Strain identifier

BacDive ID: 14241

Type strain: Yes

Species: Sphingomonas phyllosphaerae

Strain Designation: FA2

Strain history: CIP <- 2005, CECT <- 2003, E. Velasquez, Salamanca Univ., Salamanca, Spain: strain FA2

NCBI tax ID(s): 257003 (species)

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General

@ref: 6859

BacDive-ID: 14241

DSM-Number: 17258

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

description: Sphingomonas phyllosphaerae FA2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from phyllosphere of Acacia caven.

NCBI tax id

  • NCBI tax id: 257003
  • Matching level: species

strain history

@refhistory
6859<- E. Velázquez, Univers. Salamanca <-A. Abril, Córdoba, Argentinia
121816CIP <- 2005, CECT <- 2003, E. Velasquez, Salamanca Univ., Salamanca, Spain: strain FA2

doi: 10.13145/bacdive14241.20230509.8.1

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 phyllosphaerae
  • full scientific name: Sphingomonas phyllosphaerae Rivas et al. 2004

@ref: 6859

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas phyllosphaerae

full scientific name: Sphingomonas phyllosphaerae Rivas et al. 2004

strain designation: FA2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31233negative1.7 µm0.7 µmrod-shapedyes
121816negativerod-shapedyes

pigmentation

  • @ref: 31233
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6859NUTRIENT 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
39770MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121816CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
6859positivegrowth28mesophilic
39770positivegrowth25mesophilic
121816positivegrowth10-37
121816nogrowth5psychrophilic
121816nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31233aerobe
121816obligate aerobe

spore formation

  • @ref: 31233
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
121816NaClpositivegrowth0-2 %
121816NaClnogrowth4 %
121816NaClnogrowth6 %
121816NaClnogrowth8 %
121816NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3123317128adipate+carbon source
3123322599arabinose+carbon source
3123317057cellobiose+carbon source
3123328757fructose+carbon source
3123333984fucose+carbon source
3123328260galactose+carbon source
3123317716lactose+carbon source
3123325115malate+carbon source
3123328053melibiose+carbon source
31233506227N-acetylglucosamine+carbon source
3123316634raffinose+carbon source
3123317992sucrose+carbon source
3123327082trehalose+carbon source
3123318222xylose+carbon source
312334853esculin+hydrolysis
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
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-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
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
1218164853esculin+hydrolysis
12181617632nitrate-reduction
12181616301nitrite-reduction
12181617632nitrate-respiration

antibiotic resistance

  • @ref: 121816
  • 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
12181635581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31233catalase+1.11.1.6
31233cytochrome 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
121816oxidase-
121816beta-galactosidase+3.2.1.23
121816alcohol dehydrogenase-1.1.1.1
121816gelatinase+
121816amylase-
121816DNase-
121816caseinase-3.4.21.50
121816catalase+1.11.1.6
121816tween esterase-
121816lecithinase-
121816lipase-
121816lysine decarboxylase-4.1.1.18
121816ornithine decarboxylase-4.1.1.17
121816protease-
121816tryptophan deaminase-
121816urease-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
121816-+++-+++--+++++++++-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6859-----+-++++-++---++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121816---+/--+/----+/-+/-+/-+/--+/-------+/---+/---+/-+/--+/------------+/-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121816+++++-++++++++-++++-++++++--------++-----+-------+---++----+-------------------++----+---+++-+----+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
6859phyllosphere of Acacia cavenAcacia cavenArgentinaARGMiddle and South America
121816Environment, Phyllosphere, acacia cavenArgentinaARGMiddle and South AmericaCentral part

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1314.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_761;97_887;98_1039;99_1314&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AY453855
  • Sequence Identity:
  • Total samples: 877
  • soil counts: 153
  • aquatic counts: 128
  • animal counts: 324
  • plant counts: 272

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68591Risk group (German classification)
1218161Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6859
  • description: Sphingomonas phyllosphaerae 16S ribosomal RNA gene, complete sequence
  • accession: AY453855
  • length: 1481
  • database: ena
  • NCBI tax ID: 257003

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas phyllosphaerae FA2GCA_000427645scaffoldncbi1090319
66792Sphingomonas phyllosphaerae FA21090319.3wgspatric1090319
66792Sphingomonas phyllosphaerae FA22516493027draftimg1090319

GC content

  • @ref: 6859
  • GC-content: 61

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes70.365no
flagellatedno89.668no
gram-positiveno97.292yes
anaerobicno99.421yes
aerobicyes95.09no
halophileno95.672no
spore-formingno95.257no
glucose-utilyes91.425yes
thermophileno97.371yes
glucose-fermentno90.458yes

External links

@ref: 6859

culture collection no.: DSM 17258, CECT 5832, LMG 21958, CIP 108674

straininfo link

  • @ref: 83400
  • straininfo: 99921

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545449
  • title: Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina.
  • authors: Rivas R, Abril A, Trujillo ME, Velazquez E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63102-0
  • year: 2004
  • mesh: Acacia/*microbiology, Aerobiosis, Argentina, Bacterial Typing Techniques, Base Composition, Catalase/analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Esculin/metabolism, Fatty Acids/analysis/isolation & purification, Gelatin/metabolism, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phenazines, Phospholipids/analysis/isolation & purification, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Sphingomonas/*classification/cytology/*isolation & purification/physiology, Urea/metabolism, beta-Galactosidase/analysis
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6859Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17258)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17258
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
31233Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2755828776041
39770Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6329
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)
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
83400Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99921.1StrainInfo: A central database for resolving microbial strain identifiers
121816Curators of the CIPCollection of Institut Pasteur (CIP 108674)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108674