Strain identifier
BacDive ID: 13609
Type strain:
Species: Rhizobium phaseoli
Strain Designation: 3I6c15, 316c15
Strain history: CIP <- 2002, P. De Lajudie, Montpellier, France: strain ORS 662 <- LMG <- 1989, ATCC, Rhizobium leguminosarum biovar phaseoli <- U. Means, Rhizobium phaseoli, USDA: strain 316c15
NCBI tax ID(s): 396 (species)
General
@ref: 9158
BacDive-ID: 13609
DSM-Number: 30137
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Rhizobium phaseoli 3I6c15 is a mesophilic, Gram-negative, motile bacterium of the family Rhizobiaceae.
NCBI tax id
- NCBI tax id: 396
- Matching level: species
strain history
@ref | history |
---|---|
9158 | <- ATCC <- U. M. Means, USDA, 3I6c15 |
67770 | IAM 12612 <-- ATCC 14482 <-- U. M. Means 3I6c15. |
121793 | CIP <- 2002, P. De Lajudie, Montpellier, France: strain ORS 662 <- LMG <- 1989, ATCC, Rhizobium leguminosarum biovar phaseoli <- U. Means, Rhizobium phaseoli, USDA: strain 316c15 |
doi: 10.13145/bacdive13609.20230509.8.1
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 phaseoli
- full scientific name: Rhizobium phaseoli Dangeard 1926 (Approved Lists 1980)
@ref: 9158
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Rhizobium
species: Rhizobium phaseoli
full scientific name: Rhizobium phaseoli Dangeard 1926 emend. Ramírez-Bahena et al. 2008
strain designation: 3I6c15, 316c15
type strain: yes
Morphology
cell morphology
- @ref: 121793
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
colony morphology
- @ref: 9158
- incubation period: 1-2 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9158 | 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 |
38201 | MEDIUM 296 - for Rhizobium | yes | Distilled water make up to (800.000 ml);Agar (15.000 g);Yeast extract (1.000 g);Mannitol (10.000 g);Earth extract - M0541 (200.000 ml) | |
121793 | CIP Medium 296 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
9158 | positive | growth | 26 | mesophilic |
38201 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
121793 | positive | growth | 25-37 | mesophilic |
121793 | no | growth | 10 | psychrophilic |
121793 | no | growth | 41 | thermophilic |
121793 | no | growth | 45 | thermophilic |
Physiology and metabolism
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121793 | NaCl | positive | growth | 0 % |
121793 | NaCl | no | growth | 2 % |
121793 | NaCl | no | growth | 4 % |
121793 | NaCl | no | growth | 6 % |
121793 | NaCl | no | growth | 8 % |
121793 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-fructose | - | builds acid from | 15824 |
68371 | D-glucose | - | builds acid from | 17634 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
68369 | adipate | - | assimilation | 17128 |
68369 | decanoate | - | assimilation | 27689 |
68369 | gelatin | - | hydrolysis | 5291 |
68369 | urea | + | hydrolysis | 16199 |
68369 | arginine | - | hydrolysis | 29016 |
68369 | D-glucose | - | fermentation | 17634 |
68369 | tryptophan | - | energy source | 27897 |
68369 | nitrate | - | reduction | 17632 |
121793 | citrate | - | carbon source | 16947 |
121793 | esculin | + | hydrolysis | 4853 |
121793 | hippurate | - | hydrolysis | 606565 |
121793 | nitrate | - | reduction | 17632 |
121793 | nitrite | - | reduction | 16301 |
antibiotic resistance
- @ref: 121793
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121793 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test | methylred-test |
---|---|---|---|---|---|
68369 | 35581 | indole | - | ||
121793 | 15688 | acetoin | - | ||
121793 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
9158 | catalase | + | 1.11.1.6 |
9158 | cytochrome-c oxidase | + | 1.9.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | urease | + | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
121793 | oxidase | - | |
121793 | beta-galactosidase | + | 3.2.1.23 |
121793 | alcohol dehydrogenase | - | 1.1.1.1 |
121793 | gelatinase | - | |
121793 | catalase | + | 1.11.1.6 |
121793 | gamma-glutamyltransferase | - | 2.3.2.2 |
121793 | lysine decarboxylase | - | 4.1.1.18 |
121793 | ornithine decarboxylase | - | 4.1.1.17 |
121793 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121793 | tryptophan deaminase | - | |
121793 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121793 | - | + | + | - | - | + | - | - | - | - | + | + | - | + | - | + | + | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
9158 | - | - | - | - | + | - | - | + | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | - | +/- | - | - | + |
9158 | - | - | - | - | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121793 | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | geographic location | country | origin.country | continent | sample type |
---|---|---|---|---|---|
38201 | Beltsville, MD | USA | USA | North America | |
67770 | Beltsville, MD | USA | USA | North America | Plant-derived foodstuff (garden beans) |
121793 | Beltsville, Maryland | United States of America | USA | North America | Garden beans |
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: EF141340
- Sequence Identity:
- Total samples: 333
- soil counts: 50
- aquatic counts: 32
- animal counts: 28
- plant counts: 223
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
9158 | 1 | Risk group (German classification) |
121793 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rhizobium phaseoli strain ATCC 14482 16S ribosomal RNA gene, partial sequence | EF141340 | 1477 | ena | 396 |
20218 | Rhizobium phaseoli strain ATCC 14482 16S-23S ribosomal RNA intergenic spacer, partial sequence | EF141341 | 1091 | ena | 396 |
20218 | Rhizobium leguminosarum strain CCT 4168T 16S-23S ribosomal DNA intergenic spacer region, 3' end | AF091788 | 784 | ena | 384 |
20218 | Rhizobium leguminosarum strain CCT 4168T 16S-23S ribosomal DNA intergenic spacer region, 5' end | AF091789 | 743 | ena | 384 |
20218 | R.leguminosarum (LMG 8819) 16S rRNA gene | X77122 | 1099 | ena | 384 |
20218 | Rhizobium phaseoli gene for 16S rRNA, partial sequence, strain: NBRC 14785 | AB680664 | 1406 | ena | 396 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhizobium phaseoli strain ATCC 14482 | 396.115 | wgs | patric | 396 |
66792 | Rhizobium phaseoli DSM 30137 | 2738541346 | draft | img | 396 |
67770 | Rhizobium phaseoli ATCC 14482 | GCA_003985125 | scaffold | ncbi | 396 |
GC content
- @ref: 9158
- GC-content: 59.1
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 97.581 | no |
anaerobic | no | 98.745 | no |
halophile | no | 94.003 | no |
spore-forming | no | 94.069 | no |
glucose-util | yes | 83.603 | no |
aerobic | yes | 93.007 | no |
motile | yes | 83.885 | no |
thermophile | no | 99.251 | yes |
flagellated | no | 84.117 | no |
glucose-ferment | no | 88.904 | no |
External links
@ref: 9158
culture collection no.: DSM 30137, ATCC 14482, JCM 20683, NBRC 14785, NRRL L-321, VKM B-1966, IAM 12612, CIP 107329, LMG 8819, ORS 662
straininfo link
- @ref: 82796
- straininfo: 265209
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 | 22858268 | Rhizobium etli taxonomy revised with novel genomic data and analyses. | Lopez-Guerrero MG, Ormeno-Orrillo E, Velazquez E, Rogel MA, Acosta JL, Gonzalez V, Martinez J, Martinez-Romero E | Syst Appl Microbiol | 10.1016/j.syapm.2012.06.009 | 2012 | DNA, Bacterial/genetics, Databases, Genetic, *Genome, Bacterial, Genomics/methods, Nucleic Acid Hybridization, Phaseolus/microbiology, Phylogeny, Rhizobium etli/*classification/*genetics | Genetics |
Phylogeny | 25385989 | Rhizobium sophorae sp. nov. and Rhizobium sophoriradicis sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Sophora flavescens. | Jiao YS, Yan H, Ji ZJ, Liu YH, Sui XH, Wang ET, Guo BL, Chen WX, Chen WF | Int J Syst Evol Microbiol | 10.1099/ijs.0.068916-0 | 2014 | China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Phaseolus, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Sophora/*microbiology, *Symbiosis, Ubiquinone/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9158 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30137) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-30137 | |||
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 | |
38201 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/4753 | ||||
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 | |||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
82796 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265209.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121793 | Curators of the CIP | Collection of Institut Pasteur (CIP 107329) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107329 |