Strain identifier

BacDive ID: 17560

Type strain: Yes

Species: Stenotrophomonas rhizophila

Strain Designation: e-p10, p69

Strain history: CIP <- 2003, G. Berg, Rostock Univ., Rostock, Germany: strain e-p10

NCBI tax ID(s): 216778 (species)

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General

@ref: 5341

BacDive-ID: 17560

DSM-Number: 14405

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

description: Stenotrophomonas rhizophila e-p10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of oilseed rape .

NCBI tax id

  • NCBI tax id: 216778
  • Matching level: species

strain history

@refhistory
5341<- G. Berg, Univ. Rostock; e-p10 <- P. Marten, Univ. Rostock
67770DSM 14405 <-- G. Berg e-p10 <-- P. Marten.
122204CIP <- 2003, G. Berg, Rostock Univ., Rostock, Germany: strain e-p10

doi: 10.13145/bacdive17560.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Stenotrophomonas
  • species: Stenotrophomonas rhizophila
  • full scientific name: Stenotrophomonas rhizophila Wolf et al. 2002

@ref: 5341

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas rhizophila

full scientific name: Stenotrophomonas rhizophila Wolf et al. 2002

strain designation: e-p10, p69

type strain: yes

Morphology

cell morphology

  • @ref: 122204
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 122204
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5341GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54)yeshttps://mediadive.dsmz.de/medium/54Name: GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54) Composition: CaCO3 20.0 g/l Glucose 20.0 g/l Agar 17.0 g/l Yeast extract 10.0 g/l Distilled water
5341NUTRIENT 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
39946MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122204CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5341positivegrowth30mesophilic
39946positivegrowth30mesophilic
60395positivegrowth30mesophilic
67770positivegrowth30mesophilic
122204positivegrowth5-37
122204nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60395aerobe
122204obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122204NaClpositivegrowth0-2 %
122204NaClnogrowth4 %
122204NaClnogrowth6 %
122204NaClnogrowth8 %
122204NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
12220416947citrate+carbon source
1222044853esculin+hydrolysis
12220417632nitrate+reduction
12220416301nitrite-reduction
12220417632nitrate-respiration

antibiotic resistance

  • @ref: 122204
  • 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
12220435581indoleno

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
122204oxidase-
122204beta-galactosidase+3.2.1.23
122204alcohol dehydrogenase-1.1.1.1
122204gelatinase+
122204amylase-
122204DNase+
122204caseinase+3.4.21.50
122204catalase+1.11.1.6
122204tween esterase+
122204lecithinase+
122204lipase+
122204lysine decarboxylase-4.1.1.18
122204ornithine decarboxylase-4.1.1.17
122204protease+
122204tryptophan deaminase-
122204urease-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
122204-+++----+-++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5341-----++++-+-++---++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122204++-++-++-+++++-++++-+++-----------++-----+-------+-+-+-----+---------------+---++-----+--+-++++++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
5341rhizosphere of oilseed rape (Brassica napus L.)Brassica napusRostockGermanyDEUEurope
60395Rhizosphere of oilseed rape (Brassica napus L)GermanyDEUEurope
67770Rhizosphere of rape
122204Rhizospere of rapeGermanyDEUEurope1993

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2601.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_27;98_2015;99_2601&stattab=map
  • Last taxonomy: Stenotrophomonas
  • 16S sequence: AJ293463
  • Sequence Identity:
  • Total samples: 80919
  • soil counts: 24235
  • aquatic counts: 14518
  • animal counts: 31589
  • plant counts: 10577

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
53411Risk group (German classification)
1222041Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Stenotrophomonas rhizophila partial 16S rRNA gene, strain e-p10
  • accession: AJ293463
  • length: 1537
  • database: ena
  • NCBI tax ID: 216778

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas rhizophila DSM 14405GCA_000661955chromosomencbi216778
66792Stenotrophomonas rhizophila strain DSM 14405216778.7completepatric216778
66792Stenotrophomonas rhizophila DSM 144052576861471completeimg216778

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.194no
gram-positiveno98.225no
anaerobicno98.122no
aerobicyes89.703yes
halophileno94.143no
spore-formingno94.807no
glucose-utilyes90.122yes
flagellatedno79.777no
thermophileno99.7yes
glucose-fermentno89.473yes

