Strain identifier

BacDive ID: 14246

Type strain: Yes

Species: Sphingomonas azotifigens

Strain Designation: Y-39

Strain history: CIP <- 2006, IAM

NCBI tax ID(s): 1219041 (strain), 330920 (species)

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General

@ref: 7581

BacDive-ID: 14246

DSM-Number: 18530

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

description: Sphingomonas azotifigens Y-39 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from root of rice plant.

NCBI tax id

NCBI tax idMatching level
1219041strain
330920species

strain history

@refhistory
7581<- A. Yokota; IAM 15283 <- Y. Oyaizu-Masuchi and K. Komagata
374812006, IAM
67770IAM 15283 <-- A. Yokota Y-39.
116689CIP <- 2006, IAM

doi: 10.13145/bacdive14246.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas azotifigens
  • full scientific name: Sphingomonas azotifigens Xie and Yokota 2006

@ref: 7581

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas azotifigens

full scientific name: Sphingomonas azotifigens Xie and Yokota 2006

strain designation: Y-39

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31688negative01-03 µm0.5-1 µmrod-shapedyes
116689negativerod-shapedyes

colony morphology

  • @ref: 116689

pigmentation

  • @ref: 31688
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7581NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
7581R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
37481MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116689CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7581positivegrowth30mesophilic
31688positivegrowth25-40
31688positiveoptimum25-37mesophilic
37481positivegrowth30mesophilic
67770positivegrowth27mesophilic
7581positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31688aerobe
116689microaerophile

spore formation

  • @ref: 31688
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31688NaClpositivegrowth0-2 %
31688NaClpositiveoptimum0-2 %

observation

@refobservation
31688aggregates in chains
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3168830089acetate+carbon source
3168822599arabinose+carbon source
3168835391aspartate+carbon source
3168817057cellobiose+carbon source
3168828757fructose+carbon source
3168828260galactose+carbon source
3168817234glucose+carbon source
3168817716lactose+carbon source
3168825115malate+carbon source
3168817306maltose+carbon source
3168816634raffinose+carbon source
3168830031succinate+carbon source
3168817992sucrose+carbon source
3168827082trehalose+carbon source
3168818222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose+builds acid from
6837116443D-tagatose-builds acid from
6837132528turanose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
683714853esculin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11668917632nitrate-reduction
11668916301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11668935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
31688acid phosphatase+3.1.3.2
31688alkaline phosphatase+3.1.3.1
31688catalase+1.11.1.6
31688cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
116689oxidase-
116689alcohol dehydrogenase-1.1.1.1
116689catalase+1.11.1.6
116689lysine decarboxylase-4.1.1.18
116689ornithine decarboxylase-4.1.1.17
116689urease-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
116689-+++-++++-++-+++++++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7581-----+-++++-++/----+--+
7581-----+-+++/-+-++---+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116689---+-+---++++---------++/-++/-++++/-++-+/-----+/-++/--+------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7581root of rice plantMishimaJapanJPNAsia
67770Rice plantJapanJPNAsia
116689Environment, Paddy soil and the roots of Oryza sativaJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2321.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_515;98_592;99_2321&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AB217471
  • Sequence Identity:
  • Total samples: 108
  • soil counts: 18
  • aquatic counts: 50
  • animal counts: 14
  • plant counts: 26

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75811Risk group (German classification)
1166891Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas azotifigens gene for 16S rRNA, partial sequence, strain: NBRC 15497AB6808811414ena330920
7581Sphingomonas azotifigens gene for 16S rRNA, partial sequence, strain: NBRC 15497AB2174711422ena330920

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas azotifigens NBRC 15497 strain NBRC 154971219041.3wgspatric1219041
67770Sphingomonas azotifigens NBRC 15497GCA_002091475contigncbi1219041

GC content

@refGC-contentmethod
3168868
6777068high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes66.077yes
gram-positiveno96.977yes
anaerobicno99.097yes
halophileno95.415no
spore-formingno92.862yes
thermophileno97.096no
glucose-utilyes91.313no
flagellatedno90.853no
aerobicyes90.959no
glucose-fermentno91.861yes

External links

@ref: 7581

culture collection no.: DSM 18530, CCTCC AB 205007, IAM 15283, NBRC 15497, JCM 21734, IFO 15497, CIP 109209

straininfo link

  • @ref: 83405
  • straininfo: 62895

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16585711Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa.Xie CH, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64056-02006Bacterial Proteins/genetics, DNA, Ribosomal/analysis, Molecular Sequence Data, Nitrogen/*metabolism, *Nitrogen Fixation, Oryza/microbiology, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/genetics/*isolation & purificationGenetics
Phylogeny17267979Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.64441-02007Aerobiosis, Animals, *Antibiosis, Arcidae/*microbiology, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Glycosphingolipids/analysis/chemistry, Gram-Positive Bacteria/drug effects, Japan, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sphingomonas/*classification/cytology/*isolation & purification/physiologyGenetics
Phylogeny19329595Sphingomonas sanxanigenens sp. nov., isolated from soil.Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RLInt J Syst Evol Microbiol10.1099/ijs.0.000257-02009Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Sphingomonas/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny19406815Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica.Romanenko LA, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.003285-02009Animals, Anomura/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny24425812Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively.Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.055269-02013*Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny30808585Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis.Menon RR, Kumari S, Kumar P, Verma A, Krishnamurthi S, Rameshkumar NSyst Appl Microbiol10.1016/j.syapm.2019.02.0032019DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial/genetics, Genome, Bacterial/*genetics, Lipids/analysis, Nucleic Acid Hybridization, Oryza/*microbiology/physiology, *Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Salt Tolerance, Sequence Analysis, DNA, Soil Microbiology, Sphingomonas/chemistry/*classification/*geneticsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7581Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18530)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18530
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
31688Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127965
37481Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6925
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
83405Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID62895.1StrainInfo: A central database for resolving microbial strain identifiers
116689Curators of the CIPCollection of Institut Pasteur (CIP 109209)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109209