Strain identifier

BacDive ID: 2462

Type strain: Yes

Species: Rheinheimera tangshanensis

Strain Designation: JA3-B52

Strain history: X.-X. Zhang JA3-B52.

NCBI tax ID(s): 400153 (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: 8102

BacDive-ID: 2462

DSM-Number: 19460

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

description: Rheinheimera tangshanensis JA3-B52 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from roots of fresh rice plants .

NCBI tax id

  • NCBI tax id: 400153
  • Matching level: species

strain history

@refhistory
8102<- X. Zhang, Agric. Cult. Coll. of China, Inst. Agric. Res. and Regional Planning, Chinese Academy of Agric. Sci., Beijing, PR China; JA3-B52 <- L. Sun, College of Life Sci., Capital Normal Univ., Beijing , PR China
67770X.-X. Zhang JA3-B52.

doi: 10.13145/bacdive2462.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Chromatiales
  • family: Chromatiaceae
  • genus: Rheinheimera
  • species: Rheinheimera tangshanensis
  • full scientific name: Rheinheimera tangshanensis Zhang et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Pararheinheimera tangshanensis

@ref: 8102

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Chromatiales

family: Chromatiaceae

genus: Rheinheimera

species: Rheinheimera tangshanensis

full scientific name: Rheinheimera tangshanensis Zhang et al. 2008

strain designation: JA3-B52

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32513negative1.3-2.5 µm0.4-1 µmrod-shapedyes
69480yes94.695
69480negative99.888

pigmentation

  • @ref: 32513
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8102LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
8102TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8102positivegrowth28mesophilic
32513positivegrowth10-37
32513positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32513positivegrowth6-8.5alkaliphile
32513positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32513
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32513no
69481no99
69480no99.895

halophily

@refsaltgrowthtested relationconcentration
32513NaClpositivegrowth0-3 %
32513NaClpositiveoptimum1 %

observation

  • @ref: 32513
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3251330089acetate+carbon source
3251340585alpha-cyclodextrin+carbon source
3251322599arabinose+carbon source
3251335391aspartate+carbon source
3251317057cellobiose+carbon source
3251323652dextrin+carbon source
3251328260galactose+carbon source
3251317234glucose+carbon source
3251329987glutamate+carbon source
3251328087glycogen+carbon source
3251317716lactose+carbon source
3251325017leucine+carbon source
3251317306maltose+carbon source
3251328053melibiose+carbon source
32513506227N-acetylglucosamine+carbon source
3251326271proline+carbon source
3251316634raffinose+carbon source
3251317822serine+carbon source
3251330031succinate+carbon source
3251317992sucrose+carbon source
3251326986threonine+carbon source
3251327082trehalose+carbon source
325134853esculin+hydrolysis

enzymes

@refvalueactivityec
32513catalase+1.11.1.6
32513cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8102roots of fresh rice plants (Oryza sativa)Oryza sativaAgric. Exp. Demonstration Base, Sangyuan, Luannan County, Hebei ProvinceChinaCHNAsia
67770Roots of fresh rice plants (Oryza sativa) from the Agricultural Experimental Demonstration Base at the village of SangyuanOryza sativaLuannan County, Hebei ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

  • @ref: 8102
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8102
  • description: Rheinheimera sp. JA3-B52 16S ribosomal RNA gene, partial sequence
  • accession: DQ874340
  • length: 1390
  • database: ena
  • NCBI tax ID: 400153

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rheinheimera tangshanensis CGMCC 1.6362GCA_014645135scaffoldncbi400153
66792Rheinheimera tangshanensis JA3-B52GCA_008017875scaffoldncbi400153
66792Rheinheimera tangshanensis strain CGMCC 1.6362400153.4wgspatric400153

GC content

@refGC-contentmethod
810247.0thermal denaturation, midpoint method (Tm)
3251347

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
flagellatedyes84.704no
gram-positiveno99.042no
anaerobicno96.093yes
aerobicyes89.277yes
halophileno90.056yes
spore-formingno94.91no
glucose-utilyes89.92yes
thermophileno99.672yes
motileyes92.361no
glucose-fermentno79.133no

External links

@ref: 8102

culture collection no.: DSM 19460, CGMCC 1.6362, JCM 14254

straininfo link

  • @ref: 72006
  • straininfo: 396521

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842867Rheinheimera tangshanensis sp. nov., a rice root-associated bacterium.Zhang X, Sun L, Qiu F, McLean RJ, Jiang R, Song WInt J Syst Evol Microbiol10.1099/ijs.0.65605-02008Chromatiaceae/chemistry/*classification/*genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Genotype, Molecular Sequence Data, Oryza/*microbiology, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyGenetics
Phylogeny21030822Rheinheimera aquatica sp. nov., an antimicrobial activity producing bacterium isolated from freshwater culture pond.Chen WM, Lin CY, Young CC, Sheu SYJ Microbiol Biotechnol10.4014/jmb.1004.040482010Anti-Infective Agents/*metabolism, Chromatiaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny22843724Rheinheimera tilapiae sp. nov., isolated from a freshwater culture pond.Chen WM, Yang SH, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijs.0.043836-02012Animals, Bacterial Typing Techniques, Base Composition, Chromatiaceae/*classification/genetics/isolation & purification, Cichlids/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TaiwanGenetics
Phylogeny26220076Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site.Kumar A, Bajaj A, Mathan Kumar R, Kaur G, Kaur N, Kumar Singh N, Manickam N, Mayilraj SInt J Syst Evol Microbiol10.1099/ijsem.0.0004712015Bacterial Typing Techniques, Base Sequence, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, *Industrial Waste, Molecular Sequence Data, Nucleic Acid Hybridization, Pesticides, Phospholipids/chemistry, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil PollutantsGenetics
Phylogeny29160196Rheinheimera marina sp. nov., isolated from a deep-sea seamount.Wang Q, Sun YW, Liu J, Zhang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0024962017Bacterial Typing Techniques, Base Composition, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNATranscriptome
Phylogeny31800389Rheinheimera sediminis sp. nov., a marine bacterium isolated from coastal sediment.Yu Q, Qi Y, Zhang H, Pu JInt J Syst Evol Microbiol10.1099/ijsem.0.0039172020Bacterial Typing Techniques, Base Composition, China, Chromatiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny33052808Rheinheimera mangrovi sp. nov., a bacterium isolated from mangrove sediment.Zhang W, Zhu S, Cheng Y, Ding L, Li S, Peng N, He SInt J Syst Evol Microbiol10.1099/ijsem.0.0045132020Bacterial Typing Techniques, Base Composition, China, Chromatiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8102Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19460)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19460
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
32513Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2873328776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
72006Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396521.1StrainInfo: A central database for resolving microbial strain identifiers