Strain identifier

BacDive ID: 13517

Type strain: Yes

Species: Labedaea rhizosphaerae

Strain Designation: RS-49

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 598644 (species)

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General

@ref: 16409

BacDive-ID: 13517

DSM-Number: 45361

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

description: Labedaea rhizosphaerae RS-49 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from rhizosphere soil of the cliff-associated plant Peucedanum japonicum Thunb..

NCBI tax id

  • NCBI tax id: 598644
  • Matching level: species

strain history

@refhistory
16409<- S. D. Lee, Jeju National Univ., Rep. of Korea; RS-49
67770KCTC 19662 <-- S. D. Lee; Jeju Natl. Univ., South Korea; RS-49.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive13517.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Labedaea
  • species: Labedaea rhizosphaerae
  • full scientific name: Labedaea rhizosphaerae Lee 2012

@ref: 16409

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Labedaea

species: Labedaea rhizosphaerae

full scientific name: Labedaea rhizosphaerae Lee 2012

strain designation: RS-49

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
30357positiveno
67771positive
69480positive100
69480no94.788

colony morphology

@refcolony colormedium used
69388Fawn brown (8007), Pale brown (8025)suter with tyrosine
69388Ivory (1014)ISP 2
69388Ivory (1014)ISP 3
69388Ivory (1014)ISP 6
69388Light ivory (1015)ISP 4
69388Light ivory (1015)ISP 5
69388Light ivory (1015)ISP 7
69388Sepia brown (8014), Brown beige (1011)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
69388noAerial myceliumISP 2
69388noAerial myceliumISP 3
69388yesAerial myceliumISP 4Pure white (9010)
69388noAerial myceliumISP 5
69388noAerial myceliumISP 6
69388yesAerial myceliumISP 7Traffic white (9016)
69388noAerial myceliumsuter with tyrosine
69388noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
30357no
69388noMelanin
69388yessoluble pigmentOchre brown (8001)

multimedia

@refmultimedia contentcaptionintellectual property rights
69388DSM_45361_image3.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69388DSM_45361_image4.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16409GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
16409GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16409positivegrowth28mesophilic
30357positivegrowth25-42
30357positiveoptimum33.5mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30357positivegrowth5.1-10.1alkaliphile
30357positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30357aerobe
67771aerobe

spore formation

@refspore formationconfidence
30357yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
30357NaClpositivegrowth<3 %
69388NaClpositivegrowth0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-8, MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6938822599arabinose-growth
3035717057cellobiose+carbon source
3035728757fructose+carbon source
3035717234glucose+carbon source
3035717716lactose+carbon source
3035717306maltose+carbon source
3035729864mannitol+carbon source
3035728053melibiose+carbon source
3035716634raffinose+carbon source
3035726546rhamnose+carbon source
3035717992sucrose+carbon source
3035727082trehalose+carbon source
3035718222xylose+carbon source
303574853esculin+hydrolysis
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836916024D-mannose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
6938862968cellulose-growth
6938828757fructose-growth
6938817234glucose-growth
6938817268inositol-growth
6938837684mannose-growth
6938816634raffinose-growth
6938826546rhamnose-growth
6938817992sucrose-growth
6938818222xylose-growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
30357gelatinase+
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
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382leucine arylamidase+3.4.11.1
68382acid phosphatase+3.1.3.2
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase+3.2.1.52

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69388-++---+++-+--------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
16409-+/----+----++/----+/--+--
69388+/-+++/-+++/-+/-+/-+-+--+++++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
16409-----++-+/-+/--+/-+/--+/--+/-+/---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16409rhizosphere soil of the cliff-associated plant Peucedanum japonicum Thunb.Peucedanum japonicumJeju, Mara IslandRepublic of KoreaKORAsia
67770Rhizosphere soil of a cliff-associated plant (Peucedanum japonicum Thunb.) on Mara IslandPeucedanum japonicumJejuRepublic of KoreaKORAsia
67771From rhizosphere)JejuRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_58450.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_415;97_32453;98_41616;99_58450&stattab=map
  • Last taxonomy: Kibdelosporangium
  • 16S sequence: FM998036
  • Sequence Identity:
  • Total samples: 1733
  • soil counts: 946
  • aquatic counts: 43
  • animal counts: 76
  • plant counts: 668

Safety information

risk assessment

  • @ref: 16409
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16409
  • description: Labedaea rhizosphaerae partial 16S rRNA gene, type strain RS-49T
  • accession: FM998036
  • length: 1424
  • database: ena
  • NCBI tax ID: 598644

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Labedaea rhizosphaerae strain DSM 45361598644.3wgspatric598644
66792Labedaea rhizosphaerae DSM 453612795385470draftimg598644
67770Labedaea rhizosphaerae DSM 45361GCA_004362825scaffoldncbi598644

GC content

@refGC-contentmethod
1640964.2high performance liquid chromatography (HPLC)
3035764.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes86.756yes
anaerobicno98.929yes
halophileno94.022no
spore-formingyes90.211yes
glucose-utilyes89.561no
flagellatedno97.406yes
aerobicyes92.407no
thermophileno97.004yes
motileno93.932yes
glucose-fermentno92.047yes

External links

@ref: 16409

culture collection no.: DSM 45361, KCTC 19662, JCM 31489

straininfo link

  • @ref: 82708
  • straininfo: 397978

literature

  • topic: Phylogeny
  • Pubmed-ID: 21948095
  • title: Labedaea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere soil.
  • authors: Lee SD
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.034355-0
  • year: 2011
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Apiaceae/microbiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, DNA, Bacterial/genetics, Lipids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16409Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45361)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45361
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
30357Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2669728776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69388Wink, J.https://cdn.dsmz.de/wink/DSM%2045361.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
82708Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397978.1StrainInfo: A central database for resolving microbial strain identifiers