Strain identifier

BacDive ID: 132917

Type strain: Yes

Species: Pseudorhizobium tarimense

Strain Designation: PL-41

Strain history: <- NRRL; NRRL B-59556 <- E. Rahman, Wuhan Univ., China; PL-41

NCBI tax ID(s): 1079109 (species)

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General

@ref: 24705

BacDive-ID: 132917

DSM-Number: 105042

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Pseudorhizobium tarimense PL-41 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from forest soil Populus euphratica.

NCBI tax id

  • NCBI tax id: 1079109
  • Matching level: species

strain history

  • @ref: 24705
  • history: <- NRRL; NRRL B-59556 <- E. Rahman, Wuhan Univ., China; PL-41

doi: 10.13145/bacdive132917.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Pseudorhizobium
  • species: Pseudorhizobium tarimense
  • full scientific name: Pseudorhizobium tarimense (Turdahon et al. 2013) Kuzmanovi? et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Rhizobium tarimense

@ref: 24705

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium tarimense

full scientific name: Rhizobium tarimense Turdahon et al. 2013

strain designation: PL-41

type strain: yes

Morphology

cell morphology

  • @ref: 30693
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 30693
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 24705
  • 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

@refgrowthtypetemperaturerange
24705positivegrowth30mesophilic
30693positivegrowth20-37
30693positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
30693positivegrowth5.5-8.5alkaliphile
30693positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30693
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30693
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30693NaClpositivegrowth0-3 %
30693NaClpositiveoptimum0.25 %

observation

  • @ref: 30693
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30693168082-dehydro-D-gluconate+carbon source
3069315963ribitol+carbon source
3069322599arabinose+carbon source
3069318403L-arabitol+carbon source
3069317057cellobiose+carbon source
3069328757fructose+carbon source
3069333984fucose+carbon source
3069328260galactose+carbon source
3069324265gluconate+carbon source
3069317234glucose+carbon source
3069329864mannitol+carbon source
30693506227N-acetylglucosamine+carbon source
3069326546rhamnose+carbon source
3069333942ribose+carbon source
3069327082trehalose+carbon source
3069317151xylitol+carbon source
3069318222xylose+carbon source
306934853esculin+hydrolysis
3069317632nitrate+reduction
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
30693acid phosphatase+3.1.3.2
30693alkaline phosphatase+3.1.3.1
30693catalase+1.11.1.6
30693cytochrome oxidase+1.9.3.1
30693urease+3.5.1.5
68369cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
24705----++-++++++-+-----+

Isolation, sampling and environmental information

isolation

  • @ref: 24705
  • sample type: forest soil Populus euphratica
  • host species: Populus euphratica
  • geographic location: ancient Khiyik River valley, Xinjiang Uyghur Autonomous Region
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_33078.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_551;97_2821;98_24467;99_33078&stattab=map
  • Last taxonomy: Rhizobium tarimense subclade
  • 16S sequence: HM371420
  • Sequence Identity:
  • Total samples: 129
  • soil counts: 18
  • aquatic counts: 35
  • animal counts: 22
  • plant counts: 54

Safety information

risk assessment

  • @ref: 24705
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24705
  • description: Rhizobium tarimense strain PL-41 16S ribosomal RNA gene, partial sequence
  • accession: HM371420
  • length: 1444
  • database: ena
  • NCBI tax ID: 1079109

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium tarimense DSM 1050422928180846draftimg1079109
66792Rhizobium tarimense CCTCC AB 20110112738541320draftimg1079109

GC content

  • @ref: 24705
  • GC-content: 57.8

External links

@ref: 24705

culture collection no.: DSM 105042, CCTCC AB 2011011, NRRL B-59556

straininfo link

  • @ref: 91194
  • straininfo: 404301

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23203621Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River.Turdahon M, Osman G, Hamdun M, Yusuf K, Abdurehim Z, Abaydulla G, Abdukerim M, Fang C, Rahman EInt J Syst Evol Microbiol10.1099/ijs.0.042176-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Rivers, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/analysisGenetics
Phylogeny24786354Rhizobium lemnae sp. nov., a bacterial endophyte of Lemna aequinoctialis.Kittiwongwattana C, Thawai CInt J Syst Evol Microbiol10.1099/ijs.0.061622-02014Araceae/*microbiology, Base Composition, DNA, Bacterial/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Symbiosis, ThailandEnzymology
Phylogeny25391352Rhizobium pakistanensis sp. nov., isolated from groundnut (Arachis hypogaea) nodules grown in rainfed Pothwar, Pakistan.Khalid R, Zhang YJ, Ali S, Sui XH, Zhang XX, Amara U, Chen WX, Hayat RAntonie Van Leeuwenhoek10.1007/s10482-014-0326-x2014Arachis/*microbiology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Pakistan, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification, Root Nodules, Plant/microbiology, Sequence Analysis, DNAGenetics
Phylogeny26016492Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots.Zhang XX, Gao JS, Cao YH, Sheirdil RA, Wang XC, Zhang LInt J Syst Evol Microbiol10.1099/ijs.0.0003582015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNAEnzymology

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24705Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105042Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105042)
30693Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172702428776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91194Reimer, 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 identifiers10.60712/SI-ID404301.1