Strain identifier
BacDive ID: 138443
Type strain:
Species: Rhizobium leguminosarum
Strain Designation: 3Hoq18
Strain history: CIP <- 2001, IFO <- Toyama Dept Biol. <- H. Oyaizu <- IAM <- ATCC <- L.W. Erdman
NCBI tax ID(s): 384 (species)
General
@ref: 64388
BacDive-ID: 138443
DSM-Number: 106839
keywords: genome sequence, Bacteria, mesophilic, Gram-negative
description: Rhizobium leguminosarum 3Hoq18 is a mesophilic, Gram-negative bacterium of the family Rhizobiaceae.
NCBI tax id
- NCBI tax id: 384
- Matching level: species
strain history
@ref | history |
---|---|
64388 | <- C. Vereecke, LMG; LMG 14904 <- 1994, American Type Culture Collection (ATCC), Bacteriology Program (Rhizobium leguminosarum biovar. viceae) <- L.Erdman (Rhizobium leguminosarum) |
39741 | CIP <- 2001, IFO <- Toyama Dept Biol. <- H. Oyaizu <- IAM <- ATCC <- L.W. Erdman |
doi: 10.13145/bacdive138443.20230509.8.1
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: 64388
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: 3Hoq18
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.945 | ||
39741 | negative | rod-shaped | yes |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
64388 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
39741 | 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) | |
39741 | CIP Medium 296 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
64388 | positive | growth | 28 | mesophilic |
39741 | positive | growth | 30 | mesophilic |
39741 | positive | growth | 25-37 | mesophilic |
39741 | no | growth | 10 | psychrophilic |
39741 | no | growth | 41 | thermophilic |
39741 | no | growth | 45 | thermophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.995 |
halophily
- @ref: 39741
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-10 %
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | erythritol | - | builds acid from | 17113 |
68369 | malate | - | assimilation | 25115 |
68369 | adipate | - | assimilation | 17128 |
68369 | decanoate | - | assimilation | 27689 |
68369 | gluconate | - | assimilation | 24265 |
68369 | maltose | - | assimilation | 17306 |
68369 | N-acetylglucosamine | - | assimilation | 59640 |
68369 | D-mannitol | - | assimilation | 16899 |
68369 | D-mannose | - | assimilation | 16024 |
68369 | L-arabinose | - | assimilation | 30849 |
68369 | D-glucose | - | assimilation | 17634 |
68369 | gelatin | - | hydrolysis | 5291 |
68369 | esculin | + | hydrolysis | 4853 |
68369 | urea | + | hydrolysis | 16199 |
68369 | arginine | - | hydrolysis | 29016 |
68369 | D-glucose | - | fermentation | 17634 |
68369 | tryptophan | - | energy source | 27897 |
68369 | nitrate | - | reduction | 17632 |
39741 | citrate | - | carbon source | 16947 |
39741 | esculin | - | hydrolysis | 4853 |
39741 | hippurate | - | hydrolysis | 606565 |
39741 | nitrate | - | reduction | 17632 |
39741 | nitrite | - | reduction | 16301 |
antibiotic resistance
- @ref: 39741
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
39741 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test | methylred-test |
---|---|---|---|---|---|
68369 | 35581 | indole | - | ||
39741 | 15688 | acetoin | - | ||
39741 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | gelatinase | - | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | + | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
39741 | oxidase | + | |
39741 | beta-galactosidase | + | 3.2.1.23 |
39741 | alcohol dehydrogenase | - | 1.1.1.1 |
39741 | gelatinase | - | |
39741 | catalase | - | 1.11.1.6 |
39741 | gamma-glutamyltransferase | + | 2.3.2.2 |
39741 | lysine decarboxylase | - | 4.1.1.18 |
39741 | ornithine decarboxylase | - | 4.1.1.17 |
39741 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
39741 | tryptophan deaminase | - | |
39741 | urease | + | 3.5.1.5 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
64388 | - | - | - | - | - | + | - | - | +/- | - | + | - | - | - | - | + | + | +/- | - | - |
39741 | - | + | - | - | - | + | + | - | + | - | + | + | - | + | - | + | + | + | + | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
64388 | - | - | - | - | + | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
39741 | +/- | - | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | +/- | - | +/- | - | - | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | +/- | +/- | - | - | +/- | - | - | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
39741 | + | + | + | - | + | - | + | + | - | - | + | + | - | - | - | + | + | - | + | + | - | + | - | + | + | - | - | - | - | - | - | + | + | - | - | + | + | + | - | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | geographic location | sample type |
---|---|---|
64388 | country of origin unknown | |
