Strain identifier

BacDive ID: 13626

Type strain: Yes

Species: Neorhizobium galegae

Strain history: CIP <- 1998, Z. Terefework, Helsinki Univ., Helsinki, Finland: strain HAMBI 540 <- K. Lindström

NCBI tax ID(s): 399 (species)

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General

@ref: 4408

BacDive-ID: 13626

DSM-Number: 11542

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

description: Neorhizobium galegae DSM 11542 is a mesophilic, Gram-negative bacterium that was isolated from root nodules from Galega orientalis.

NCBI tax id

  • NCBI tax id: 399
  • Matching level: species

strain history

@refhistory
4408<- ATCC <- K. Lindström, HAMBI 540
67770IAM 13631 <-- HAMBI 540 <-- K. Lindström gal1261.
119505CIP <- 1998, Z. Terefework, Helsinki Univ., Helsinki, Finland: strain HAMBI 540 <- K. Lindström

doi: 10.13145/bacdive13626.20230509.8.1

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 galegae
  • full scientific name: Neorhizobium galegae (Lindström 1989) Mousavi et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Rhizobium galegae

@ref: 4408

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Neorhizobium

species: Neorhizobium galegae

full scientific name: Neorhizobium galegae (Lindström 1989) Mousavi et al. 2015

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.978
119505negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4408RHIZOBIUM 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
34062MEDIUM 1 - for Acetobacter, Azotobacter, Gluconobacter, Gluconacetobacter, Mesorhizodium ciceri and Pseudomonas doudoroffiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (5.000 g);Peptone (3.000 g);Mannitol (25.000 g)
119505CIP Medium 1yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=1

culture temp

@refgrowthtypetemperaturerange
4408positivegrowth30mesophilic
34062positivegrowth25mesophilic
67770positivegrowth25mesophilic
119505positivegrowth10-30
119505nogrowth37mesophilic
119505nogrowth41thermophilic
119505nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
119505NaClpositivegrowth0 %
119505NaClnogrowth2 %
119505NaClnogrowth4 %
119505NaClnogrowth6 %
119505NaClnogrowth8 %
119505NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1195054853esculin+hydrolysis
119505606565hippurate-hydrolysis
11950517632nitrate-reduction
11950516301nitrite+reduction
11950517632nitrate-respiration

antibiotic resistance

  • @ref: 119505
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119505
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11950515688acetoin-
11950517234glucose-

enzymes

@refvalueactivityec
119505oxidase+
119505beta-galactosidase+3.2.1.23
119505alcohol dehydrogenase-1.1.1.1
119505gelatinase-
119505catalase-1.11.1.6
119505gamma-glutamyltransferase-2.3.2.2
119505lysine decarboxylase-4.1.1.18
119505ornithine decarboxylase-4.1.1.17
119505phenylalanine ammonia-lyase+4.3.1.24
119505tryptophan deaminase-
119505urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119505-++--+-++-++----+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119505------------------+++---+-------------------+-+-++----+-------+-+------+-------++------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
4408root nodules from Galega orientalisGalega orientalisFinlandFINEurope
48993Galega orientalisFinlandFINEurope
67770Galega orientalisGalega orientalisFinlandFINEurope
119505Plant, Root nodule, Galega orientalisFinlandFINEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

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: X67226
  • Sequence Identity:
  • Total samples: 3783
  • soil counts: 1052
  • aquatic counts: 391
  • animal counts: 295
  • plant counts: 2045

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
44081Risk group (German classification)
1195051Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhizobium galegae gene for 16S rRNA, complete sequence, type strain: ATCC 43677D113431466ena399
20218Rhizobium galegae strain HAMBI 540 16S-23S intergenic spacer, partial sequenceAF2716461160ena1028800
20218R.galegae gene for 16S ribosomal RNA (partial)X63823260ena1028800
20218Rhizobium galegae 16S rRNA gene, partial, strain HAMBI540Y12355818ena1028800
20218Rhizobium galegae gene for 16S rRNA, strain: IAM 13631D127931434ena399
20218Rhizobium galegae partial 16S rRNA gene, strain LMG 6214X672261433ena399
20218Rhizobium galegae gene for 16S rRNA, partial sequence, strain: NBRC 14965AB6807261406ena399

