Strain identifier

BacDive ID: 13546

Type strain: Yes

Species: Ensifer meliloti

Strain Designation: 3D0a2

Strain history: CIP <- 2002, P. De Lajudie, Montpellier, France: strain ORS 665T <- LMG <- 1984, B. Jarvis, Rhizobium meliloti

NCBI tax ID(s): 382 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9156

BacDive-ID: 13546

DSM-Number: 30135

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

description: Ensifer meliloti 3D0a2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Medicago sativa.

NCBI tax id

  • NCBI tax id: 382
  • Matching level: species

strain history

@refhistory
9156<- ATCC <- N.R. Smith, 3D0a2
67770IAM 12611 <-- ATCC 9930 <-- N. R. Smith 3DOa2.
120885CIP <- 2002, P. De Lajudie, Montpellier, France: strain ORS 665T <- LMG <- 1984, B. Jarvis, Rhizobium meliloti

doi: 10.13145/bacdive13546.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Ensifer
  • species: Ensifer meliloti
  • full scientific name: Ensifer meliloti (Dangeard 1926) Young 2003
  • synonyms

    @refsynonym
    20215Rhizobium meliloti
    20215Sinorhizobium meliloti

@ref: 9156

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Ensifer

species: Ensifer meliloti

full scientific name: Ensifer meliloti (Dangeard 1926) Young 2003

strain designation: 3D0a2

type strain: yes

Morphology

cell morphology

  • @ref: 120885
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refincubation period
91561-2 days
120885

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9156RHIZOBIUM 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
33771MEDIUM 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)
120885CIP Medium 296yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=296

culture temp

@refgrowthtypetemperaturerange
9156positivegrowth26mesophilic
33771positivegrowth30mesophilic
48992positivegrowth30mesophilic
67770positivegrowth25mesophilic
120885positivegrowth25-37mesophilic
120885nogrowth10psychrophilic
120885nogrowth41thermophilic
120885nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 48992
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
120885NaClpositivegrowth0-4 %
120885NaClnogrowth6 %
120885NaClnogrowth8 %
120885NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371D-fucose+builds acid from28847
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371inulin-builds acid from15443
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371methyl beta-D-xylopyranoside+builds acid from74863
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannose+assimilation16024
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin-hydrolysis5291
68369urea+hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
120885citrate-carbon source16947
120885esculin-hydrolysis4853
120885hippurate-hydrolysis606565
120885nitrate+reduction17632
120885nitrite-reduction16301
120885nitrate+respiration17632

antibiotic resistance

  • @ref: 120885
  • 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
12088535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12088515688acetoin-
12088517234glucose-

enzymes

@refvalueactivityec
9156catalase+1.11.1.6
9156cytochrome-c oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
120885oxidase+
120885beta-galactosidase+3.2.1.23
120885alcohol dehydrogenase-1.1.1.1
120885gelatinase-
120885amylase-
120885DNase-
120885caseinase-3.4.21.50
120885catalase+1.11.1.6
120885tween esterase-
120885gamma-glutamyltransferase+2.3.2.2
120885lecithinase-
120885lipase-
120885lysine decarboxylase-4.1.1.18
120885ornithine decarboxylase-4.1.1.17
120885phenylalanine ammonia-lyase-4.3.1.24
120885tryptophan deaminase-
120885urease+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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    48992C16:0816
    48992C17:01.617
    48992C18:01.918
    48992C14:0 3OH/C16:1 ISO I13.715.485
    48992C15:0 ISO 3OH1.316.135
    48992C16:1 ω7c0.915.819
    48992C17:0 CYCLO1.216.888
    48992C18:1 ω7c /12t/9t5117.824
    48992C18:2 ω6,9c/C18:0 ANTE1.217.724
    48992C19:0 CYCLO ω8c15.318.9
    48992Unidentified1.318.091
    48992Unidentified2.718.135
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120885-++--++-+-+----+++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
9156+---++-+++++/-++---+--+
9156+/----++/--+++++/-++---+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120885+/-+/-+/-+++/-+/-+/-++/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+---++/-+/-+/-+/-+/-+/-+/--+/-+/---+/-+/-+/-+/-+/-++/-+/-+/----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120885--++----+-------+-+--++---++-+++++++++-++--------+-------+++--+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
48992Medicago sativaNew ZealandNZLAustralia and Oceania
120885Medicago sativaUnited States of AmericaUSANorth AmericaVirginia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_106.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_84;97_88;98_97;99_106&stattab=map
  • Last taxonomy: Sinorhizobium
  • 16S sequence: X67222
  • Sequence Identity:
  • Total samples: 10577
  • soil counts: 5488
  • aquatic counts: 1757
  • animal counts: 1189
  • plant counts: 2143

