Strain identifier

BacDive ID: 2055

Type strain: Yes

Species: Limnobacter thiooxidans

Strain Designation: CS-K2

Strain history: CIP <- 2001, DSMZ <- 1997, S. Spring, Munich Univ., Munich, Germany: strain CS-K2

NCBI tax ID(s): 131080 (species)

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General

@ref: 5113

BacDive-ID: 2055

DSM-Number: 13612

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

description: Limnobacter thiooxidans CS-K2 is an obligate aerobe, chemolithoautotroph, mesophilic bacterium that forms circular colonies and was isolated from littoral sediment of a freshwater lake.

NCBI tax id

  • NCBI tax id: 131080
  • Matching level: species

strain history

@refhistory
5113<- S. Spring, Techn. Univ. München; CS-K2
123525CIP <- 2001, DSMZ <- 1997, S. Spring, Munich Univ., Munich, Germany: strain CS-K2

doi: 10.13145/bacdive2055.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Limnobacter
  • species: Limnobacter thiooxidans
  • full scientific name: Limnobacter thiooxidans Spring et al. 2001

@ref: 5113

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Limnobacter

species: Limnobacter thiooxidans

full scientific name: Limnobacter thiooxidans Spring et al. 2001

strain designation: CS-K2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23161negative1.5-3.7 µm0.6-1.5 µmrod-shapedyes
69480yes92.82
69480negative99.999
123525negativerod-shapedno

colony morphology

  • @ref: 23161
  • colony size: 0.8-1.0 mm
  • colony shape: circular
  • medium used: R2A medium

pigmentation

  • @ref: 123525
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5113R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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
5113LIMNOBACTER MEDIUM (DSMZ Medium 919)yeshttps://mediadive.dsmz.de/medium/919Name: LIMNOBACTER MEDIUM (DSMZ Medium 919) 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 Sodium pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
23161Reasoner's 2A agar (R2A)yes
33761MEDIUM 407 - for Limnobacter thiooxidansyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.050 g);Agar (15.000 g);Glucose (0.500 g);Yeast extract (0.500 g);Pyruvic acid (0.300g);Starch maize (0.500 g);Casamino acids (0.500 g);Di Potassium monohydrogenophosphate (0.300 g
123525CIP Medium 407yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=407

culture temp

@refgrowthtypetemperaturerange
5113positivegrowth28mesophilic
5113positivegrowth30mesophilic
23161positivegrowth4psychrophilic
23161nogrowth40thermophilic
33761positivegrowth30mesophilic
123525positivegrowth5-37
123525nogrowth41thermophilic

culture pH

  • @ref: 23161
  • ability: positive
  • type: growth
  • pH: 5.5-10.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23161obligate aerobe
123525obligate aerobe

nutrition type

  • @ref: 23161
  • type: chemolithoautotroph

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
123525NaClpositivegrowth0 %
123525NaClnogrowth2 %
123525NaClnogrowth4 %
123525NaClnogrowth6 %
123525NaClnogrowth8 %
123525NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23161161933-hydroxybenzoate-carbon source
2316116865gamma-aminobutyric acid-carbon source
23161178794-hydroxybenzoate-carbon source
2316115963ribitol-carbon source
2316116383cis-aconitate-carbon source
2316116947citrate-carbon source
2316115570D-alanine-carbon source
2316117057cellobiose-carbon source
2316115824D-fructose-carbon source
2316112936D-galactose-carbon source
2316117634D-glucose-carbon source
2316117306maltose-carbon source
2316116899D-mannitol-carbon source
2316116024D-mannose-carbon source
2316163150D-rhamnose-carbon source
2316116988D-ribose-carbon source
2316117924D-sorbitol-carbon source
2316116551D-trehalose-carbon source
2316165327D-xylose-carbon source
2316117859glutaric acid-carbon source
2316117240itaconate-carbon source
2316130849L-arabinose-carbon source
2316115971L-histidine-carbon source
2316115729L-ornithine-carbon source
2316117295L-phenylalanine-carbon source
2316117203L-proline-carbon source
2316117115L-serine-carbon source
2316116828L-tryptophan-carbon source
2316168428maltitol-carbon source
2316118401phenylacetate-carbon source
2316117272propionate-carbon source
2316117148putrescine-carbon source
2316117992sucrose-carbon source
2316115708trans-aconitate-carbon source
231614853esculin-hydrolysis
2316117203L-proline-hydrolysis
23161320055methyl beta-D-glucopyranoside-hydrolysis
2316117632nitrate-reduction
2316129985L-glutamate+carbon source
2316130089acetate+carbon source
2316135391aspartate+carbon source
2316129806fumarate+carbon source
2316115361pyruvate+carbon source
2316130031succinate+carbon source
2316116094thiosulfate+energy source
2316129985L-glutamate+growth
2316129806fumarate+growth
2316129991L-aspartate+growth
2316115589L-malate+growth
2316130031succinate+growth
231613122bis-4-nitrophenyl phosphate+hydrolysis
2316116977L-alanine+hydrolysis
23161309162-oxoglutarate+/-carbon source
2316124996lactate+/-carbon source
2316115589L-malate+/-carbon source
12352516947citrate-carbon source
1235254853esculin-hydrolysis
12352517632nitrate-reduction
12352516301nitrite-reduction