39741 | Effective nodules of Pisum sativum |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
64388 | 1 | Risk group (German classification) |
39741 | 1 | Risk group (French classification) |
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhizobium leguminosarum DSM 106839 | GCA_014202125 | scaffold | ncbi | 384 |
66792 | Rhizobium leguminosarum strain DSM 106839 | 384.421 | wgs | patric | 384 |
66792 | Rhizobium leguminosarum DSM 106839 | 2861339494 | draft | img | 384 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 76.966 | no |
gram-positive | no | 97.671 | no |
anaerobic | no | 98.773 | no |
aerobic | yes | 93.604 | no |
halophile | no | 93.679 | no |
spore-forming | no | 92.577 | no |
glucose-util | yes | 83.293 | yes |
thermophile | no | 99.344 | yes |
motile | yes | 86.031 | no |
glucose-ferment | no | 89.086 | yes |
External links
@ref: 64388
culture collection no.: CIP 106959, ATCC 10004, IAM 12609, OUT 30008, IFO 14778, DSM 106839, LMG 14904
straininfo link
- @ref: 95170
- straininfo: 4782
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 1377901 | Phylogenetic position of Rhizobium sp. strain Or 191, a symbiont of both Medicago sativa and Phaseolus vulgaris, based on partial sequences of the 16S rRNA and nifH genes. | Eardly BD, Young JP, Selander RK | Appl Environ Microbiol | 10.1128/aem.58.6.1809-1815.1992 | 1992 | Base Sequence, DNA, Bacterial/genetics, Fabaceae/microbiology, Genes, Bacterial, Hydrogen-Ion Concentration, Medicago sativa/microbiology, Microscopy, Electron, Molecular Sequence Data, Nitrogen Fixation/*genetics, Phylogeny, Plants, Medicinal, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/*genetics, Rhizobium/classification/*genetics/ultrastructure, Sequence Homology, Nucleic Acid, Symbiosis, Temperature | Genetics |
Phylogeny | 9336913 | Classification of Austrian rhizobia and the Mexican isolate FL27 obtained from Phaseolus vulgaris L. as Rhizobium gallicum. | Sessitsch A, Ramirez-Saad H, Hardarson G, Akkermans AD, de Vos WM | Int J Syst Bacteriol | 10.1099/00207713-47-4-1097 | 1997 | Austria, DNA, Bacterial/*analysis, Fabaceae/microbiology/physiology, Mexico, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plants, Medicinal, Plasmids/genetics, RNA, Ribosomal, 16S/*analysis, Rhizobium/*classification/*genetics, Rickettsiaceae/physiology | Genetics |
Metabolism | 12029033 | Atypical processing in domain III of 23S rRNA of Rhizobium leguminosarum ATCC 10004(T) at a position homologous to an rRNA fragmentation site in protozoa. | Klein F, Samorski R, Klug G, Evguenieva-Hackenberg E | J Bacteriol | 10.1128/JB.184.12.3176-3185.2002 | 2002 | Animals, Base Sequence, Crithidia, Endoribonucleases/metabolism, Introns, Molecular Sequence Data, Nucleic Acid Conformation, *RNA Processing, Post-Transcriptional, RNA, Bacterial/metabolism, RNA, Protozoan/*chemistry/metabolism, RNA, Ribosomal, 23S/*chemistry/genetics/*metabolism, Rhizobium leguminosarum/genetics/growth & development/*metabolism, Ribonuclease III, Trypanosomatina/*genetics/metabolism | Genetics |
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 | 19567587 | Rhizobium mesosinicum sp. nov., isolated from root nodules of three different legumes. | Lin DX, Chen WF, Wang FQ, Hu D, Wang ET, Sui XH, Chen WX | Int J Syst Evol Microbiol | 10.1099/ijs.0.006387-0 | 2009 | Aerobiosis, Bacterial Proteins/genetics, Bacterial Typing Techniques, China, Cluster Analysis, DNA Fingerprinting/methods, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, Fabaceae/*microbiology, Locomotion, Molecular Sequence Data, N-Acetylglucosaminyltransferases/genetics, Nucleic Acid Hybridization, Phylogeny, Plant Roots/*microbiology, Proteome/analysis, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Transcription Factors/genetics | Genetics |
Phylogeny | 29881978 | A new Rhizobium species isolated from the water of a crater lake, description of Rhizobium aquaticum sp. nov. | Mathe I, Toth E, Mentes A, Szabo A, Marialigeti K, Schumann P, Felfoldi T | Antonie Van Leeuwenhoek | 10.1007/s10482-018-1110-0 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Lakes/*microbiology, Phylogeny, Rhizobium/classification/genetics/*isolation & purification/metabolism | Metabolism |
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 | |
39741 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106959 | Collection of Institut Pasteur (CIP 106959) | |
64388 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-106839 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106839) | |
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 | |||
68371 | Automatically annotated from API 50CH acid | |||
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
95170 | 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-ID4782.1 |