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
91561Risk group (German classification)
1208851Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhizobium meliloti 16S ribosomal RNA, partialM55241260ena382
9156Sinorhizobium meliloti strain LMTR32 16S ribosomal RNA gene, partial sequenceAY1969631479ena382
67770Sinorhizobium meliloti gene for 16S rRNA, partial sequence, strain: NBRC 14782AB6806621410ena382
67770Sinorhizobium meliloti gene for 16S rRNA, strain: IAM 12611D127831421ena382
67770Sinorhizobium meliloti gene for 16S rRNA, complete sequence, type strain: IAM 12611D145091480ena382
67770Sinorhizobium meliloti partial 16S rRNA gene, strain LMG 6133X672221437ena382

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sinorhizobium meliloti strain NBRC 14782382.1072wgspatric382
67770Sinorhizobium meliloti NBRC 14782GCA_006539625contigncbi382

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.936no
anaerobicno98.352yes
halophileno91.469no
spore-formingno94.341no
glucose-utilyes92.081yes
aerobicyes93.519no
motileyes90.331no
flagellatedno74.298no
thermophileno99.451no
glucose-fermentno91.05yes

External links

@ref: 9156

culture collection no.: DSM 30135, ATCC 9930, CCUG 27879, LMG 6133, JCM 20682, CFBP 5561, HAMBI 2148, IAM 12611, ICMP 12623, IFO 14782, NBRC 14782, NCAIM B.01520, NRRL L-45, NZP 4027, OUT 30010, USDA 1002, CIP 107332, ORS 665T

