Strain identifier

BacDive ID: 4370

Type strain: Yes

Species: Kosakonia radicincitans

Strain Designation: D5/23

Strain history: CIP <- 2004, S. Ruppel, Leibniz Inst. Vegetable Ornamental crops, Grossbeeren, Germany: strain D5/23, Enterobacter radicincitans <- DSMZ

NCBI tax ID(s): 1177180 (strain), 283686 (species)

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General

@ref: 6554

BacDive-ID: 4370

DSM-Number: 16656

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Kosakonia radicincitans D5/23 is an aerobe, mesophilic, motile bacterium that was isolated from phyllosphere of winter wheat.

NCBI tax id

NCBI tax idMatching level
1177180strain
283686species

strain history

@refhistory
6554<- S. Ruppel, Institut f. Gemuese- und Zierpflanzenbau Grossbeeren, Germany; D5/23 <- S. Ruppel and R. Schmelzer
122115CIP <- 2004, S. Ruppel, Leibniz Inst. Vegetable Ornamental crops, Grossbeeren, Germany: strain D5/23, Enterobacter radicincitans <- DSMZ

doi: 10.13145/bacdive4370.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Kosakonia
  • species: Kosakonia radicincitans
  • full scientific name: Kosakonia radicincitans (Kämpfer et al. 2005) Brady et al. 2013

  • synonyms

    • @ref: 20215
    • synonym: Enterobacter radicincitans

@ref: 6554

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Kosakonia

species: Kosakonia radicincitans

full scientific name: Kosakonia radicincitans (Kämpfer et al. 2005) Brady et al. 2013

strain designation: D5/23

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.068
6948099.983negative
122115yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6554CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
6554NUTRIENT 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
34218MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122115CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6554positivegrowth28mesophilic
34218positivegrowth30mesophilic
59043positivegrowth30-37mesophilic
122115positivegrowth30-41
122115nogrowth5psychrophilic
122115nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59043aerobe
122115facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no98.791

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate+builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol+builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368nitrate-reduction17632
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368sucrose+fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol+fermentation30911
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine+hydrolysis29016
122115mannitol+fermentation29864
122115citrate+carbon source16947
122115glucose+fermentation17234
122115lactose-fermentation17716
122115nitrate-reduction17632
122115nitrite-reduction16301
122115malonate+assimilation15792
122115sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 122115
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12211535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12211515688acetoin+
12211517234glucose-

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
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
122115oxidase-
122115beta-galactosidase+3.2.1.23
122115alcohol dehydrogenase+1.1.1.1
122115gelatinase-
122115catalase+1.11.1.6
122115lysine decarboxylase-4.1.1.18
122115ornithine decarboxylase-4.1.1.17
122115phenylalanine ammonia-lyase-4.3.1.24
122115tryptophan deaminase-
122115urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122115-+---+----++-+--++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
6554++--+----+-+++++++++---
6554++--+----+-++-++++/-++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122115+--+++---++++-++-++-+/-++/-++++++-++------+--------++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6554phyllosphere of winter wheatMünchebergGermanyDEUEurope
59043Phyllosphere of winter wheatGermanyDEUEurope1986
122115Environment, Phyllosphere of winter wheatMünchebergGermanyDEUEurope1986

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65541Risk group (German classification)
1221152Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterobacter radicincitans partial 16S rRNA gene, type strain DSM 16656THF5690431530ena283686
6554UNVERIFIED: Kosakonia radicincitans strain D5/23 16S ribosomal RNA gene, partial sequenceAY5631341479ena283686

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kosakonia radicincitans DSM 16656GCA_000280495completencbi1177180
66792Enterobacter radicincitans DSM 166561177180.3wgspatric1177180
66792Kosakonia radicincitans DSM 166561177180.10plasmidpatric1177180
66792Kosakonia radicincitans DSM 166561177180.11plasmidpatric1177180
66792Kosakonia radicincitans DSM 166561177180.18wgspatric1177180
66792Kosakonia radicincitans DSM 166562811995038completeimg1177180

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.302no
motileyes90.302no
flagellatedyes53.88no
flagellatedyes53.88no
gram-positiveno98.272no
gram-positiveno98.272no
anaerobicno94.887yes
anaerobicno94.887yes
aerobicno64.886yes
aerobicno64.886yes
halophileno95.917no
halophileno95.917no
spore-formingno91.388no
spore-formingno91.388no
thermophileno99.76yes
thermophileno99.76yes
glucose-utilyes95.469no
glucose-utilyes95.469no
glucose-fermentyes90.287no
glucose-fermentyes90.287no