External links

@ref: 5341

culture collection no.: DSM 14405, ATCC BAA 473, CCUG 54934, JCM 13333, CCUG 47042, CIP 107801

straininfo link

  • @ref: 86556
  • straininfo: 100967

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508851Stenotrophomonas rhizophila sp. nov., a novel plant-associated bacterium with antifungal properties.Wolf A, Fritze A, Hagemann M, Berg GInt J Syst Evol Microbiol10.1099/00207713-52-6-19372002Antifungal Agents/metabolism, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/metabolism, Humans, Molecular Sequence Data, Phenotype, Phylogeny, Plants/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityMetabolism
12851735Highly sensitive determination of ectoine and other compatible solutes by anion-exchange chromatography and pulsed amperometric detection.Riis V, Maskow T, Babel WAnal Bioanal Chem10.1007/s00216-003-2085-92003
Metabolism15668022Synthesis of the compatible solutes glucosylglycerol and trehalose by salt-stressed cells of Stenotrophomonas strains.Roder A, Hoffmann E, Hagemann M, Berg GFEMS Microbiol Lett10.1016/j.femsle.2004.12.0052005Biotechnology/methods, Glucosides/*metabolism, Heat-Shock Response, Sodium Chloride/*pharmacology, Stenotrophomonas/growth & development/*physiology, Stenotrophomonas maltophilia/growth & development/physiology, Trehalose/*metabolismStress
Phylogeny20221726Stenotrophomonas panacihumi sp. nov., isolated from soil of a ginseng field.Yi H, Srinivasan S, Kim MKJ Microbiol10.1007/s12275-010-0006-02010Carotenoids/analysis, Fatty Acids/analysis, Genes, Bacterial, *Panax, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Stenotrophomonas/chemistry/classification/genetics/*isolation & purificationEnzymology
Stress23717321Root-microbe systems: the effect and mode of interaction of Stress Protecting Agent (SPA) Stenotrophomonas rhizophila DSM14405(T.).Alavi P, Starcher MR, Zachow C, Muller H, Berg GFront Plant Sci10.3389/fpls.2013.001412013
Phylogeny28820086Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations.Sanchez-Castro I, Ruiz-Fresneda MA, Bakkali M, Kampfer P, Glaeser SP, Busse HJ, Lopez-Fernandez M, Martinez-Rodriguez P, Merroun MLInt J Syst Evol Microbiol10.1099/ijsem.0.0020162017Bacterial Typing Techniques, Base Composition, *Bentonite, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Stenotrophomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny29638210Stenotrophomonas lactitubi sp. nov. and Stenotrophomonas indicatrix sp. nov., isolated from surfaces with food contact.Weber M, Schunemann W, Fuss J, Kampfer P, Lipski AInt J Syst Evol Microbiol10.1099/ijsem.0.0027322018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Dairying/instrumentation, Fatty Acids/chemistry, *Food Microbiology, Genes, Bacterial, Germany, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Stenotrophomonas/*classification/genetics/isolation & purificationBiotechnology
Phylogeny34559247Stenotrophomonas nematodicola sp. nov., isolated from Caenorhabditis elegans.Wei X, Lei S, Deng Y, Zhang Y, Zhang L, Niu QArch Microbiol10.1007/s00203-021-02586-y2021Animals, Bacterial Typing Techniques, *Caenorhabditis elegans, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Stenotrophomonas/geneticsTranscriptome
Metabolism35469877Diffusible signal factor enhances the saline-alkaline resistance and rhizosphere colonization of Stenotrophomonas rhizophila by coordinating optimal metabolism.Liu Y, Gao J, Wang N, Li X, Fang N, Zhuang XSci Total Environ10.1016/j.scitotenv.2022.1554032022*Bacterial Proteins/genetics, Quorum Sensing, *Rhizosphere, Stenotrophomonas/metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5341Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14405)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14405
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
39946Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5276
60395Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54934)https://www.ccug.se/strain?id=54934
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
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
86556Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100967.1StrainInfo: A central database for resolving microbial strain identifiers
122204Curators of the CIPCollection of Institut Pasteur (CIP 107801)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107801