Strain identifier

BacDive ID: 17442

Type strain: Yes

Species: Pseudoxanthobacter soli

Strain Designation: CC-CC4, CC-4

Strain history: CIP <- 2007, P. Kämpfer, Giesssen Univ., Giessen, Germany: strain CC-4

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8202

BacDive-ID: 17442

DSM-Number: 19599

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

description: Pseudoxanthobacter soli CC-CC4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil sample collected at a regional agricultural research field station.

NCBI tax id

NCBI tax idMatching level
1123029strain
433840species

strain history

@refhistory
8202<- C.-C. Young, Dept. Soil and Environmental Sci., Natl. Chung Hsing Univ., Taichung, Taiwan; CC4
122663CIP <- 2007, P. Kämpfer, Giesssen Univ., Giessen, Germany: strain CC-4

doi: 10.13145/bacdive17442.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Pseudoxanthobacteraceae
  • genus: Pseudoxanthobacter
  • species: Pseudoxanthobacter soli
  • full scientific name: Pseudoxanthobacter soli Arun et al. 2008

@ref: 8202

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Pseudoxanthobacteraceae

genus: Pseudoxanthobacter

species: Pseudoxanthobacter soli

full scientific name: Pseudoxanthobacter soli Arun et al. 2008

strain designation: CC-CC4, CC-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32256negative2 µm0.2 µmrod-shapedyes
69480negative99.987
122663negativerod-shapedyes

colony morphology

  • @ref: 60225
  • incubation period: 1 day

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_19599_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19599_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19599_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19599_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_19599_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8202NUTRIENT 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
37749MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122663CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8202positivegrowth28mesophilic
32256positivegrowth10-37
32256positiveoptimum37mesophilic
37749positivegrowth30mesophilic
60225positivegrowth28-37mesophilic

culture pH

@refabilitytypepHPH range
32256positivegrowth5.5-10alkaliphile
32256positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32256aerobe
60225aerobe
122663obligate aerobe

spore formation

@refspore formationconfidence
32256no
69481no100
69480no99.986

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3225630089acetate+carbon source
3225615963ribitol+carbon source
3225621217L-alaninamide+carbon source
3225616449alanine+carbon source
3225622599arabinose+carbon source
3225618403L-arabitol+carbon source
3225622653asparagine+carbon source
3225615740formate+carbon source
3225628757fructose+carbon source
3225633984fucose+carbon source
3225628260galactose+carbon source
3225617234glucose+carbon source
3225629987glutamate+carbon source
3225617754glycerol+carbon source
3225624996lactate+carbon source
3225629864mannitol+carbon source
3225637684mannose+carbon source
3225617268myo-inositol+carbon source
3225626271proline+carbon source
3225626546rhamnose+carbon source
3225630911sorbitol+carbon source
3225630031succinate+carbon source
3225617151xylitol+carbon source
12266317632nitrate-reduction
12266316301nitrite-reduction

metabolite production

  • @ref: 122663
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32256catalase+1.11.1.6
32256cytochrome oxidase+1.9.3.1
122663oxidase+
122663catalase+1.11.1.6
122663urease+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
122663-++++++++-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
8202soil sample collected at a regional agricultural research field stationKaohsiung CountyTaiwanTWNAsia
60225SoilChyai CountyTaiwanTWNAsia2000
122663Environment, SoilChyai countyTaiwanTWNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_90344.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_37398;97_47548;98_62331;99_90344&stattab=map
  • Last taxonomy: Pseudoxanthobacter
  • 16S sequence: EF465533
  • Sequence Identity:
  • Total samples: 296
  • soil counts: 33
  • aquatic counts: 152
  • animal counts: 79
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82021Risk group (German classification)
1226631Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8202
  • description: Pseudoxanthobacter soli DSM 19599 16S ribosomal RNA gene, partial sequence
  • accession: EF465533
  • length: 1436
  • database: ena
  • NCBI tax ID: 1123029

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoxanthobacter soli DSM 19599GCA_900148505scaffoldncbi1123029
66792Pseudoxanthobacter soli DSM 195991123029.3wgspatric1123029
66792Pseudoxanthobacter soli DSM 195992585428043draftimg1123029
66792Pseudoxanthobacter soli DSM 19599 MsE-30jul19-87GCA_945898215scaffoldncbi1123029
66792Pseudoxanthobacter soli DSM 19599 strain MsE-30jul19-871123029.10wgspatric1123029

GC content

@refGC-content
820268.0
3225668

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes78.322no
flagellatedno80.677no
gram-positiveno97.499yes
anaerobicno98.078no
aerobicyes89.188yes
halophileno93.217no
spore-formingno95.639yes
thermophileno97.227yes
glucose-utilyes92.296yes
glucose-fermentno89.986no

External links

@ref: 8202

culture collection no.: DSM 19599, CIP 109513, CCUG 54547, CC 4

straininfo link

  • @ref: 86438
  • straininfo: 358831

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599697Pseudoxanthobacter soli gen. nov., sp. nov., a nitrogen-fixing alphaproteobacterium isolated from soil.Arun AB, Schumann P, Chu HI, Tan CC, Chen WM, Lai WA, Kampfer P, Shen FT, Rekha PD, Hung MH, Chou JH, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.65206-02008Alphaproteobacteria/chemistry/*classification/genetics/growth & development, Lipids/chemistry, Molecular Sequence Data, Nitrogen Fixation/*physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity, TaiwanGenetics
Phylogeny25013230Pseudoxanthobacter liyangensis sp. nov., isolated from dichlorodiphenyltrichloroethane-contaminated soil.Liu XM, Chen K, Meng C, Zhang L, Zhu JC, Huang X, Li SP, Jiang JDInt J Syst Evol Microbiol10.1099/ijs.0.056507-02014Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DDT/*chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/chemistry, Ubiquinone/chemistryGenetics
Phylogeny31800387Segnochrobactrum spirostomi gen. nov., sp. nov., isolated from the ciliate Spirostomum yagiui and description of a novel family, Segnochrobactraceae fam. nov. within the order Rhizobiales of the class Alphaproteobacteria.Akter S, Shazib SUA, Shin MKInt J Syst Evol Microbiol10.1099/ijsem.0.0039072020Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Ciliophora/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
8202Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19599)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19599
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
32256Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2849728776041
37749Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7265
60225Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54547)https://www.ccug.se/strain?id=54547
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
86438Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID358831.1StrainInfo: A central database for resolving microbial strain identifiers
122663Curators of the CIPCollection of Institut Pasteur (CIP 109513)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109513