Strain identifier

BacDive ID: 17517

Type strain: Yes

Species: Rhodanobacter fulvus

Strain history: CIP <- 2005, IAM <- ST Lee, KAIST: strain Jip2

NCBI tax ID(s): 1163408 (strain), 219571 (species)

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General

@ref: 7478

BacDive-ID: 17517

DSM-Number: 18449

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

description: Rhodanobacter fulvus DSM 18449 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rotten rice straw with soil.

NCBI tax id

NCBI tax idMatching level
219571species
1163408strain

strain history

@refhistory
7478<- S.-T. Lee, KAIST Daejeon; Jip02
67770IAM 15025 <-- W.-T. Im Jip2.
67771<- ST Lee, KAIST
119488CIP <- 2005, IAM <- ST Lee, KAIST: strain Jip2

doi: 10.13145/bacdive17517.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Rhodanobacter
  • species: Rhodanobacter fulvus
  • full scientific name: Rhodanobacter fulvus Im et al. 2005

@ref: 7478

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Rhodanobacteraceae

genus: Rhodanobacter

species: Rhodanobacter fulvus

full scientific name: Rhodanobacter fulvus Im et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771negative
119488negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7478REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)yeshttps://mediadive.dsmz.de/medium/830cName: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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
38305MEDIUM 339 - for Photorhabdus asymbioticayesDistilled water make up to (1000.000 ml);Nutrient agar 1,5% (31.000 g)
119488CIP Medium 339yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=339

culture temp

@refgrowthtypetemperature
7478positivegrowth28
38305positivegrowth25
59191positivegrowth25
67770positivegrowth30
67771positivegrowth25
119488positivegrowth15-30
119488nogrowth5
119488nogrowth37
119488nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59191aerobe
67771aerobe
119488obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119488NaClpositivegrowth0-2 %
119488NaClnogrowth4 %
119488NaClnogrowth6 %
119488NaClnogrowth8 %
119488NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11948816947citrate-carbon source
1194884853esculin+hydrolysis
11948817234glucose-fermentation
11948817716lactose-fermentation
11948817632nitrate+reduction
11948816301nitrite+reduction
119488132112sodium thiosulfate-builds gas from
11948817234glucose+degradation
11948817632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117266L-sorbose-builds acid from
6837117754glycerol-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
683714853esculin+builds acid from
6837127613amygdalin-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

metabolite production

  • @ref: 119488
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11948815688acetoin+
11948817234glucose-

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
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
119488oxidase+
119488beta-galactosidase+3.2.1.23
119488alcohol dehydrogenase-1.1.1.1
119488gelatinase-
119488amylase-
119488DNase-
119488caseinase-3.4.21.50
119488catalase+1.11.1.6
119488tween esterase-
119488gamma-glutamyltransferase+2.3.2.2
119488lecithinase-
119488lipase-
119488lysine decarboxylase-4.1.1.18
119488ornithine decarboxylase-4.1.1.17
119488phenylalanine ammonia-lyase-4.3.1.24
119488protease-
119488tryptophan deaminase-
119488urease-3.5.1.5
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119488-+++-++---++++++++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119488-----+/----+/-+/-+/-+/---------+/--+/-++/-+/-+/-+/-+/------+/---+/-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119488+-+-+-+--+++---++++--++------------------+-----------------+--------------------------+--++-+----+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7478rotten rice straw with soilDaejonRepublic of KoreaKORAsia
59191Soil mixed with rotten strawDeajonRepublic of KoreaKORAsia
67770Soil mixed with rotten strawDaejeonRepublic of KoreaKORAsia
67771From soil mixed with rotten strawRepublic of KoreaKORAsia
119488Environment, Soil, rotten rice strawDaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Decomposing plant
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6597.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_114;96_316;97_352;98_397;99_6597&stattab=map
  • Last taxonomy: Rhodanobacter
  • 16S sequence: AB100608
  • Sequence Identity:
  • Total samples: 769
  • soil counts: 613
  • aquatic counts: 61
  • animal counts: 52
  • plant counts: 43

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74781Risk group (German classification)
1194881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7478Swingsiella fulva gene for 16S rRNA, partial sequenceAB1006081480nuccore1163408
124043Rhodanobacter fulvus gene for 16S rRNA, partial sequence, strain: NBRC 103168.AB6819751470nuccore1163408

GC content

  • @ref: 67771
  • GC-content: 65.3

External links

@ref: 7478

culture collection no.: DSM 18449, IAM 15025, KCTC 12098, CCUG 51445, LMG 23003, JCM 21488, NBRC 103168, Jip 02, Jip 2, CIP 108727

straininfo link

  • @ref: 86514
  • straininfo: 99569

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15486823Rhodanobacter fulvus sp. nov., a beta-galactosidase-producing gammaproteobacterium.Im WT, Lee ST, Yokota AJ Gen Appl Microbiol10.2323/jgam.50.1432004Base Composition, Base Sequence, DNA Primers, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gammaproteobacteria/classification/*enzymology/genetics, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, beta-Galactosidase/*metabolismGenetics
Phylogeny16902003Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix.De Clercq D, Van Trappen S, Cleenwerck I, Ceustermans A, Swings J, Coosemans J, Ryckeboer JInt J Syst Evol Microbiol10.1099/ijs.0.64131-02006Antibiosis, Araceae/growth & development/*microbiology, Base Composition, Catalase/analysis, Culture Media, DNA, Bacterial, Fatty Acids/analysis, Gammaproteobacteria/chemistry/*classification/isolation & purification/physiology, Hypocreales/physiology, Molecular Sequence Data, Oxidoreductases/analysis, Phylogeny, Plant Diseases/microbiology, Plant Roots/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Soil, Soil Microbiology, Species SpecificityCultivation
Phylogeny17684255Rhodanobacter thiooxydans sp. nov., isolated from a biofilm on sulfur particles used in an autotrophic denitrification process.Lee CS, Kim KK, Aslam Z, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.65086-02007Autotrophic Processes, Biofilms/*classification, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, Sulfur/*metabolism, Xanthomonadaceae/chemistry/*classification/*isolation & purification/physiologyGenetics
Phylogeny18048729Rhodanobacter ginsengisoli sp. nov. and Rhodanobacter terrae sp. nov., isolated from soil cultivated with Korean ginseng.Weon HY, Kim BY, Hong SB, Jeon YA, Kwon SW, Go SJ, Koo BSInt J Syst Evol Microbiol10.1099/ijs.0.65018-02007Base Composition, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Xanthomonadaceae/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny19329589Rhodanobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field in South Korea.An DS, Lee HG, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.001784-02009Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny28126050Rhodanobacter rhizosphaerae sp. nov., isolated from soil of ginseng rhizosphere.Cho GY, Lee JC, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0018252017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7478Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18449)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18449
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
38305Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6388
59191Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51445)https://www.ccug.se/strain?id=51445
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
68371Automatically annotated from API 50CH acid
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
86514Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99569.1StrainInfo: A central database for resolving microbial strain identifiers
119488Curators of the CIPCollection of Institut Pasteur (CIP 108727)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108727
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy