Strain identifier

BacDive ID: 13638

Type strain: Yes

Species: Neorhizobium alkalisoli

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

NCBI tax ID(s): 528178 (species)

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General

@ref: 15974

BacDive-ID: 13638

DSM-Number: 21826

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

description: Neorhizobium alkalisoli DSM 21826 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from root nodules of Caragana intermedia grown in saline-alkaline soils.

NCBI tax id

  • NCBI tax id: 528178
  • Matching level: species

strain history

  • @ref: 15974
  • history: <- X. Sui, China Agric. Univ., College Biol. Sci., Beijing <- Y. L. Lu

doi: 10.13145/bacdive13638.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Neorhizobium
  • species: Neorhizobium alkalisoli
  • full scientific name: Neorhizobium alkalisoli (Lu et al. 2009) Mousavi et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Rhizobium alkalisoli

@ref: 15974

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Neorhizobium

species: Neorhizobium alkalisoli

full scientific name: Neorhizobium alkalisoli (Lu et al. 2009) Mousavi et al. 2015

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29143negative2 µm0.4 µmrod-shapedyes
69480yes92.913
69480negative99.987

Culture and growth conditions

culture medium

  • @ref: 15974
  • name: YMA-MEDIUM (MODIFIED) (DSMZ Medium 1031a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1031a
  • composition: Name: YMA-MEDIUM (modified) (DSMZ Medium 1031a) Composition: Agar 20.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l K2HPO4 0.5 g/l Na glutamate 0.5 g/l MgSO4 x 7 H2O 0.1 g/l CaCl2 x 2 H2O 0.0528 g/l NaCl 0.05 g/l FeCl3 x 6 H2O 0.00666 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15974positivegrowth28mesophilic
29143positivegrowth12-37
29143positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
29143positivegrowth05-10alkaliphile
29143positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29143
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29143no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
29143NaClpositivegrowth0-3 %
29143NaClpositiveoptimum1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2914316449alanine+carbon source
2914322599arabinose+carbon source
2914329016arginine+carbon source
2914335391aspartate+carbon source
2914328757fructose+carbon source
2914328260galactose+carbon source
2914317234glucose+carbon source
2914329987glutamate+carbon source
2914315428glycine+carbon source
29143182404-hydroxy-L-proline+carbon source
2914324996lactate+carbon source
2914325115malate+carbon source
2914337684mannose+carbon source
2914328044phenylalanine+carbon source
2914326271proline+carbon source
2914316634raffinose+carbon source
2914326546rhamnose+carbon source
2914333942ribose+carbon source
2914317814salicin+carbon source
2914330911sorbitol+carbon source
2914317992sucrose+carbon source
2914326986threonine+carbon source
2914327082trehalose+carbon source
2914316199urea+carbon source

metabolite production

  • @ref: 29143
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 29143
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
29143catalase+1.11.1.6
29143cytochrome oxidase+1.9.3.1
29143urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 15974
  • sample type: root nodules of Caragana intermedia grown in saline-alkaline soils
  • host species: Caragana intermedia
  • geographic location: Inner Mongolia, Qingshuihe city
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root nodule
#Condition#Alkaline
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_939.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_551;97_637;98_736;99_939&stattab=map
  • Last taxonomy: Neorhizobium
  • 16S sequence: EU074168
  • Sequence Identity:
  • Total samples: 3783
  • soil counts: 1052
  • aquatic counts: 391
  • animal counts: 295
  • plant counts: 2045

Safety information

risk assessment

  • @ref: 15974
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15974
  • description: Neorhizobium alkalisoli strain CCBAU 01393 16S ribosomal RNA gene, partial sequence
  • accession: EU074168
  • length: 1307
  • database: ena
  • NCBI tax ID: 528178

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Neorhizobium alkalisoli DSM 21826GCA_002968635contigncbi528178
66792Neorhizobium alkalisoli strain DSM 21826528178.3wgspatric528178
66792Neorhizobium alkalisoli DSM 218262854896431draftimg528178

GC content

@refGC-contentmethod
1597465.47thermal denaturation, midpoint method (Tm)
2914365.47

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.972yes
anaerobicno98.106yes
halophileno92.858yes
spore-formingno94.964yes
glucose-utilyes89.556yes
motileyes86.497yes
aerobicyes88.404no
thermophileno99.058no
flagellatedno80.479no
glucose-fermentno86.586no

External links

@ref: 15974

culture collection no.: DSM 21826, CCBAU 01393, HAMBI 3051, LMG 24763

straininfo link

  • @ref: 82821
  • straininfo: 364848

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19643906Rhizobium alkalisoli sp. nov., isolated from Caragana intermedia growing in saline-alkaline soils in the north of China.Li Lu Y, Chen WF, Li Han L, Wang ET, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.007237-02009Alkalies/analysis, Caragana/growth & development/*microbiology, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification, Root Nodules, Plant/microbiology, Sodium Chloride/analysis, Soil/*analysis, *Soil MicrobiologyGenetics
Phylogeny20382786Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species.Ren DW, Chen WF, Sui XH, Wang ET, Chen WXInt J Syst Evol Microbiol10.1099/ijs.0.023143-02010Bacterial Typing Techniques, China, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer/genetics, Fabaceae/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification, Sequence Analysis, DNAGenetics
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
Phylogeny25376852Rhizobium yantingense sp. nov., a mineral-weathering bacterium.Chen W, Sheng XF, He LY, Huang ZInt J Syst Evol Microbiol10.1099/ijs.0.064428-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
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
Phylogeny26374202Rhizobium marinum sp. nov., a malachite-green-tolerant bacterium isolated from seawater.Liu Y, Wang RP, Ren C, Lai QL, Zeng RYInt J Syst Evol Microbiol10.1099/ijsem.0.0005932015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fabaceae/microbiology, Fatty Acids/chemistry, Genes, Bacterial, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Root Nodulation, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water MicrobiologyGenetics
Phylogeny30259064Rhizobium panacihumi sp. nov., an isolate from ginseng-cultivated soil, as a potential plant growth promoting bacterium.Kang JP, Huo Y, Kim YJ, Ahn JC, Hurh J, Yang DU, Yang DCArch Microbiol10.1007/s00203-018-1578-z2018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Essential/genetics, Nucleic Acid Hybridization, Oxidoreductases/genetics, Panax/*microbiology, Phylogeny, Plant Development/*physiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizobium/*classification/genetics/*isolation & purification, Sequence Analysis, DNA, Soil, Soil MicrobiologyEnzymology
Phylogeny31768560Neorhizobium lilium sp. nov., an endophytic bacterium isolated from Lilium pumilum bulbs in Hebei province.Liu L, Shi S, Liang L, Xu L, Chi M, Zhang X, Li LArch Microbiol10.1007/s00203-019-01774-12019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/classification/genetics/*isolation & purification/metabolism, Fatty Acids/chemistry/metabolism, Lilium/*microbiology, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/classification/genetics/*isolation & purification/metabolism, Sequence Analysis, DNAMetabolism
Phylogeny31982965Rhizobium terrae sp. nov., Isolated from an Oil-Contaminated Soil in China.Ruan ZP, Cao WM, Zhang X, Liu JT, Zhu JC, Hu B, Jiang JDCurr Microbiol10.1007/s00284-020-01889-52020Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genome, Bacterial/genetics, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Rhizobium/chemistry/*classification/cytology/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Species Specificity, TemperatureGenetics
Phylogeny35604458Neorhizobium xiangyangii sp. nov., isolated from a highland barley cultivation soil in Qamdo, Tibet.Pan H, Zhou ZQ, He GW, Zhou J, Jin K, Liu HH, Wang C, Yang H, Yu YB, Tian YArch Microbiol10.1007/s00203-022-02961-32022Bacterial Typing Techniques, DNA, Bacterial/genetics, Ethanolamines, Fatty Acids/analysis, *Hordeum, Phosphatidylglycerols/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizobiaceae, Sequence Analysis, DNA, Soil, Soil Microbiology, TibetTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15974Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21826)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21826
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
29143Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2556728776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
82821Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364848.1StrainInfo: A central database for resolving microbial strain identifiers