Strain identifier

BacDive ID: 13548

Type strain: Yes

Species: Ensifer fredii

Strain history: CIP <- 2002, P. de Lajudie, Montpellier, France: strain ORS 669T <- LMG <- 1984, B. Jarvis, Rhizobium sp.

NCBI tax ID(s): 380 (species)

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General

@ref: 2339

BacDive-ID: 13548

DSM-Number: 5851

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

description: Ensifer fredii DSM 5851 is a mesophilic, Gram-negative, motile bacterium that was isolated from soybean nodules.

NCBI tax id

  • NCBI tax id: 380
  • Matching level: species

strain history

@refhistory
2339<- Wen-Xin Chen <- Yang Su-Scheng <- H.H. Keyser
67770IAM 13625 <-- USDA 205.
119450CIP <- 2002, P. de Lajudie, Montpellier, France: strain ORS 669T <- LMG <- 1984, B. Jarvis, Rhizobium sp.

doi: 10.13145/bacdive13548.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Ensifer
  • species: Ensifer fredii
  • full scientific name: Ensifer fredii (Scholla and Elkan 1984) Young 2003

  • synonyms

    @refsynonym
    20215Sinorhizobium xinjiangensis
    20215Rhizobium fredii
    20215Sinorhizobium fredii
    20215Ensifer xinjiangensis
    20215Sinorhizobium xinjiangense

@ref: 2339

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Ensifer

species: Ensifer fredii

full scientific name: Ensifer fredii (Scholla and Elkan 1984) Young 2003

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119450negativerod-shapedyes
125438negative98.833
125439negative99.5

colony morphology

  • @ref: 119450

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2339RHIZOBIUM 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
38202MEDIUM 296 - for RhizobiumyesDistilled water make up to (800.000 ml);Agar (15.000 g);Yeast extract (1.000 g);Mannitol (10.000 g);Earth extract - M0541 (200.000 ml)
119450CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperature
2339positivegrowth28
38202positivegrowth30
67770positivegrowth25
119450positivegrowth25-30
119450nogrowth10
119450nogrowth37
119450nogrowth41
119450nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 97.3

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.1

halophily

@refsaltgrowthtested relationconcentration
119450NaClpositivegrowth0 %
119450NaClnogrowth2 %
119450NaClnogrowth4 %
119450NaClnogrowth6 %
119450NaClnogrowth8 %
119450NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11945016947citrate-carbon source
1194504853esculin+hydrolysis
119450606565hippurate-hydrolysis
11945017632nitrate-reduction
11945016301nitrite+reduction
6836925115malate+assimilation
6836927689decanoate-assimilation
6836917306maltose+assimilation
6836916899D-mannitol+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

  • @ref: 119450
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11945035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11945015688acetoin-
11945017234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
119450oxidase+
119450beta-galactosidase+3.2.1.23
119450alcohol dehydrogenase-1.1.1.1
119450gelatinase-
119450amylase-
119450DNase-
119450caseinase-3.4.21.50
119450catalase+1.11.1.6
119450tween esterase-
119450gamma-glutamyltransferase-2.3.2.2
119450lecithinase-
119450lipase-
119450lysine decarboxylase-4.1.1.18
119450ornithine decarboxylase-4.1.1.17
119450phenylalanine ammonia-lyase-4.3.1.24
119450tryptophan deaminase-
119450urease+3.5.1.5
68369urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119450-+++-+--+-++-+-++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2339----++-++/--+/-+-+---+--+
2339----++-++++++++/--++--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119450+++++-++++++++++++++-++++-+----+++--++--+--------+---------+--+--+----++-+-----+------+--+++-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2339soybean nodules
48991Soy bean,Glycine max,root noduleHonanChinaCHNAsia
67770Root nodule of soybeanHonanChinaCHNAsia
119450Plant, Glycine max, soybean root noduleHonanChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_273.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_84;97_88;98_232;99_273&stattab=map
  • Last taxonomy: Rhizobiaceae
  • 16S sequence: NR_036957
  • Sequence Identity:
  • Total samples: 9487
  • soil counts: 5353
  • aquatic counts: 1562
  • animal counts: 1094
  • plant counts: 1478

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
23391Risk group (German classification)
1194501Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sinorhizobium fredii gene for 16S rRNA, complete sequence, type strain: ATCC 35423D145161481nuccore380
20218Sinorhizobium fredii gene for 16S rRNA, strain: IAM 13625D127921438nuccore380
20218Sinorhizobium fredii strain LMG 6217 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequenceAF3452821060nuccore380
20218Sinorhizobium fredii partial 16S rRNA gene, strain LMG 6217X672311437nuccore380
20218Sinorhizobium fredii gene for 16S rRNA, partial sequence, strain: NBRC 14780AB6806611410nuccore380
20218Sinorhizobium fredii gene for 16S rRNA, partial sequence, strain: USDA 205AB4333531407nuccore380
20218Sinorhizobium fredii DNA, 16S-23S ribosomal RNA intergenic spacer region, clone: 205-A-2AB4333591081nuccore380
20218Sinorhizobium fredii DNA, 16S-23S ribosomal RNA intergenic spacer region, clone: 205-B-1AB4333601063nuccore380
20218Sinorhizobium fredii strain USDA 205 16S-23S ribosomal RNA intergenic spacer regionAF2844511142nuccore380
20218Sinorhizobium fredii strain USDA205 16S ribosomal RNA gene, partial sequenceAY2601491421nuccore380
20218Sinorhizobium fredii strain USDA205 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHQ143405821nuccore380
20218Rhizobium fredii 16S ribosomal RNA gene, partialM74163260nuccore380
2339Sinorhizobium fredii strain USDA 205 16S ribosomal RNA, partial sequenceNR_0369571437nuccore380
2339Ficus variegata Roding, 1798 isolate X6723 cytochrome c oxidase subunit I (COI) gene, partial cds; mitochondrialX6723616ena1030158

