Strain identifier

BacDive ID: 13627

Type strain: Yes

Species: Rhizobium hainanense

Strain Designation: I66

Strain history: CIP <- 1998, W.X. Chen, China Agric. Univ., Beijing, China: strain I66

NCBI tax ID(s): 52131 (species)

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General

@ref: 4538

BacDive-ID: 13627

DSM-Number: 11917

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Rhizobium hainanense I66 is a mesophilic, motile bacterium that was isolated from root nodules of Desmodium sinuatum.

NCBI tax id

  • NCBI tax id: 52131
  • Matching level: species

strain history

@refhistory
4538<- G. Cheng, CCBAU; strain I66
401551998, W. Chen, Beijing, China: strain I66
119786CIP <- 1998, W.X. Chen, China Agric. Univ., Beijing, China: strain I66

doi: 10.13145/bacdive13627.20230509.8.1

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 hainanense
  • full scientific name: Rhizobium hainanense Chen et al. 1997

@ref: 4538

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium hainanense

full scientific name: Rhizobium hainanense Chen et al. 1997

strain designation: I66

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.71
6948099.989negative
119786yesnegativerod-shaped

colony morphology

  • @ref: 119786

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4538RHIZOBIUM 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
40155MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119786CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4538positivegrowth30mesophilic
40155positivegrowth30mesophilic
119786positivegrowth25-30mesophilic
119786nogrowth10psychrophilic
119786nogrowth37mesophilic
119786nogrowth41thermophilic
119786nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
119786NaClpositivegrowth0 %
119786NaClnogrowth2 %
119786NaClnogrowth4 %
119786NaClnogrowth6 %
119786NaClnogrowth8 %
119786NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose+builds acid from28847
68371D-lyxose+builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
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
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371erythritol+builds acid from17113
68371glycerol+builds acid from17754
119786citrate+carbon source16947
119786esculin+hydrolysis4853
119786hippurate-hydrolysis606565
119786nitrate+reduction17632
119786nitrite-reduction16301
119786nitrate-respiration17632

antibiotic resistance

  • @ref: 119786
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119786
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11978615688acetoin+
11978617234glucose-

enzymes

@refvalueactivityec
119786oxidase+
119786beta-galactosidase+3.2.1.23
119786alcohol dehydrogenase-1.1.1.1
119786gelatinase-
119786amylase-
119786DNase-
119786caseinase-3.4.21.50
119786catalase-1.11.1.6
119786tween esterase-
119786gamma-glutamyltransferase+2.3.2.2
119786lecithinase-
119786lipase-
119786lysine decarboxylase-4.1.1.18
119786ornithine decarboxylase-4.1.1.17
119786phenylalanine ammonia-lyase-4.3.1.24
119786protease-
119786tryptophan deaminase-
119786urease+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
119786-++--+--+-++-+-+++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119786+++/-+++--+/-+/-+/-+/-+/--+------+-++++++-++------++++/-++-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119786+++-+--+++++++++++-++++++-+-++++++++++-++--++---++------+--++-+++-----++---+---++-----+--++--+++--+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
4538root nodules of Desmodium sinuatumDesmodium sinuatumHainan provinceChinaCHNAsia
119786Nodules of D. SinuatumChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1577.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_62;97_65;98_1244;99_1577&stattab=map
  • Last taxonomy: Rhizobiaceae
  • 16S sequence: U71078
  • Sequence Identity:
  • Total samples: 5839
  • soil counts: 3171
  • aquatic counts: 403
  • animal counts: 1252
  • plant counts: 1013

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
45381Risk group (German classification)
1197861Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhizobium hainanensis strain I66 16S-23S ribosomal RNA intergenic spacer regionAF3218721062ena52131
20218Rhizobium hainanense strain I66 16S ribosomal RNA gene, partial sequenceU710781370ena52131
20218Rhizobium hainanense strain USDA 3588 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequenceAF3452691065ena52131

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhizobium hainanense CCBAU 57015GCA_900094555scaffoldncbi52131
66792Rhizobium hainanense strain CCBAU 5701552131.3wgspatric52131
66792Rhizobium hainanense CCBAU 570152615840609draftimg52131

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.213no
flagellatedno78.334no
gram-positiveno98.09no
anaerobicno98.328no
aerobicyes92.355no
halophileno92.297no
spore-formingno93.617no
glucose-fermentno87.217no
thermophileno99.23yes
glucose-utilyes92.243no

External links

@ref: 4538

culture collection no.: DSM 11917, CCBAU 57015, CIP 105503

straininfo link

  • @ref: 82813
  • straininfo: 18651

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9226920Rhizobium hainanense sp. nov., isolated from tropical legumes.Chen WX, Tan ZY, Gao JL, Li Y, Wang ETInt J Syst Bacteriol10.1099/00207713-47-3-8701997China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fabaceae/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, *Plants, Medicinal, Rhizobium/*classification/genetics/*isolation & purification, RickettsiaceaeGenetics
Phylogeny32804605Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species).Ouyabe M, Tanaka N, Shiwa Y, Fujita N, Kikuno H, Babil P, Shiwachi HInt J Syst Evol Microbiol10.1099/ijsem.0.0043812020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dioscorea/*microbiology, Endophytes, Fatty Acids/chemistry, Japan, Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/isolation & purification, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4538Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11917)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11917
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
40155Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17529
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)
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
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
82813Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID18651.1StrainInfo: A central database for resolving microbial strain identifiers
119786Curators of the CIPCollection of Institut Pasteur (CIP 105503)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105503