Strain identifier

BacDive ID: 7339

Type strain: Yes

Species: Leifsonia aquatica

Strain Designation: 150

Strain history: CIP <- 1964, E. Leifson: strain 150

NCBI tax ID(s): 1358026 (strain), 144185 (species)

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General

@ref: 8570

BacDive-ID: 7339

DSM-Number: 20146

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

description: Leifsonia aquatica 150 is a mesophilic, Gram-positive bacterium that was isolated from distilled water.

NCBI tax id

NCBI tax idMatching level
144185species
1358026strain

strain history

@refhistory
8570<- ATCC <- E. Leifson, 150 (Corynebacterium aquaticum)
376111964, E. Leifson: strain 150
67770K. Suzuki CNF 038 <-- AJ 1413 <-- ATCC 14665 <-- E. Leifson 150.
116431CIP <- 1964, E. Leifson: strain 150

doi: 10.13145/bacdive7339.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leifsonia
  • species: Leifsonia aquatica
  • full scientific name: Leifsonia aquatica (ex Leifson 1962) Evtushenko et al. 2000

  • synonyms

    @refsynonym
    20215Leifsonia aquatica
    20215Corynebacterium aquaticum

@ref: 8570

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leifsonia

species: Leifsonia aquatica

full scientific name: Leifsonia aquatica (ex Leifson 1962) Evtushenko et al. 2000

strain designation: 150

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
18306Cream (9001)10-14 daysISP 2
18306Lemon yellow (1012)10-14 daysISP 3
18306Lemon yellow (1012)10-14 daysISP 4
1830610-14 daysISP 5
18306Lemon yellow (1012)10-14 daysISP 6
1830610-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18306noISP 2
18306noISP 3
18306noISP 4
18306noISP 5
18306noISP 6
18306noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8570CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
18306ISP 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
18306ISP 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:
18306ISP 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
18306ISP 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
18306ISP 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
18306ISP 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
37611MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116431CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18306positiveoptimum28mesophilic
8570positivegrowth30mesophilic
37611positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

  • @ref: 18306
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8570
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1830662968cellulose+
1830616634raffinose-
1830626546rhamnose+
1830628757fructose+
1830629864mannitol+
1830617268myo-inositol-
1830618222xylose+
1830617992sucrose+
1830622599arabinose+
1830617234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
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

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

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
68368gelatinase-
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368beta-galactosidase-3.2.1.23

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18306-+-+-+++++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18306-+-++++--++++-++++-

API 20E

@refONPGODCCITH2SUREINDVPGEL
18306----+-+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
8570distilled water
48900Distilled water
67770Distilled water
116431Environment, Distilled waterFranceFRAEurope1962

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Engineered#Industrial#Engineered product
#Engineered#Treatment#Sterilized (Desinfected)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5106.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_671;97_777;98_901;99_5106&stattab=map
  • Last taxonomy: Leifsonia
  • 16S sequence: X77450
  • Sequence Identity:
  • Total samples: 1088
  • soil counts: 509
  • aquatic counts: 123
  • animal counts: 333
  • plant counts: 123

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85701Risk group (German classification)
183061Risk group (German classification)
1164311Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Leifsonia aquatica 16S ribosomal RNA gene, partial sequenceAF299364435ena144185
8570C.aquaticum (DSM 20146) 16S rRNA geneX774501475ena144185
67770Leifsonia aquatica gene for 16S ribosomal RNAD450571468ena144185
67770Leifsonia aquatica strain VKM Ac-1400 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceDQ2326182111ena144185

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leifsonia aquatica DSM 20146GCA_014190775contigncbi144185
66792Leifsonia aquatica ATCC 146651358026.3wgspatric1358026
66792Leifsonia aquatica strain DSM 20146144185.6wgspatric144185
66792Leifsonia aquatica DSM 201462821241899draftimg144185
66792Leifsonia aquatica ATCC 146652602041580draftimg1358026
67770Leifsonia aquatica ATCC 14665GCA_000469485scaffoldncbi1358026

GC content

@refGC-contentmethod
857069.3
6777073.2thermal denaturation, midpoint method (Tm)
6777069.3thermal denaturation, midpoint method (Tm)
6777070.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes61.013no
gram-positiveyes89.613no
anaerobicno99.685no
halophileno94.724no
spore-formingno88.26no
thermophileno99.451yes
glucose-utilyes86.478yes
flagellatedno94.016no
aerobicyes92.606no
glucose-fermentno89.592yes

External links

@ref: 8570

culture collection no.: DSM 20146, ATCC 14665, NCIB 9460, CCUG 27700, CCTM La 2040, JCM 1368, BCRC 11574, CECT 535, CIP 64.13, IAM 12441, IFO 12154, IFO 15710, KCTC 9098, KCTC 9233, NBRC 12154, NBRC 15710, NCIMB 9460, NRIC 1848, VKM Ac-1400

straininfo link

  • @ref: 76789
  • straininfo: 389265

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10826825Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov.Evtushenko LI, Dorofeeva LV, Subbotin SA, Cole JR, Tiedje JMInt J Syst Evol Microbiol10.1099/00207713-50-1-3712000Actinomycetales/*classification/cytology/isolation & purification/physiology, Animals, Cell Wall/chemistry, Culture Media, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, *Nematoda, Nucleic Acid Hybridization, Phenotype, Plant Tumors/*microbiology/parasitology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNACultivation
12501368Leifsonia gen. nov., a genus for 2,4-diaminobutyric acid-containing actinomycetes to accommodate "Corynebacterium aquaticum" Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al. 1984.Suzuki KI, Suzuki M, Sasaki J, Park YH, Komagata KKJ Gen Appl Microbiol10.2323/jgam.45.2531999
Phylogeny19126716Leifsonia kribbensis sp. nov., isolated from soil.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.001925-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Korea, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny23728372Rudaibacter terrae gen. nov., sp. nov., isolated from greenhouse soil.Kim SJ, Moon JY, Hamada M, Tamura T, Weon HY, Suzuki KI, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.049817-02013Actinomycetales/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Environment, Controlled, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8570Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20146)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20146
18306Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20146.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
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
37611Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10113
48900Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27700)https://www.ccug.se/strain?id=27700
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/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
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
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
76789Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389265.1StrainInfo: A central database for resolving microbial strain identifiers
116431Curators of the CIPCollection of Institut Pasteur (CIP 64.13)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2064.13