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Neorhizobium galegae bv. orientalis str. HAMBI 540GCA_000731315completencbi1028800
66792Neorhizobium galegae bv. orientalis str. HAMBI 5401028800.3completepatric1028800
66792Neorhizobium galegae bv. orientalis str. HAMBI 5401028800.16plasmidpatric1028800
66792Neorhizobium galegae bv. orientalis HAMBI 5402585427634completeimg1028800

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.159no
flagellatedno82.922no
gram-positiveno98.146no
anaerobicno98.533no
aerobicyes91.762no
halophileno92.94no
spore-formingno95.624no
thermophileno98.971yes
glucose-utilyes89.58no
glucose-fermentno87.611no

External links

@ref: 4408

culture collection no.: DSM 11542, ATCC 43677, CIP 105585, JCM 20973, LMG 6214, NBRC 14965, CCUG 27880, HAMBI 540, IAM 13631, IFO 14965, NZP 5563, OUT 30006

straininfo link

  • @ref: 82812
  • straininfo: 4763

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734023Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae.Wang ET, van Berkum P, Beyene D, Sui XH, Dorado O, Chen WX, Martinez-Romero EInt J Syst Bacteriol10.1099/00207713-48-3-6871998Base Sequence, DNA, Bacterial/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plasmids, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification, SymbiosisGenetics
16348119Stability of Markers Used for Identification of Two Rhizobium galegae Inoculant Strains after Five Years in the Field.Lindstrom K, Lipsanen P, Kaijalainen SAppl Environ Microbiol10.1128/aem.56.2.444-450.19901990
19719586Persistence, population dynamics and competitiveness for nodulation of marker gene-tagged Rhizobium galegae strains in field lysimeters in the boreal climatic zone.Pitkajarvi J, Rasanen LA, Langenskiold J, Wallenius K, Niemi M, Lindstrom KFEMS Microbiol Ecol10.1016/S0168-6496(03)00210-12003
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
Metabolism25933608Genomic features separating ten strains of Neorhizobium galegae with different symbiotic phenotypes.Osterman J, Mousavi SA, Koskinen P, Paulin L, Lindstrom KBMC Genomics10.1186/s12864-015-1576-32015Amino Acid Sequence, Bacterial Proteins/chemistry/genetics/metabolism, DNA, Bacterial/analysis/isolation & purification/metabolism, Galega/growth & development/microbiology, *Genome, Bacterial, Molecular Sequence Data, Nitrogen Fixation/genetics, Phenotype, Rhizobiaceae/*genetics, Seeds/growth & development/metabolism/microbiology, Sequence Alignment, Sequence Analysis, DNA, Sigma Factor/chemistry/genetics/metabolism, Symbiosis/*geneticsGenetics
Phylogeny26078205Pseudorhizobium pelagicum gen. nov., sp. nov. isolated from a pelagic Mediterranean zone.Kimes NE, Lopez-Perez M, Flores-Felix JD, Ramirez-Bahena MH, Igual JM, Peix A, Rodriguez-Valera F, Velazquez ESyst Appl Microbiol10.1016/j.syapm.2015.05.0032015Bacterial Typing Techniques, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Mediterranean Sea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Rhizobiaceae/*classification/genetics/*isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Spain, Transcription Factors/geneticsGenetics
Phylogeny30268635Neorhizobium tomejilense sp. nov., first non-symbiotic Neorhizobium species isolated from a dryland agricultural soil in southern Spain.Soenens A, Gomila M, Imperial JSyst Appl Microbiol10.1016/j.syapm.2018.09.0012018Agriculture, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Operon, RNA, Ribosomal, 16S, Rhizobiaceae/*classification/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, SpainTranscriptome
Phylogeny31820041Rhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China.Liu L, Liang L, Xu L, Chi M, Zhang X, Li LCurr Microbiol10.1007/s00284-019-01831-42019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/isolation & purification, Sand/microbiology, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
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/urltitlejournalpubmed
4408Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11542)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11542
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
34062Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17620
48993Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27880)https://www.ccug.se/strain?id=27880
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
82812Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4763.1StrainInfo: A central database for resolving microbial strain identifiers
119505Curators of the CIPCollection of Institut Pasteur (CIP 105585)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105585