antibiotic resistance

  • @ref: 123525
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123525
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
123525oxidase+
123525beta-galactosidase+3.2.1.23
123525alcohol dehydrogenase-1.1.1.1
123525gelatinase-
123525amylase-
123525DNase-
123525caseinase-3.4.21.50
123525catalase+1.11.1.6
123525tween esterase+
123525lecithinase-
123525lipase-
123525lysine decarboxylase-4.1.1.18
123525ornithine decarboxylase-4.1.1.17
123525protease-
123525tryptophan deaminase-
123525urease-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
123525--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5113littoral sediment of a freshwater lakeBavaria, Lake ChiemseeGermanyDEUEurope
123525Environment, Fresh water, lakeChiemsee lakeGermanyDEUEurope1997

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51131Risk group (German classification)
1235251Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5113
  • description: Limnobacter thiooxidans 16S rRNA gene, strain CS-K2
  • accession: AJ289885
  • length: 1522
  • database: ena
  • NCBI tax ID: 131080

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Limnobacter thiooxidans DSM 13612GCA_004291335scaffoldncbi131080
66792Limnobacter thiooxidans strain DSM 13612131080.4wgspatric131080
66792Limnobacter thiooxidans DSM 136122785510713draftimg131080
66792Limnobacter thiooxidans DSM 136122795386119draftimg131080
66792Limnobacter thiooxidans DSM 13612 re-run2786546107draftimg131080

GC content

  • @ref: 5113
  • GC-content: 55

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.651no
flagellatedyes72.337no
gram-positiveno98.952no
anaerobicno98.959no
aerobicyes90.596no
halophileno81.488no
spore-formingno96.311no
thermophileno96.072no
glucose-utilno86.336no
glucose-fermentno94.171no

External links

@ref: 5113

culture collection no.: DSM 13612, CIP 107302, LMG 19593

straininfo link

  • @ref: 71702
  • straininfo: 14965

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491347Limnobacter thiooxidans gen. nov., sp. nov., a novel thiosulfate-oxidizing bacterium isolated from freshwater lake sediment.Spring S, Kampfer P, Schleifer KHInt J Syst Evol Microbiol10.1099/00207713-51-4-14632001Base Composition, Betaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Burkholderia/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Fresh Water/microbiology, Geologic Sediments/microbiology, Germany, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Thiosulfates/metabolismMetabolism
Phylogeny20348326Limnobacter litoralis sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from a volcanic deposit, and emended description of the genus Limnobacter.Lu H, Sato Y, Fujimura R, Nishizawa T, Kamijo T, Ohta HInt J Syst Evol Microbiol10.1099/ijs.0.020206-02010Bacterial Typing Techniques, Burkholderiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thiosulfates/metabolism, Volcanic EruptionsGenetics
Phylogeny28664518Limnobacter humi sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from humus soil, and emended description of the genus Limnobacter Spring et al. 2001.Nguyen TM, Kim JJ Microbiol10.1007/s12275-017-6645-72017Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial, DNA, Ribosomal, Fatty Acids/analysis, Heterotrophic Processes, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Thiosulfates/*metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5113Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13612)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13612
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
23161S Spring, P Kämpferr, K H Schleifer10.1099/00207713-51-4-1463Limnobacter thiooxidans gen. nov., sp. nov., a novel thiosulfate-oxidizing bacterium isolated from freshwater lake sedimentIJSEM 51: 1463-1470 200111491347
33761Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4722
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)
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
71702Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14965.1StrainInfo: A central database for resolving microbial strain identifiers
123525Curators of the CIPCollection of Institut Pasteur (CIP 107302)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107302