Strain identifier

BacDive ID: 3034

Type strain: Yes

Species: Limnohabitans parvus

Strain Designation: II-B4

Strain history: CIP <- 2008, V. Kasalicky, CAS Center, Ceske Budejovice, Czech Republic: strain II-B4

NCBI tax ID(s): 540061 (species)

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General

@ref: 15832

BacDive-ID: 3034

DSM-Number: 21592

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

description: Limnohabitans parvus II-B4 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from meso-eutrophic freshwater reservoir.

NCBI tax id

  • NCBI tax id: 540061
  • Matching level: species

strain history

@refhistory
15832<- V. Kasalický, Inst. of Hydrobiology, Ceské Budéjovice
121613CIP <- 2008, V. Kasalicky, CAS Center, Ceske Budejovice, Czech Republic: strain II-B4

doi: 10.13145/bacdive3034.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Limnohabitans
  • species: Limnohabitans parvus
  • full scientific name: Limnohabitans parvus Kasalický et al. 2010

@ref: 15832

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Limnohabitans

species: Limnohabitans parvus

full scientific name: Limnohabitans parvus Kasalický et al. 2010

strain designation: II-B4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23094negative0.46-0.74 µm0.25-0.35 µmrod-shapedno
69480negative99.987
121613negativerod-shapedno

colony morphology

@refcolony sizeincubation period
230941.0-2.0 mm2-5 days
610902 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15832R2A 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
23094Brain Heart Infusion agaryes
23094Casitone agaryes
23094lysogeny broth agaryes
23094nutrient broth soyotone yeast extract mediumyes
23094peptone agaryes
23094Reasoner's 2A agar (R2A)yes
23094standards method agaryes
23094tryptic soy broth agaryes
40072MEDIUM 701 - for -Limnicolayes
121613CIP Medium 701yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=701

culture temp

@refgrowthtypetemperaturerange
15832positivegrowth28mesophilic
23094positivegrowth4.0-34.0
40072positivegrowth21psychrophilic
61090positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23094aerobe
23094facultative anaerobe
61090aerobe
121613obligate aerobe

nutrition type

  • @ref: 23094
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
23094NaClnogrowth>0.5 %
23094NaClpositivegrowth0.0-0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2309430089acetate-assimilation
2309417750betaine-assimilation
2309412936D-galactose-assimilation
230948391D-gluconate-assimilation
2309416988D-ribose-assimilation
2309424996lactate-assimilation
2309416236ethanol-assimilation
2309429805glycolate-assimilation
2309436655glyoxylate-assimilation
2309416467L-arginine-assimilation
2309416347L-carnitine-assimilation
2309415971L-histidine-assimilation
2309417295L-phenylalanine-assimilation
2309417115L-serine-assimilation
2309417266L-sorbose-assimilation
2309415792malonate-assimilation
23094506227N-acetylglucosamine-assimilation
2309430623oxalate-assimilation
2309416452oxaloacetate-assimilation
2309417272propionate-assimilation
2309416610spermidine-assimilation
2309417992sucrose-assimilation
23094309162-oxoglutarate+assimilation
2309417968butyrate+assimilation
2309416947citrate+assimilation
2309417634D-glucose+assimilation
2309416024D-mannose+assimilation
2309433871glycerate+assimilation
2309425115malate+assimilation
2309429806fumarate+assimilation
2309428300glutamine+assimilation
2309417754glycerol+assimilation
2309429985L-glutamate+assimilation
2309417203L-proline+assimilation
2309416828L-tryptophan+assimilation
2309415361pyruvate+assimilation
2309430031succinate+assimilation
12161317632nitrate-reduction
12161316301nitrite-reduction

metabolite production

  • @ref: 121613
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
23094catalase+1.11.1.6
23094cytochrome 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
121613oxidase+
121613catalase-1.11.1.6
121613urease+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
121613-+++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culturesampling date
15832meso-eutrophic freshwater reservoirRimovCzech RepublicCZEEurope
23094Nutrient broth soyotone yeast extract (NSY) medium
61090FreshwaterRimov reservoirCzech RepublicCZEEurope2006-10-09
121613Environment, Water, pelagialRimovCzech RepublicCZEEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Environmental#Aquatic#Freshwater

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158321Risk group (German classification)
1216131Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15832
  • description: Limnohabitans parvus partial 16S rRNA, IGS, tRNA-Ile, tRNA-Ala and 23S rRNA genes, type strain II-B4T
  • accession: FM165536
  • length: 2324
  • database: ena
  • NCBI tax ID: 1293052

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Limnohabitans parvus II-B4GCA_003063455contigncbi1293052
66792Limnohabitans parvus II-B41293052.5wgspatric1293052
66792Limnohabitans parvus II-B42834088864draftimg1293052

GC content

@refGC-contentmethod
1583259.9high performance liquid chromatography (HPLC)
2309459.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.776no
gram-positiveno98.201no
anaerobicno99.088yes
aerobicyes95.691no
halophileno91.356yes
spore-formingno97.332no
glucose-utilyes60.253yes
flagellatedno93.753yes
thermophileno95.995yes
glucose-fermentno90.158no

External links

@ref: 15832

culture collection no.: DSM 21592, CIP 109845, CCUG 56787

straininfo link

  • @ref: 72554
  • straininfo: 371486

literature

  • topic: Phylogeny
  • Pubmed-ID: 20061501
  • title: Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans.
  • authors: Kasalicky V, Jezbera J, Simek K, Hahn MW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.018952-0
  • year: 2010
  • mesh: Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, Czech Republic, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Phenotype, Phospholipids/blood, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15832Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21592)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21592
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
23094Vojtech Kasalický,Jan Jezbera,Karel Simek,Martin W. Hahn10.1099/ijs.0.018952-0Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus LimnohabitansIJSEM 60: 2710-2714 201020061501
40072Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7636
61090Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56787)https://www.ccug.se/strain?id=56787
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
72554Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID371486.1StrainInfo: A central database for resolving microbial strain identifiers
121613Curators of the CIPCollection of Institut Pasteur (CIP 109845)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109845