Strain identifier
BacDive ID: 13643
Type strain:
Species: Pararhizobium herbae
Strain history: <- LMG <- X. Sui, China Agric. Univ., College Biol. Sci., Beijing <- Y. Li
NCBI tax ID(s): 508661 (species)
General
@ref: 18217
BacDive-ID: 13643
DSM-Number: 26427
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Pararhizobium herbae DSM 26427 is a mesophilic, Gram-negative bacterium that was isolated from root nodules of herb legumes Astragalus membranaceus.
NCBI tax id
- NCBI tax id: 508661
- Matching level: species
strain history
- @ref: 18217
- history: <- LMG <- X. Sui, China Agric. Univ., College Biol. Sci., Beijing <- Y. Li
doi: 10.13145/bacdive13643.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Rhizobiaceae
- genus: Pararhizobium
- species: Pararhizobium herbae
- full scientific name: Pararhizobium herbae (Ren et al. 2011) Mousavi et al. 2016
synonyms
- @ref: 20215
- synonym: Rhizobium herbae
@ref: 18217
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Pararhizobium
species: Pararhizobium herbae
full scientific name: Pararhizobium herbae (Ren et al. 2011) Mousavi et al. 2016
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.967
colony morphology
- @ref: 18217
- incubation period: 2-3 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
18217 | 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 |
18217 | 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 |
culture temp
- @ref: 18217
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.997 |
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 |
---|---|---|---|
18217 | catalase | + | 1.11.1.6 |
18217 | cytochrome-c 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18217 | - | - | - | - | + | + | - | + | + | + | + | + | + | + | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 18217
- sample type: root nodules of herb legumes Astragalus membranaceus
- host species: Astragalus membranaceus
- geographic location: Xinjiang
- country: China
- origin.country: CHN
- continent: Asia
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_252.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_84;97_191;98_214;99_252&stattab=map
- Last taxonomy: Rhizobiaceae
- 16S sequence: GU565534
- Sequence Identity:
- Total samples: 2054
- soil counts: 902
- aquatic counts: 390
- animal counts: 330
- plant counts: 432
Safety information
risk assessment
- @ref: 18217
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rhizobium giardinii strain CCBAU 83011 16S ribosomal RNA gene, partial sequence | EU399716 | 1345 | ena | 56731 |
18217 | Rhizobium herbae strain CCBAU 83011 16S ribosomal RNA gene, partial sequence | GU565534 | 1320 | ena | 508661 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhizobium herbae DSM 26427 | GCA_017873135 | contig | ncbi | 508661 |
66792 | Rhizobium herbae strain DSM 26427 | 508661.3 | wgs | patric | 508661 |
66792 | Rhizobium herbae DSM 26427 | 2913313856 | draft | img | 508661 |
66792 | Rhizobium herbae LMG 25718 | 2739367693 | draft | img | 508661 |
GC content
- @ref: 18217
- GC-content: 58.9
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.186 | no |
anaerobic | no | 98.915 | no |
halophile | no | 92.146 | no |
spore-forming | no | 94.663 | no |
glucose-util | yes | 87.591 | no |
aerobic | yes | 94.095 | no |
thermophile | no | 99.327 | no |
motile | yes | 88.442 | no |
flagellated | no | 71.369 | no |
glucose-ferment | no | 88.497 | yes |
External links
@ref: 18217
culture collection no.: DSM 26427, CCBAU 83011, HAMBI 3117, LMG 25718
straininfo link
- @ref: 82826
- straininfo: 369639
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20833881 | Rhizobium herbae sp. nov. and Rhizobium giardinii-related bacteria, minor microsymbionts of various wild legumes in China. | Ren DW, Wang ET, Chen WF, Sui XH, Zhang XX, Liu HC, Chen WX | Int J Syst Evol Microbiol | 10.1099/ijs.0.024943-0 | 2010 | China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fabaceae/*microbiology/physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, *Symbiosis | Genetics |
Phylogeny | 27026286 | Pararhizobium polonicum sp. nov. isolated from tumors on stone fruit rootstocks. | Pulawska J, Kuzmanovic N, Willems A, Pothier JF | Syst Appl Microbiol | 10.1016/j.syapm.2016.03.002 | 2016 | *Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Tumors/microbiology, Poland, Prunus avium/*microbiology, Prunus domestica/*microbiology, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, *Rhizobiaceae/classification/genetics/isolation & purification, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Transcription Factors/genetics | Phenotype |
Phylogeny | 27474082 | Rhizobium gei sp. nov., a bacterial endophyte of Geum aleppicum. | Shi X, Li C, Zhao L, Si M, Zhu L, Xin K, Chen C, Wang Y, Shen X, Zhang L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001348 | 2016 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification, Fatty Acids/chemistry, Genes, Bacterial, Geum/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA | Transcriptome |
Phylogeny | 28141485 | Pararhizobium antarcticum sp. nov., isolated from Antarctic water samples. | Naqvi SU, Qin Y, Tahir A, Stougaard P | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001828 | 2017 | Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
18217 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26427) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26427 | |||
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) | |||
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 | |||
82826 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID369639.1 | StrainInfo: A central database for resolving microbial strain identifiers |