straininfo link

  • @ref: 82735
  • straininfo: 92703

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1377901Phylogenetic position of Rhizobium sp. strain Or 191, a symbiont of both Medicago sativa and Phaseolus vulgaris, based on partial sequences of the 16S rRNA and nifH genes.Eardly BD, Young JP, Selander RKAppl Environ Microbiol10.1128/aem.58.6.1809-1815.19921992Base Sequence, DNA, Bacterial/genetics, Fabaceae/microbiology, Genes, Bacterial, Hydrogen-Ion Concentration, Medicago sativa/microbiology, Microscopy, Electron, Molecular Sequence Data, Nitrogen Fixation/*genetics, Phylogeny, Plants, Medicinal, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/*genetics, Rhizobium/classification/*genetics/ultrastructure, Sequence Homology, Nucleic Acid, Symbiosis, TemperatureGenetics
Enzymology8416894Detection of a nitrous oxide reductase structural gene in Rhizobium meliloti strains and its location on the nod megaplasmid of JJ1c10 and SU47.Chan YK, Wheatcroft RJ Bacteriol10.1128/jb.175.1.19-26.19931993Blotting, Southern, Genes, Bacterial/*genetics, Genetic Variation, Nitrous Oxide/metabolism, Nucleic Acid Hybridization, Oxidoreductases/*genetics, Plasmids/*genetics, Restriction Mapping, Rhizobiaceae/genetics, Sequence Homology, Nucleic Acid, Sinorhizobium meliloti/enzymology/*geneticsPhylogeny
Phylogeny16110948[A Sinorhizoboium meliloti strain that can nodulate soybean plants].Lin RS, Du BH, Li XH, Wang L, Yang SSWei Sheng Wu Xue Bao2004Medicago sativa/microbiology, Nitrogen Fixation, Plant Roots/microbiology, Sinorhizobium meliloti/classification/*physiology, Soybeans/*microbiology, *Symbiosis
Genetics16269751Novel DNA sequences from natural strains of the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti.Guo H, Sun S, Finan TM, Xu JAppl Environ Microbiol10.1128/AEM.71.11.7130-7138.20052005*Base Sequence, DNA, Bacterial/genetics, Gene Library, *Genome, Bacterial, Genotype, *Nitrogen Fixation, Phylogeny, Sinorhizobium meliloti/*classification/genetics, *SymbiosisPhylogeny
Phylogeny16413160Nitrogen-fixing sinorhizobia with Medicago laciniata constitute a novel biovar (bv. medicaginis) of S. meliloti.Villegas Mdel C, Rome S, Maure L, Domergue O, Gardan L, Bailly X, Cleyet-Marel JC, Brunel BSyst Appl Microbiol10.1016/j.syapm.2005.12.0082006Acyltransferases/chemistry/genetics, Bacterial Proteins/chemistry/genetics, Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal Spacer/chemistry/genetics, France, Genetic Variation, Medicago/*microbiology, Molecular Sequence Data, Nitrogen Fixation/*physiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/chemistry/genetics, Root Nodules, Plant/microbiology, Sequence Analysis, DNA, Sinorhizobium meliloti/*classification/genetics/isolation & purification/metabolism, Symbiosis/physiology, TunisiaGenetics
Metabolism16788172Flavin adenine dinucleotide-dependent 4-phospho-D-erythronate dehydrogenase is responsible for the 4-phosphohydroxy-L-threonine pathway in vitamin B6 biosynthesis in Sinorhizobium meliloti.Tazoe M, Ichikawa K, Hoshino TJ Bacteriol10.1128/JB.01999-052006Acetaldehyde/analogs & derivatives/analysis/metabolism, Amino Acid Sequence, Bacterial Proteins/genetics, Flavin-Adenine Dinucleotide/*metabolism, *Genes, Bacterial, Isomerases/metabolism, Molecular Sequence Data, Open Reading Frames/genetics, Organophosphates/metabolism, Oxidation-Reduction, Oxidoreductases/genetics/metabolism/*physiology, Phosphotransferases/metabolism, Sequence Alignment, Sinorhizobium meliloti/*metabolism, Threonine/analogs & derivatives/metabolism, Transketolase/metabolism, Vitamin B 6/*biosynthesisEnzymology
Enzymology18256491Cloning of the pyridoxine 5'-phosphate phosphatase gene (pdxP) and vitamin B6 production in pdxP recombinant Sinorhizobium meliloti.Nagahashi Y, Tazoe M, Hoshino TBiosci Biotechnol Biochem10.1271/bbb.705392008Amino Acid Sequence, Animals, Base Sequence, Cloning, Molecular, DNA Primers, Electrophoresis, Polyacrylamide Gel, Mice, Molecular Sequence Data, Open Reading Frames, Phosphoprotein Phosphatases/chemistry/genetics/*metabolism, Recombinant Proteins/chemistry/genetics/metabolism, Sequence Homology, Amino Acid, Sinorhizobium meliloti/*genetics, Vitamin B 6/*biosynthesisGenetics
Phylogeny23898997Ensifer meliloti is the preferred symbiont of Medicago arborea in eastern Morocco soils.Guerrouj K, Perez-Valera E, Abdelmoumen H, Bedmar EJ, Missbah El Idrissi MCan J Microbiol10.1139/cjm-2013-02682013Bacterial Proteins/genetics, Genetic Variation, Medicago/*microbiology, Morocco, N-Acetylglucosaminyltransferases/genetics, Phenotype, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sinorhizobium meliloti/genetics/*physiology, *Soil Microbiology, *SymbiosisPhenotype
Phylogeny29750490[Isolation and phylogenetic analysis of major capsid gene (g23) of bacteriophages infecting Sinorhizobium meliloti].Yu H, Liu J, Fan G, Wang GWei Sheng Wu Xue Bao2017Bacteriophage T4/classification/*isolation & purification/*metabolism, Capsid Proteins/*genetics/metabolism, Genome, Viral, Myoviridae/classification/genetics/*isolation & purification/*metabolism, *Phylogeny, Sinorhizobium meliloti/*virologyMetabolism
31418203[Biological characteristics of bacteriophages infecting three typic rhizobia of legume].Liu JJ, Liu ZX, Yu H, Yao Q, Yu ZH, Wang GHYing Yong Sheng Tai Xue Bao10.13287/j.1001-9332.201908.0292019*Bacteriophages, *Bradyrhizobium, Fabaceae/*microbiology/virology, Nitrogen Fixation, Rhizobium/*virology
33255180Exogenous ACC Deaminase Is Key to Improving the Performance of Pasture Legume-Rhizobial Symbioses in the Presence of a High Manganese Concentration.Paco A, da-Silva JR, Torres DP, Glick BR, Brigido CPlants (Basel)10.3390/plants91216302020
33820122A Rhizobium strain that nodulates and fixes nitrogen in association with alfalfa and soybean plants.Gao WM, Yang SSMicrobiology (Reading)10.1099/13500872-141-8-19571995

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9156Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30135)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30135
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
33771Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4756
48992Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27879)https://www.ccug.se/strain?id=27879
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
68371Automatically annotated from API 50CH acid
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
82735Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92703.1StrainInfo: A central database for resolving microbial strain identifiers
120885Curators of the CIPCollection of Institut Pasteur (CIP 107332)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107332