Strain identifier

BacDive ID: 14230

Type strain: Yes

Species: Sphingomonas melonis

Strain Designation: EY 4350

Strain history: CIP <- 2003, R. Buonaurio, Perugia, Italy: strain DAPP-PG 224

NCBI tax ID(s): 1090320 (strain), 152682 (species)

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General

@ref: 5357

BacDive-ID: 14230

DSM-Number: 14444

keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, rod-shaped, plant pathogen

description: Sphingomonas melonis EY 4350 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from fruits of yellow spanish melons .

NCBI tax id

NCBI tax idMatching level
1090320strain
152682species

strain history

@refhistory
5357<- R. Buonaurio; DAPP-PG 224
120888CIP <- 2003, R. Buonaurio, Perugia, Italy: strain DAPP-PG 224

doi: 10.13145/bacdive14230.20230509.8.1

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 melonis
  • full scientific name: Sphingomonas melonis Buonaurio et al. 2002

@ref: 5357

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas melonis

full scientific name: Sphingomonas melonis Buonaurio et al. 2002

strain designation: EY 4350

type strain: yes

Morphology

cell morphology

  • @ref: 120888
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 120888
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5357NUTRIENT 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
39769MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120888CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5357positivegrowth28mesophilic
39769positivegrowth30mesophilic
120888positivegrowth30mesophilic
120888nogrowth5psychrophilic
120888nogrowth10psychrophilic
120888nogrowth25mesophilic
120888nogrowth37mesophilic
120888nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120888
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120888NaClpositivegrowth0 %
120888NaClnogrowth2 %
120888NaClnogrowth4 %
120888NaClnogrowth6 %
120888NaClnogrowth8 %
120888NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-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
12088816947citrate-carbon source
1208884853esculin+hydrolysis
12088817632nitrate-reduction
12088816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12088835581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120888oxidase-
120888beta-galactosidase+3.2.1.23
120888alcohol dehydrogenase-1.1.1.1
120888gelatinase-
120888amylase-
120888DNase-
120888caseinase-3.4.21.50
120888catalase+1.11.1.6
120888tween esterase-
120888lecithinase-
120888lipase-
120888lysine decarboxylase-4.1.1.18
120888ornithine decarboxylase-4.1.1.17
120888protease-
120888tryptophan deaminase-
120888urease-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
120888-+++-++-+-++---+++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5357-----+-++++-++++-+-++
5357-----+-++++-++---+-++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120888+++++--+-++-------+--+---------------------------+---------+-------------------++--------+++-+-----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
5357fruits of yellow spanish melons (Cucumis melo var. inodorus)Cucumis melo var. inodorusAlmeriaSpainESPEurope
120888Yellow Spanish melon fruitsSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_548.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_388;98_445;99_548&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AB055863
  • Sequence Identity:
  • Total samples: 2932
  • soil counts: 447
  • aquatic counts: 1091
  • animal counts: 1087
  • plant counts: 307

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
5357yes1Risk group (German classification)
1208881Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Sphingomonas melonis gene for 16S rRNA, partial sequence
  • accession: AB055863
  • length: 1439
  • database: ena
  • NCBI tax ID: 152682

GC content

  • @ref: 5357
  • GC-content: 65

External links

@ref: 5357

culture collection no.: DSM 14444, LMG 19484, DAPP-PG 224, CIP 107880

straininfo link

  • @ref: 83389
  • straininfo: 13322

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508872Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits.Buonaurio R, Stravato VM, Kosako Y, Fujiwara N, Naka T, Kobayashi K, Cappelli C, Yabuuchi EInt J Syst Evol Microbiol10.1099/00207713-52-6-20812002Cucumis melo/microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fruit/microbiology, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sphingomonas/*classification/genetics/*pathogenicity, Terminology as TopicGenetics
Phylogeny16280528Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni sp. nov.Busse HJ, Hauser E, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.63872-02005DNA, Bacterial/analysis/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Species Specificity, Sphingomonas/*classification/genetics/isolation & purification/metabolismGenetics
Phylogeny17590230Sphingomonas astaxanthinifaciens sp. nov., a novel astaxanthin-producing bacterium of the family Sphingomonadaceae isolated from Misasa, Tottori, Japan.Asker D, Beppu T, Ueda KFEMS Microbiol Lett10.1111/j.1574-6968.2007.00760.x2007Carotenoids/chemistry/classification, Fresh Water/*microbiology, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/chemistry/classification, Sequence Analysis, DNA, Sphingomonas/*classification/isolation & purification/metabolism, Xanthophylls/biosynthesisGenetics
Phylogeny17625171Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan.Asker D, Beppu T, Ueda KInt J Syst Evol Microbiol10.1099/ijs.0.64828-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, Carotenoids/*biosynthesis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Gamma Rays, Genes, rRNA, Glycolipids/analysis, Japan, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sphingomonas/chemistry/*classification/genetics/*isolation & purification, Ubiquinone/analysisGenetics
Phylogeny20511462Sphingomonas rubra sp. nov., isolated from bioreactor wastewater.Huo YY, Xu XW, Liu SP, Cui HL, Li X, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.020958-02010Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, Sphingomonas/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny23687058Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field.Son HM, Yang JE, Park Y, Han CK, Kim SG, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.051649-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Panax/*microbiology, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/analysis, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analysisGenetics
Phylogeny36477930Sphingomonas liriopis sp. nov., Sphingomonas donggukensis sp. nov., and Sphingomonas tagetis sp. nov., isolated from Liriope platyphylla fruit, soil, and Tagetes patula roots.Kim I, Chhetri G, So Y, Jung Y, Park S, Seo TArch Microbiol10.1007/s00203-022-03360-42022*Tagetes, Soil, *Sphingomonas/genetics, Fruit, RNA, Ribosomal, 16S/genetics, Phylogeny, DNA

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5357Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14444)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14444
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
39769Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5440
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
83389Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13322.1StrainInfo: A central database for resolving microbial strain identifiers
120888Curators of the CIPCollection of Institut Pasteur (CIP 107880)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107880