Strain identifier

BacDive ID: 6318

Type strain: Yes

Species: Kineococcus rhizosphaerae

Strain Designation: RP-B16

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 559628 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8041

BacDive-ID: 6318

DSM-Number: 19711

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive

description: Kineococcus rhizosphaerae RP-B16 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rhizosphere soil of Peucedanum japonicum , a cliff-associated plant.

NCBI tax id

  • NCBI tax id: 559628
  • Matching level: species

strain history

@refhistory
8041<- S. D. Lee, Department of Science Education, Cheju National University; RP-B16
67770DSM 19711 <-- S. D. Lee RP-B16.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive6318.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kineosporiales
  • family: Kineosporiaceae
  • genus: Kineococcus
  • species: Kineococcus rhizosphaerae
  • full scientific name: Kineococcus rhizosphaerae Lee 2009

@ref: 8041

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kineosporiaceae

genus: Kineococcus

species: Kineococcus rhizosphaerae

full scientific name: Kineococcus rhizosphaerae Lee 2009

strain designation: RP-B16

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
67771positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19785Yellow orange (2000)10-14 daysISP 2
19785Dahlia yellow (1033)10-14 daysISP 3
19785Light ivory (1015)10-14 daysISP 4
19785Light ivory (1015)10-14 daysISP 5
19785Beige red (3012)10-14 daysISP 6
19785Yellow orange (2000)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19785noISP 2
19785noISP 3
19785noISP 4
19785noISP 5
19785noISP 6
19785noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8041R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
19785ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19785ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19785ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19785ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19785ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19785ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
8041positivegrowth28mesophilic
19785positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 95.601

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1978562968cellulose-
1978516634raffinose+/-
1978526546rhamnose+
1978528757fructose+/-
1978529864mannitol+/-
1978517268myo-inositol+/-
1978518222xylose+/-
1978517992sucrose+
1978522599arabinose+
1978517234glucose+
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837916899D-mannitol-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19785+/---+-++-+--+/-+/-+/--+/-+/---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19785+++-+----+++++-+-+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8041rhizosphere soil of Peucedanum japonicum (thunb.), a cliff-associated plantPeucedanum japonicumJeju, Mara IslandRepublic of KoreaKORAsia
67770Rhizosphere soil of a cliff-associated plant (Peucedanum japonicum Thunb.)Peucedanum japonicumMara Island, JejuRepublic of KoreaKORAsia
67771From rhizosphere of plantMara island, JejuRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 8041
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8041
  • description: Kineococcus rhizosphaerae partial 16S rRNA gene, type strain RP-B16T
  • accession: FM210338
  • length: 1420
  • database: ena
  • NCBI tax ID: 559628

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kineococcus rhizosphaerae strain DSM 19711559628.3wgspatric559628
66792Kineococcus rhizosphaerae DSM 197112728369276draftimg559628
67770Kineococcus rhizosphaerae DSM 19711GCA_003002055contigncbi559628

GC content

  • @ref: 8041
  • GC-content: 73.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno73no
gram-positiveyes90.829yes
anaerobicno99.109yes
halophileno90.452no
spore-formingno79.219no
glucose-utilyes88.855yes
aerobicyes89.126yes
thermophileno99.684no
motileyes66.708no
flagellatedno91.22no
glucose-fermentno73.345no

External links

@ref: 8041

culture collection no.: DSM 19711, JCM 16541, KCTC 19366

straininfo link

  • @ref: 75792
  • straininfo: 403248

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19605726Kineococcus rhizosphaerae sp. nov., isolated from rhizosphere soil.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.008599-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisEnzymology
Phylogeny22669199Kineococcus endophytica sp. nov., a novel endophytic actinomycete isolated from a coastal halophyte in Jiangsu, China.Bian GK, Feng ZZ, Qin S, Xing K, Wang Z, Cao CL, Liu CH, Dai CC, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-012-9757-42012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny26703438Kineococcus mangrovi sp. nov., isolated from mangrove sediment.Duangmal K, Muangham S, Mingma R, Yimyai T, Srisuk N, Kitpreechavanich V, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijsem.0.0008602015
Phylogeny28984560Kineococcus terrestris sp. nov. and Kineococcus aureolus sp. nov., isolated from saline sediment.Xu FJ, Li QY, Li GD, Chen X, Jiang Y, Jiang CLInt J Syst Evol Microbiol10.1099/ijsem.0.0023802017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8041Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19711)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19711
19785Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19711.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
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)
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
75792Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403248.1StrainInfo: A central database for resolving microbial strain identifiers