants9121630 | 2020 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9165 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30141) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-30141 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 82789 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4783.1 | StrainInfo: A central database for resolving microbial strain identifiers |