Strain identifier

BacDive ID: 3035

Type strain: Yes

Species: Limnohabitans planktonicus

Strain Designation: II-D5

Strain history: CIP <- 2008, V. Kasalicky, Center CAS, HBU, Ceske Budejovice, Czech Republic: strain II-D5

NCBI tax ID(s): 540060 (species)

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General

@ref: 15834

BacDive-ID: 3035

DSM-Number: 21594

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

description: Limnohabitans planktonicus II-D5 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from meso-eutrophic freshwater reservoir.

NCBI tax id

  • NCBI tax id: 540060
  • Matching level: species

strain history

@refhistory
15834<- V. Kasalický, Inst. of Hydrobiology, Ceské Budejovice, Czech Republic; II-D5
121852CIP <- 2008, V. Kasalicky, Center CAS, HBU, Ceske Budejovice, Czech Republic: strain II-D5

doi: 10.13145/bacdive3035.20230509.8.1

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 planktonicus
  • full scientific name: Limnohabitans planktonicus Kasalický et al. 2010

@ref: 15834

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Limnohabitans

species: Limnohabitans planktonicus

full scientific name: Limnohabitans planktonicus Kasalický et al. 2010

strain designation: II-D5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23094negative0.64-1.16 mm0.23-0.37 mmrod-shapedno
121852negativerod-shapedno

colony morphology

@refcolony sizeincubation period
230941.0-2.0 mm2-5 days
610914 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15834R2A 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
37665MEDIUM 701 - for -Limnicolayes
15834NUTRIENT 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
121852CIP Medium 701yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=701

culture temp

@refgrowthtypetemperaturerange
15834positivegrowth28mesophilic
23094positivegrowth4.0-34.0
37665positivegrowth21psychrophilic
61091positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23094aerobe
23094facultative anaerobe
61091aerobe
121852obligate aerobe

nutrition type

  • @ref: 23094
  • type: chemoorganotroph

halophily

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2309417750betaine-assimilation
2309412936D-galactose-assimilation
230948391D-gluconate-assimilation
2309416988D-ribose-assimilation
2309424996lactate-assimilation
2309416467L-arginine-assimilation
2309416347L-carnitine-assimilation
2309417266L-sorbose-assimilation
2309415792malonate-assimilation
23094506227N-acetylglucosamine-assimilation
2309430623oxalate-assimilation
2309416610spermidine-assimilation
2309417992sucrose-assimilation
23094309162-oxoglutarate+assimilation
2309430089acetate+assimilation
2309417968butyrate+assimilation
2309416947citrate+assimilation
2309417634D-glucose+assimilation
2309416024D-mannose+assimilation
2309433871glycerate+assimilation
2309425115malate+assimilation
2309416236ethanol+assimilation
2309429806fumarate+assimilation
2309428300glutamine+assimilation
2309417754glycerol+assimilation
2309429805glycolate+assimilation
2309436655glyoxylate+assimilation
2309429985L-glutamate+assimilation
2309415971L-histidine+assimilation
2309417295L-phenylalanine+assimilation
2309417203L-proline+assimilation
2309417115L-serine+assimilation
2309416828L-tryptophan+assimilation
2309416452oxaloacetate+assimilation
2309415361pyruvate+assimilation
2309430031succinate+assimilation
12185217632nitrate-reduction
12185216301nitrite-reduction

metabolite production

  • @ref: 121852
  • 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
121852oxidase-
121852catalase+1.11.1.6
121852urease+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
121852-+++-+----++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment culturesampling date
15834meso-eutrophic freshwater reservoirRimovCzech RepublicCZEEurope
23094Nutrient broth soyotone yeast extract (NSY) medium
61091FreshwaterRimov reservoirCzech RepublicCZEEurope2006-10-09
121852Environment, Water, pelagialRimovCzech RepublicCZEEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3902.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_269;97_2286;98_2813;99_3902&stattab=map
  • Last taxonomy: Limnohabitans planktonicus
  • 16S sequence: FM165535
  • Sequence Identity:
  • Total samples: 779
  • soil counts: 12
  • aquatic counts: 652
  • animal counts: 111
  • plant counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158341Risk group (German classification)
1218521Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15834
  • description: Limnohabitans planktonicus partial 16S rRNA, IGS, tRNA-Ile, tRNA-Ala and 23S rRNA genes, type strain II-D5T
  • accession: FM165535
  • length: 2330
  • database: ena
  • NCBI tax ID: 1293045

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Limnohabitans planktonicus II-D5GCA_001270065contigncbi1293045
66792Limnohabitans planktonicus II-D51293045.4wgspatric1293045

GC content

@refGC-contentmethod
1583459.9high performance liquid chromatography (HPLC)
2309459.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes64.729yes
gram-positiveno98.379yes
anaerobicno97.897yes
aerobicyes91.448no
halophileno93.975yes
spore-formingno95.604no
glucose-utilyes61.486yes
flagellatedyes54.197no
thermophileno97.112yes
glucose-fermentno89.932no

External links

@ref: 15834

culture collection no.: CCUG 56788, DSM 21594, CIP 109844

straininfo link

  • @ref: 72555
  • straininfo: 371487

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20061501Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans.Kasalicky V, Jezbera J, Simek K, Hahn MWInt J Syst Evol Microbiol10.1099/ijs.0.018952-02010Bacterial 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/chemistryGenetics
Enzymology26014379Betaproteobacteria Limnohabitans strains increase fecundity in the crustacean Daphnia magna: symbiotic relationship between major bacterioplankton and zooplankton in freshwater ecosystem.Peerakietkhajorn S, Kato Y, Kasalicky V, Matsuura T, Watanabe HEnviron Microbiol10.1111/1462-2920.129192015Animals, Betaproteobacteria/genetics/growth & development/isolation & purification/*physiology, Daphnia/*microbiology/*physiology, Ecosystem, Fertility, Food Chain, Fresh Water/microbiology, *Symbiosis, Zooplankton/*microbiology/*physiologyPhylogeny
Metabolism29030444Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans.Kasalicky V, Zeng Y, Piwosz K, Simek K, Kratochvilova H, Koblizek MAppl Environ Microbiol10.1128/AEM.02116-172017Aerobiosis, Bacterial Proteins/*genetics/metabolism, Comamonadaceae/*genetics/metabolism, Genes, Bacterial/*physiology, Multigene Family/*physiology, Photosynthesis/*genetics, PhylogenyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15834Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21594)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21594
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
37665Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7634
61091Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56788)https://www.ccug.se/strain?id=56788
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
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
72555Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID371487.1StrainInfo: A central database for resolving microbial strain identifiers
121852Curators of the CIPCollection of Institut Pasteur (CIP 109844)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109844