Strain identifier

BacDive ID: 13643

Type strain: Yes

Species: Pararhizobium herbae

Strain history: <- LMG <- X. Sui, China Agric. Univ., College Biol. Sci., Beijing <- Y. Li

NCBI tax ID(s): 508661 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refnamegrowthlinkcomposition
18217RHIZOBIUM MEDIUM (DSMZ Medium 98)yeshttps://mediadive.dsmz.de/medium/98Name: 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
18217NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: 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

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
18217catalase+1.11.1.6
18217cytochrome-c oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
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

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhizobium giardinii strain CCBAU 83011 16S ribosomal RNA gene, partial sequenceEU3997161345ena56731
18217Rhizobium herbae strain CCBAU 83011 16S ribosomal RNA gene, partial sequenceGU5655341320ena508661

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium herbae DSM 26427GCA_017873135contigncbi508661
66792Rhizobium herbae strain DSM 26427508661.3wgspatric508661
66792Rhizobium herbae DSM 264272913313856draftimg508661
66792Rhizobium herbae LMG 257182739367693draftimg508661

GC content

  • @ref: 18217
  • GC-content: 58.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.186no
anaerobicno98.915no
halophileno92.146no
spore-formingno94.663no
glucose-utilyes87.591no
aerobicyes94.095no
thermophileno99.327no
motileyes88.442no
flagellatedno71.369no
glucose-fermentno88.497yes

External links

@ref: 18217

culture collection no.: DSM 26427, CCBAU 83011, HAMBI 3117, LMG 25718

straininfo link

  • @ref: 82826
  • straininfo: 369639

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20833881Rhizobium 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 WXInt J Syst Evol Microbiol10.1099/ijs.0.024943-02010China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fabaceae/*microbiology/physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, *SymbiosisGenetics
Phylogeny27026286Pararhizobium polonicum sp. nov. isolated from tumors on stone fruit rootstocks.Pulawska J, Kuzmanovic N, Willems A, Pothier JFSyst Appl Microbiol10.1016/j.syapm.2016.03.0022016*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/geneticsPhenotype
Phylogeny27474082Rhizobium 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 LInt J Syst Evol Microbiol10.1099/ijsem.0.0013482016Bacterial 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, DNATranscriptome
Phylogeny28141485Pararhizobium antarcticum sp. nov., isolated from Antarctic water samples.Naqvi SU, Qin Y, Tahir A, Stougaard PInt J Syst Evol Microbiol10.1099/ijsem.0.0018282017Antarctic 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 MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18217Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26427)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26427
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82826Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID369639.1StrainInfo: A central database for resolving microbial strain identifiers