External links

@ref: 6554

culture collection no.: CCUG 50898, DSM 16656, CIP 108468, LMG 23767

straininfo link

  • @ref: 73861
  • straininfo: 214847

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15900968Enterobacter radicincitans sp. nov., a plant growth promoting species of the family Enterobacteriaceae.Kampfer P, Ruppel S, Remus RSyst Appl Microbiol10.1016/j.syapm.2004.12.0072005Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Enterobacter/*classification/isolation & purification/physiology, Fatty Acids/analysis/chemistry, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Leaves/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Triticum/*microbiologyGenetics
19556746Interaction between plants and bacteria: glucosinolates and phyllospheric colonization of cruciferous vegetables by Enterobacter radicincitans DSM 16656.Schreiner M, Krumbein A, Ruppel SJ Mol Microbiol Biotechnol10.1159/0002265892009Brassicaceae/chemistry/*microbiology, Colony Count, Microbial/methods, Enterobacter/*growth & development, Glucosinolates/*analysis, Plant Leaves/chemistry/*microbiology, Polymerase Chain Reaction/methods, *Symbiosis, Vegetables/chemistry/*microbiology
Phylogeny19578150Enterobacter oryzae sp. nov., a nitrogen-fixing bacterium isolated from the wild rice species Oryza latifolia.Peng G, Zhang W, Luo H, Xie H, Lai W, Tan ZInt J Syst Evol Microbiol10.1099/ijs.0.65484-02009Anti-Bacterial Agents/pharmacology, Bacterial Proteins/chemistry, Bacterial Typing Techniques, DNA, Bacterial/analysis, Drug Resistance, Bacterial, Enterobacter/*classification/genetics/isolation & purification/physiology, Fatty Acids/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, *Nitrogen Fixation, Oryza/*microbiology, Phenotype, Phylogeny, Plant Roots/microbiology, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Genetics22965092Genome sequence of Enterobacter radicincitans DSM16656(T), a plant growth-promoting endophyte.Witzel K, Gwinn-Giglio M, Nadendla S, Shefchek K, Ruppel SJ Bacteriol10.1128/JB.01193-122012Enterobacter/*classification/*genetics, *Genome, Bacterial, Molecular Sequence Data, Plant Roots/growth & development/microbiology, Plant Shoots/growth & development/microbiology, Soil Microbiology, Triticum/growth & developmentPhylogeny
23242136Impact of the PGPB Enterobacter radicincitans DSM 16656 on growth, glucosinolate profile, and immune responses of Arabidopsis thaliana.Brock AK, Berger B, Mewis I, Ruppel SMicrob Ecol10.1007/s00248-012-0146-32012Arabidopsis/genetics/*growth & development/immunology/*microbiology, Arabidopsis Proteins/genetics/immunology, Cyclopentanes/immunology, Endophytes/*physiology, Enterobacter/*physiology, Ethylenes/immunology, Gene Expression Regulation, Plant, Glucosinolates/*immunology, Oxylipins/immunology, Plant Growth Regulators/immunology, Salicylic Acid/immunology
Phylogeny26597455Kosakonia pseudosacchari sp. nov., an endophyte of Zea mays.Kampfer P, McInroy JA, Doijad S, Chakraborty T, Glaeser SPSyst Appl Microbiol10.1016/j.syapm.2015.09.0042015Alabama, Base Sequence, DNA Gyrase/genetics, DNA, Bacterial/genetics, DNA-Directed RNA Polymerases/genetics, Endophytes, Enterobacteriaceae/*classification/genetics/*isolation & purification, Multilocus Sequence Typing, Phylogeny, Plant Roots/*microbiology, Prokaryotic Initiation Factor-2/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Transcription Factors/genetics, Zea mays/*microbiologyTranscriptome
Biotechnology28382622The plant growth-promoting bacterium Kosakonia radicincitans improves fruit yield and quality of Solanum lycopersicum.Berger B, Baldermann S, Ruppel SJ Sci Food Agric10.1002/jsfa.83572017Agricultural Inoculants/physiology, Amino Acids/analysis, Enterobacteriaceae/*physiology, Fruit/chemistry/*growth & development/microbiology, Gene Expression Regulation, Plant, Lycopersicon esculentum/chemistry/growth & development/*microbiology, Seeds/growth & development/microbiology, Volatile Organic Compounds/analysis
