Strain identifier

BacDive ID: 140985

Type strain: Yes

Species: Rhizobium wenxiniae

Strain Designation: 166

NCBI tax ID(s): 1737357 (species)

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General

@ref: 64870

BacDive-ID: 140985

DSM-Number: 100734

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

description: Rhizobium wenxiniae 166 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize, Fangshan District, Beijing, PR China.

NCBI tax id

  • NCBI tax id: 1737357
  • Matching level: species

doi: 10.13145/bacdive140985.20230509.8.1

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 wenxiniae
  • full scientific name: Rhizobium wenxiniae Gao et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Alirhizobium wenxiniae

@ref: 64870

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium wenxiniae

full scientific name: Rhizobium wenxiniae Gao et al. 2017

strain designation: 166

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43873negative1.2-2.2 µm0.3-0.4 µmrod-shapedno
69480negative99.995

colony morphology

  • @ref: 43873
  • colony size: 3-4 mm
  • colony color: milky
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Yeast mannitol agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43873Tryptic soy agaryes
43873Yeast mannitol agaryes
64870RHIZOBIUM 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

culture temp

@refgrowthtypetemperaturerange
43873positivegrowth15-37
43873positiveoptimum30mesophilic
64870positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43873positivegrowth6.0-9.0alkaliphile
43873positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43873
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.987

halophily

  • @ref: 43873
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
438738391D-gluconate-carbon source
4387317924D-sorbitol-carbon source
4387351850methyl pyruvate-carbon source
43873100147nalidixic acid-carbon source
4387375248potassium tellurite-carbon source
4387317234glucose-fermentation
43873casein-hydrolysis
4387328017starch-hydrolysis
4387316651(S)-lactate+carbon source
43873739183-O-methyl-D-glucose+carbon source
4387330089acetate+carbon source
4387328847D-fucose+carbon source
4387315748D-glucuronate+carbon source
4387323652dextrin+carbon source
4387328066gentiobiose+carbon source
4387317754glycerol+carbon source
4387329991L-aspartate+carbon source
4387317464L-galactonic acid gamma-lactone+carbon source
43873506227N-acetylglucosamine+carbon source
4387326490quinate+carbon source
4387362968cellulose+hydrolysis
4387317632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836927897tryptophan-energy source
6836917632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4387328971ampicillinyesyes50 µg/mL
4387348923erythromycinyesyes50 µg/mL
4387317833gentamicinyesyes5 µg/mL
438736104kanamycinyesyes5 µg/mL
4387317076streptomycinyesyes5 µg/mL
4387327902tetracyclineyesyes5 µg/mL
438736472lincomycinyesyes300 µg/mL
4387328971ampicillinyesyes5 µg/mL
4387348923erythromycinyesyes5 µg/mL

metabolite production

@refChebi-IDmetaboliteproduction
4387315688acetoinyes
6836935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
43873cytochrome oxidase+1.9.3.1
43873catalase+1.11.1.6
43873alkaline phosphatase+3.1.3.1
43873esterase (C 4)+
43873esterase Lipase (C 8)+
43873leucine arylamidase+3.4.11.1
43873valine arylamidase+
43873cystine arylamidase+3.4.11.3
43873trypsin+3.4.21.4
43873alpha-chymotrypsin+3.4.21.1
43873acid phosphatase+3.1.3.2
43873naphthol-AS-BI-phosphohydrolase+
43873alpha-glucosidase+3.2.1.20
43873beta-glucosidase+3.2.1.21
43873lipase (C 14)-
43873alpha-galactosidase-3.2.1.22
43873beta-galactosidase-3.2.1.23
43873beta-glucuronidase-3.2.1.31
43873N-acetyl-beta-glucosaminidase-3.2.1.52
43873alpha-mannosidase-3.2.1.24
43873alpha-fucosidase-3.2.1.51
43873arginine dihydrolase-3.5.3.6
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43873C12:0 aldehyde / unknown 10.9286.8
    43873C13:1 at 12-130.4
    43873C14:00.4
    43873C15:0 3OH0.2
    43873C16:07.8
    43873C16:0 3OH3.1
    43873C16:1ω6c / C16:1ω7c3
    43873C17:00.4
    43873C17:0 3OH0.3
    43873C17:1ω6c0.3
    43873C17:1ω8c0.5
    43873C18:00.3
    43873C18:0 3OH0.2
    43873C18:1ω5c0.1
    43873C18:1ω7c / C18:1ω6c71.1
    4387310-methyl C19:00.9
    43873C19:0ω8c cyclo4
    43873C15:1 iso h / C13:0 3OH0.3
    43873unknown 18.846 / C19:1ω6c0.1
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar
  • agar/liquid: agar
  • incubation temperature: 30
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph
  • method/protocol: Sasser, 1990

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64870+-+/--++-+++++++/-+/---+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
43873surface-sterilized root tissue of maize, Fangshan District, Beijing, PR ChinaFangshan District, BeijingChinaCHNAsiaLuria-Bertani agar2-3 daysroom temperature
64870surface-sterilized root tissue of maizeFangshan District of BeijingChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

  • @ref: 64870
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64870
  • description: Rhizobium wenxiniae strain 166 16S ribosomal RNA gene, partial sequence
  • accession: KR610521
  • length: 1348
  • database: ena
  • NCBI tax ID: 1737357

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium wenxiniae DSM 100734GCA_014201355scaffoldncbi1737357
66792Rhizobium wenxiniae CGMCC 1.15279GCA_014641515scaffoldncbi1737357
66792Rhizobium wenxiniae strain CGMCC 1.152791737357.4wgspatric1737357
66792Rhizobium wenxiniae strain DSM 1007341737357.3wgspatric1737357
66792Rhizobium wenxiniae DSM 1007342861144075draftimg1737357

GC content

  • @ref: 64870
  • GC-content: 59.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno80.554yes
gram-positiveno98.426no
anaerobicno96.778no
aerobicyes84.339no
halophileno94.591no
spore-formingno95.488no
glucose-utilyes92.73no
thermophileno99.636yes
motileyes79.872yes
glucose-fermentno90.726yes

External links

@ref: 64870

culture collection no.: CGMCC 1.15279, DSM 100734

straininfo link

  • @ref: 96823
  • straininfo: 405935

literature

  • topic: Phylogeny
  • Pubmed-ID: 28820092
  • title: Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root.
  • authors: Gao JL, Sun P, Wang XM, Lv FY, Mao XJ, Sun JG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002025
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Zea mays/*microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
43873Jun-lian Gao, Pengbo Sun, Xu-ming Wang, Fan-yang Lv, Xiao-jie Mao, Jian-guang SunRhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root10.1099/ijsem.0.002025IJSEM 67: 2798-2803 201728820092
64870Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100734Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100734)
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96823Reimer, 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-ID405935.1