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sinorhizobium fredii strain NBRC 14780380.55wgspatric380
67770Sinorhizobium fredii NBRC 14780GCA_006539605contigncbi380

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.833no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.397no
125438spore-formingspore-formingAbility to form endo- or exosporesno86.273no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.063no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.417no
125438motile2+flagellatedAbility to perform flagellated movementyes72.305no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.1
125439BacteriaNetmotilityAbility to perform movementyes52.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.3

External links

@ref: 2339

culture collection no.: DSM 5851, ATCC 35423, LMG 6217, USDA 205, CCUG 27877, JCM 20967, HAMBI 2075, IAM 13625, ICMP 11139, IFO 14780, NBRC 14780, NCIMB 12104, NRRL B-14241, NRRL B-14594, OUT 30005, CIP 107333, ORS 669T

straininfo link

  • @ref: 82737
  • straininfo: 4760

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity8012042Production of cell-associated polysaccharides of Rhizobium fredii USDA205 is modulated by apigenin and host root extract.Reuhs BL, Kim JS, Badgett A, Carlson RWMol Plant Microbe Interact10.1094/mpmi-7-02401994Chamomile, Chromatography, Gas, Chromatography, Gel, Chromatography, Ion Exchange, Flavonoids/*pharmacology, Gene Expression Regulation, Bacterial, Genes, Bacterial, Magnetic Resonance Spectroscopy, Oils, Volatile/*pharmacology, Plant Extracts/*pharmacology, Plants, Medicinal, Polysaccharides, Bacterial/*biosynthesis/chemistry, Rhizobium/genetics/*metabolism, Symbiosis/geneticsBiotechnology
Genetics8501061Rhizobium fredii and Rhizobium meliloti produce 3-deoxy-D-manno-2-octulosonic acid-containing polysaccharides that are structurally analogous to group II K antigens (capsular polysaccharides) found in Escherichia coli.Reuhs BL, Carlson RW, Kim JSJ Bacteriol10.1128/jb.175.11.3570-3580.19931993*Antigens, Bacterial, Antigens, Surface/*chemistry, Bacterial Capsules/*chemistry, Carbohydrate Sequence, Chromatography, High Pressure Liquid, Disaccharides/chemistry, Escherichia coli/*chemistry, Galactose/analogs & derivatives, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Polysaccharides, Bacterial/*chemistry, Rhizobium/*chemistry, Sinorhizobium meliloti/chemistry, Species Specificity, Spectrometry, Mass, Fast Atom Bombardment, Sugar Acids/*analysisPhylogeny
Phylogeny12549015[A sinorhizobium fredll strain that effectively nodulate Medicago sativa].Zhang H, Zhang H, Li X, Yang SWei Sheng Wu Xue Bao2001Base Sequence, DNA, Bacterial/genetics, Medicago sativa/*microbiology, Nitrogen Fixation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sinorhizobium fredii/genetics/*growth & development/isolation & purification, Soybeans/microbiology, *SymbiosisTranscriptome
16347190Growth of fast- and slow-growing rhizobia on ethanol.Sadowsky MJ, Bohlool BBAppl Environ Microbiol10.1128/aem.52.4.951-953.19861986
16347404Serological Relatedness of Rhizobium fredii to Other Rhizobia and to the Bradyrhizobia.Sadowsky MJ, Bohlool BB, Keyser HHAppl Environ Microbiol10.1128/aem.53.8.1785-1789.19871987
27303417RNA-Seq Analysis of Differential Gene Expression Responding to Different Rhizobium Strains in Soybean (Glycine max) Roots.Yuan S, Li R, Chen S, Chen H, Zhang C, Chen L, Hao Q, Shan Z, Yang Z, Qiu D, Zhang X, Zhou XFront Plant Sci10.3389/fpls.2016.007212016
Phylogeny28771124Notoacmeibacter marinus gen. nov., sp. nov., isolated from the gut of a limpet and proposal of Notoacmeibacteraceae fam. nov. in the order Rhizobiales of the class Alphaproteobacteria.Huang Z, Guo F, Lai Q, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0019512017Alphaproteobacteria/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Chin, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastropoda/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
28936222The Soybean Rfg1 Gene Restricts Nodulation by Sinorhizobium fredii USDA193.Fan Y, Liu J, Lyu S, Wang Q, Yang S, Zhu HFront Plant Sci10.3389/fpls.2017.015482017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2339Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5851)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5851
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
38202Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4757
48991Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27877)https://www.ccug.se/strain?id=27877
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/
68369Automatically annotated from API 20NE
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
82737Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4760.1StrainInfo: A central database for resolving microbial strain identifiers
119450Curators of the CIPCollection of Institut Pasteur (CIP 107333)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107333
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1