28491076A Proteomic Approach Suggests Unbalanced Proteasome Functioning Induced by the Growth-Promoting Bacterium Kosakonia radicincitans in Arabidopsis.Witzel K, Ustun S, Schreiner M, Grosch R, Bornke F, Ruppel SFront Plant Sci10.3389/fpls.2017.006612017
Enzymology29059532Site-directed mutagenesis to deactivate two nitrogenase isozymes of Kosakonia radicincitans DSM16656(T).Ekandjo LK, Ruppel S, Remus R, Witzel K, Patz S, Becker YCan J Microbiol10.1139/cjm-2017-05322017Enterobacteriaceae/*enzymology/*genetics, Enzyme Activation/genetics, Isoenzymes/chemistry/genetics/metabolism, Mutagenesis, Site-Directed, Nitrogen Fixation/genetics, Nitrogenase/chemistry/*genetics/*metabolismMetabolism
Cultivation29789802Successful Formulation and Application of Plant Growth-Promoting Kosakonia radicincitans in Maize Cultivation.Berger B, Patz S, Ruppel S, Dietel K, Faetke S, Junge H, Becker MBiomed Res Int10.1155/2018/64394812018Agriculture, Enterobacteriaceae/*physiology, Germany, Silage, Soil Microbiology, Zea mays/*growth & development/*microbiology
Phylogeny29876800Isolation, characterization, genomic sequencing, and GFP-marked insertional mutagenesis of a high-performance nitrogen-fixing bacterium, Kosakonia radicincitans GXGL-4A and visualization of bacterial colonization on cucumber roots.Sun S, Chen Y, Cheng J, Li Q, Zhang Z, Lan ZFolia Microbiol (Praha)10.1007/s12223-018-0608-12018Cucumis sativus/*microbiology, Enterobacteriaceae/*genetics/growth & development/isolation & purification/*metabolism, Genome, Bacterial, Green Fluorescent Proteins/genetics/metabolism, Microscopy, Fluorescence, Mutagenesis, Insertional, Nitrogen/metabolism, *Nitrogen Fixation, Phylogeny, Plant Roots/microbiologyMetabolism
Metabolism30120551Plant growth-promoting bacteria Kosakonia radicincitans mediate anti-herbivore defense in Arabidopsis thaliana.Brock AK, Berger B, Schreiner M, Ruppel S, Mewis IPlanta10.1007/s00425-018-2964-02018Animals, Aphids/growth & development/*microbiology, Arabidopsis/growth & development/immunology/*microbiology, *Disease Resistance, Enterobacteriaceae/*physiology, Glucosinolates/metabolism, Herbivory, Larva, Mutation, Phloem/growth & development/immunology/microbiology, Plant Diseases/immunology/*microbiology/parasitology, Plant Proteins/genetics, Signal Transduction, Spodoptera/growth & development/*microbiology
Genetics30214433Comparative Genomics Reveal a Flagellar System, a Type VI Secretion System and Plant Growth-Promoting Gene Clusters Unique to the Endophytic Bacterium Kosakonia radicincitans.Becker M, Patz S, Becker Y, Berger B, Drungowski M, Bunk B, Overmann J, Sproer C, Reetz J, Tchuisseu Tchakounte GV, Ruppel SFront Microbiol10.3389/fmicb.2018.019972018
Stress31341674Salt stress and hydroxyectoine enhance phosphate solubilisation and plant colonisation capacity of Kosakonia radicincitans.Cruz Barrera M, Jakobs-Schoenwandt D, Gomez MI, Becker M, Patel AV, Ruppel SJ Adv Res10.1016/j.jare.2019.03.0122019
32405468Formulating bacterial endophyte: Pre-conditioning of cells and the encapsulation in amidated pectin beads.Cruz Barrera M, Jakobs-Schoenwandt D, Gomez MI, Serrato J, Ruppel S, Patel AVBiotechnol Rep (Amst)10.1016/j.btre.2020.e004632020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6554Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16656)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16656
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34218Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6093
59043Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50898)https://www.ccug.se/strain?id=50898
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)
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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)
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
73861Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID214847.1StrainInfo: A central database for resolving microbial strain identifiers
122115Curators of the CIPCollection of Institut Pasteur (CIP 108468)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108468