Strain identifier

BacDive ID: 7354

Type strain: Yes

Species: Leucobacter tardus

Strain Designation: K 70/01

Strain history: LMG 24388 <-- U. Behrendt K 70/01.

NCBI tax ID(s): 501483 (species)

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General

@ref: 8330

BacDive-ID: 7354

DSM-Number: 19811

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

description: Leucobacter tardus K 70/01 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from phyllosphere of potato plants, Solanum tuberosum L..

NCBI tax id

  • NCBI tax id: 501483
  • Matching level: species

strain history

@refhistory
8330<- U. Behrendt; K 70/01
67770LMG 24388 <-- U. Behrendt K 70/01.

doi: 10.13145/bacdive7354.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leucobacter
  • species: Leucobacter tardus
  • full scientific name: Leucobacter tardus Behrendt et al. 2008

@ref: 8330

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leucobacter

species: Leucobacter tardus

full scientific name: Leucobacter tardus Behrendt et al. 2008

strain designation: K 70/01

type strain: yes

Morphology

cell morphology

  • @ref: 31201
  • gram stain: positive
  • cell length: 0.8-1.6 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18615Corn yellow (1006)10-14 daysISP 2
18615Corn yellow (1006)10-14 daysISP 3
18615Beige (1001)10-14 daysISP 4
18615Corn yellow (1006)10-14 daysISP 5
18615Corn yellow (1006)10-14 daysISP 6
18615Corn yellow (1006)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18615noISP 2
18615noISP 3
18615noISP 4
18615noISP 5
18615noISP 6
18615noISP 7

pigmentation

  • @ref: 31201
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8330TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18615ISP 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
18615ISP 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:
18615ISP 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
18615ISP 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
18615ISP 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
18615ISP 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

culture temp

@refgrowthtypetemperaturerange
8330positivegrowth28mesophilic
18615positiveoptimum28mesophilic
31201positivegrowth04-37
31201positiveoptimum21-30
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31201positivegrowth7
31201positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31201
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31201
  • spore formation: no

observation

@refobservation
31201aggregates in chains
67770quinones: MK-10, MK-11, MK-9 (9:7:1)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3120122599arabinose+carbon source
3120128757fructose+carbon source
3120124265gluconate+carbon source
3120117234glucose+carbon source
3120117754glycerol+carbon source
3120124996lactate+carbon source
3120129864mannitol+carbon source
3120115361pyruvate+carbon source
3120133942ribose+carbon source
3120117822serine+carbon source
3120130911sorbitol+carbon source
3120130031succinate+carbon source
3120153423tween 40+carbon source
3120153426tween 80+carbon source
3120118222xylose+carbon source
312014853esculin+hydrolysis

enzymes

@refvalueactivityec
31201catalase+1.11.1.6
31201cytochrome oxidase+1.9.3.1
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

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18615-++-+----+---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8330phyllosphere of potato plants, Solanum tuberosum L.Solanum tuberosumDahnsdorfGermanyDEUEurope
67770Phyllosphere of potato plantsDahnsdorfGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_61503.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_7696;97_9245;98_11340;99_61503&stattab=map
  • Last taxonomy: Leucobacter tardus subclade
  • 16S sequence: AM940158
  • Sequence Identity:
  • Total samples: 1026
  • soil counts: 168
  • aquatic counts: 148
  • animal counts: 453
  • plant counts: 257

Safety information

risk assessment

  • @ref: 8330
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8330
  • description: Leucobacter tardus partial 16S rRNA gene, type strain DSM 19811T
  • accession: AM940158
  • length: 1484
  • database: ena
  • NCBI tax ID: 501483

Genome sequences

  • @ref: 66792
  • description: Leucobacter tardus K 70/01
  • accession: GCA_017583045
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 501483

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno98.2yes
gram-positiveyes92.932no
anaerobicno99.526no
aerobicyes94.9yes
halophileyes58.867no
spore-formingno94.79yes
thermophileno99.004yes
glucose-utilyes87.992yes
motileno87.474no
glucose-fermentno89.204no

External links

@ref: 8330

culture collection no.: DSM 19811, LMG 24388, JCM 16030

straininfo link

  • @ref: 76804
  • straininfo: 323087

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18984695Leucobacter tardus sp. nov., isolated from the phyllosphere of Solanum tuberosum L.Behrendt U, Ulrich A, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.2008/001065-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Aminobutyrates/analysis, Bacterial Typing Techniques, Cell Wall/chemistry, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Solanum tuberosum/*microbiology, Species SpecificityGenetics
Phylogeny20081017Leucobacter aerolatus sp. nov., from the air of a duck barn.Martin E, Lodders N, Jackel U, Schumann P, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.021303-02010Actinomycetales/*classification/genetics/isolation & purification, *Air Microbiology, Aminobutyrates/chemistry, Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Ducks, Fatty Acids/chemistry, *Housing, Animal, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
Phylogeny28792377Leucobacter ruminantium sp. nov., isolated from the bovine rumen.Chun BH, Lee HJ, Jeong SE, Schumann P, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0020032017Actinomycetales/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Glycolipids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rumen/*microbiology, Sequence Analysis, DNATranscriptome
Phylogeny34319867Leucobacter chromiisoli sp. nov., isolated from chromium-containing chemical plant soil.Xu Z, Li X, Tian J, Gan L, Tian YInt J Syst Evol Microbiol10.1099/ijsem.0.0049232021Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, *Chromium, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8330Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19811)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19811
18615Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19811.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
31201Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2752828776041
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/
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
76804Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID323087.1StrainInfo: A central database for resolving microbial strain identifiers