Strain identifier

BacDive ID: 18155

Type strain: Yes

Species: Solimonas soli

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 1123261 (strain), 413479 (species)

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General

@ref: 15950

BacDive-ID: 18155

DSM-Number: 21787

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

description: Solimonas soli DSM 21787 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of a ginseng field near Daejeon.

NCBI tax id

NCBI tax idMatching level
413479species
1123261strain

strain history

@refhistory
15950<- KCTC <- D.-C. Yang, Kyung Hee University, Giheung-gu Yongin, South Korea
67771<- DC Yang, Kyunghee Univ.

doi: 10.13145/bacdive18155.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Nevskiales
  • family: Nevskiaceae
  • genus: Solimonas
  • species: Solimonas soli
  • full scientific name: Solimonas soli Kim et al. 2007

  • synonyms

    • @ref: 20215
    • synonym: Sinobacter soli

@ref: 15950

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Nevskiaceae

genus: Solimonas

species: Solimonas soli

full scientific name: Solimonas soli Kim et al. 2007 emend. Sheu et al. 2011

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32085negative0.4 µm0.3 µmrod-shapedno
67771negative
69480negative99.994

pigmentation

  • @ref: 32085
  • production: no

Culture and growth conditions

culture medium

  • @ref: 15950
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15950positivegrowth28mesophilic
32085positivegrowth25-37mesophilic
32085positiveoptimum30mesophilic
62483positivegrowth37mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32085positivegrowth07-09alkaliphile
32085positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32085aerobe
62483aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

observation

  • @ref: 67771
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32085370543-hydroxybutyrate+carbon source
3208530089acetate+carbon source
3208517128adipate+carbon source
3208522599arabinose+carbon source
3208533984fucose+carbon source
3208524265gluconate+carbon source
3208517234glucose+carbon source
3208527570histidine+carbon source
3208526271proline+carbon source
3208517272propionate+carbon source
3208517822serine+carbon source
3208530911sorbitol+carbon source
3208516199urea+carbon source
3208531011valerate+carbon source
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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
32085acid phosphatase+3.1.3.2
32085alkaline phosphatase+3.1.3.1
32085catalase+1.11.1.6
32085urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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
62483-+-+-+--------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
62483--------+-----------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15950soil of a ginseng field near DaejeonDaejeonRepublic of KoreaKORAsia
62483Soil of a ginseng fieldDaejeonRepublic of KoreaKORAsia2006
67771From soilRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3162.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_146;96_1648;97_1972;98_2426;99_3162&stattab=map
  • Last taxonomy: Solimonas soli subclade
  • 16S sequence: EF067861
  • Sequence Identity:
  • Total samples: 401
  • soil counts: 168
  • aquatic counts: 69
  • animal counts: 84
  • plant counts: 80

Safety information

risk assessment

  • @ref: 15950
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15950
  • description: Solimonas soli strain DCY12 16S ribosomal RNA gene, partial sequence
  • accession: EF067861
  • length: 1480
  • database: ena
  • NCBI tax ID: 1123261

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Solimonas soli DSM 21787GCA_000474945scaffoldncbi1123261
66792Solimonas soli DSM 217871123261.3wgspatric1123261
66792Solimonas soli DSM 217872528768146draftimg1123261

GC content

@refGC-contentmethod
1595068.4high performance liquid chromatography (HPLC)
1595040.5
3208540.53

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes82.924no
flagellatedno65.02no
gram-positiveno98.858yes
anaerobicno99.411yes
aerobicyes94.915no
halophileno96.346no
spore-formingno95.316no
thermophileno94.049no
glucose-utilyes71.738no
glucose-fermentno92.749yes

External links

@ref: 15950

culture collection no.: DSM 21787, KCTC 12834, LMG 24014, CCUG 60890, LMG 23841, DCY 12

straininfo link

  • @ref: 87139
  • straininfo: 294637

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978223Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field.Kim MK, Kim YJ, Cho DH, Yi TH, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64938-02007Bacterial Typing Techniques, DNA, Ribosomal/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Molecular Sequence Data, *Panax/growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny20971835Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli.Sheu SY, Cho NT, Arun AB, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.023010-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, Flagella/physiology, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Taiwan, TemperatureGenetics
Phylogeny22407788Fontimonas thermophila gen. nov., sp. nov., a moderately thermophilic bacterium isolated from a freshwater hot spring, and proposal of Solimonadaceae fam. nov. to replace Sinobacteraceae Zhou et al. 2008.Losey NA, Stevenson BS, Verbarg S, Rudd S, Moore ERB, Lawson PAInt J Syst Evol Microbiol10.1099/ijs.0.037127-02012Arkansas, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Gammaproteobacteria/*classification/genetics/isolation & purification, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny24421276Solimonas terrae sp. nov., isolated from soil.Kim SJ, Moon JY, Weon HY, Ahn JH, Chen WM, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.055574-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny30016233Solimonas fluminis sp. nov., isolated from a freshwater river.Lee Y, Lee B, Lee K, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0028652018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15950Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21787)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21787
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
32085Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2833128776041
62483Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60890)https://www.ccug.se/strain?id=60890
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
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
87139Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294637.1StrainInfo: A central database for resolving microbial strain identifiers