Strain identifier

BacDive ID: 2983

Type strain: Yes

Species: Polaromonas hydrogenivorans

Strain Designation: DQ094183

Strain history: CIP <- 2007, DSMZ <- M. Sizova, Stevens Inst., Hoboken, USA: strain DQ094183

NCBI tax ID(s): 335476 (species)

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General

@ref: 6927

BacDive-ID: 2983

DSM-Number: 17735

keywords: 16S sequence, Bacteria, aerobe, chemolithotroph, psychrophilic, Gram-negative, coccus-shaped, colony-forming

description: Polaromonas hydrogenivorans DQ094183 is an aerobe, chemolithotroph, psychrophilic bacterium that forms circular colonies and was isolated from seasonally frozen forest soil.

NCBI tax id

  • NCBI tax id: 335476
  • Matching level: species

strain history

@refhistory
6927<- M. Sizova
120002CIP <- 2007, DSMZ <- M. Sizova, Stevens Inst., Hoboken, USA: strain DQ094183

doi: 10.13145/bacdive2983.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Polaromonas
  • species: Polaromonas hydrogenivorans
  • full scientific name: Polaromonas hydrogenivorans Sizova and Panikov 2007

@ref: 6927

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Polaromonas

species: Polaromonas hydrogenivorans

full scientific name: Polaromonas hydrogenivorans Sizova and Panikov 2007

strain designation: DQ094183

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
23089negative0.8-2.8 µmcoccus-shapedno
120002negativeoval-shapedno

colony morphology

@refcolony sizecolony colorcolony shapemedium used
230890.5-2 mmwhitecircularmineral agar
230892.0-5.0 mmshiny beigecircularnutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6927NUTRIENT 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
23089mineral agaryes
23089Nutrient agar (NA)yes
120002CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
6927positivegrowth10psychrophilic
23089positivegrowth0.0-25.0
23089nogrowth28.0mesophilic
23089positiveoptimum15.0-20.0psychrophilic

culture pH

  • @ref: 23089
  • ability: positive
  • type: optimum
  • pH: 6.0-7.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23089aerobe
120002obligate aerobe

nutrition type

@reftype
23089chemolithotroph
23089organotroph

spore formation

  • @ref: 23089
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2308915963ribitol-carbon source
2308918333D-arabitol-carbon source
2308912931D-galactonate-carbon source
2308930612D-glucarate-carbon source
2308917784D-glucosaminic acid-carbon source
2308916899D-mannitol-carbon source
2308923652dextrin-carbon source
2308916000ethanolamine-carbon source
2308928066gentiobiose-carbon source
2308917754glycerol-carbon source
2308973804glycyl L-aspartic acid-carbon source
2308930849L-arabinose-carbon source
2308918183L-pyroglutamic acid-carbon source
230896359lactulose-carbon source
2308917268myo-inositol-carbon source
2308973784glycyl-l-glutamate-carbon source
2308916452oxaloacetate-carbon source
2308927248urocanic acid-carbon source
2308917521(-)-quinic acid+carbon source
23089645522-hydroxybutyrate+carbon source
23089167632-oxobutanoate+carbon source
23089286442-oxopentanoate+carbon source
23089620642,3-butanediol+carbon source
23089370543-hydroxybutyrate+carbon source
23089167244-hydroxybutyrate+carbon source
23089181014-hydroxyphenylacetic acid+carbon source
2308930089acetate+carbon source
2308940585alpha-cyclodextrin+carbon source
2308973706bromosuccinate+carbon source
2308916383cis-aconitate+carbon source
2308915570D-alanine+carbon source
2308915824D-fructose+carbon source
2308912936D-galactose+carbon source
2308918024D-galacturonic acid+carbon source
230898391D-gluconate+carbon source
2308914314D-glucose 6-phosphate+carbon source
2308915748D-glucuronate+carbon source
2308927605D-psicose+carbon source
2308916236ethanol+carbon source
2308915740formate+carbon source
2308916865gamma-aminobutyric acid+carbon source
2308917234glucose+carbon source
2308928087glycogen+carbon source
2308917240itaconate+carbon source
2308929991L-aspartate+carbon source
2308962345L-rhamnose+carbon source
2308917115L-serine+carbon source
2308916857L-threonine+carbon source
2308915792malonate+carbon source
2308928053melibiose+carbon source
23089320055methyl beta-D-glucopyranoside+carbon source
2308951850methyl pyruvate+carbon source
2308975146monomethyl succinate+carbon source
2308916634raffinose+carbon source
2308941865sebacic acid+carbon source
23089143136succinamate+carbon source
2308917992sucrose+carbon source
2308927082trehalose+carbon source
2308932528turanose+carbon source
2308953423tween 40+carbon source
2308953426tween 80+carbon source
2308917151xylitol+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12000217632nitrate+reduction
12000216301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
230897507neomycinyesyes30 µg (disc)
2308928368novobiocinyesyes30 µg (disc)
2308917833gentamicinyesyes10 µg (disc)
2308917076streptomycinyesyes10 µg (disc)
2308927902tetracyclineyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12000235581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
23089catalase+1.11.1.6
23089cytochrome 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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
120002oxidase+
120002catalase+1.11.1.6
120002urease-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
120002-++--+----+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6927+---+---------------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture composition
6927seasonally frozen forest soilAlaska, FairbanksUSAUSANorth America
23089mineral mediumcontaining (l-1): 2 g K2HPO4, 1.5 g NaH2PO4, 1 g (NH4)2SO4, 0.1 g CaCl2, 0.4 g MgSO4, 0.01 g Na-EDTA, 1x10-3 g FeCl3.6H2O, 2x10-4 g KI, 2x10-4 g CoCl2.6H2O, 8x10-4 g MnCl2.4H2O, 8x10-4 g ZnSO4, 1x10-4 g H3BO3 , 1x10-4 g Na2MoO4.2H2O, 1x10-4 g CuCl2 and 10-4 g NiCl2.6H2O
120002Environment, Soil, seasonally frozen forestFairbanks, AlaskaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1546.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_884;97_1032;98_1221;99_1546&stattab=map
  • Last taxonomy: Polaromonas
  • 16S sequence: DQ094183
  • Sequence Identity:
  • Total samples: 2817
  • soil counts: 683
  • aquatic counts: 1647
  • animal counts: 380
  • plant counts: 107

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69271Risk group (German classification)
1200021Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6927
  • description: Polaromonas hydrogenivorans strain DSM 17735 16S ribosomal RNA gene, partial sequence
  • accession: DQ094183
  • length: 1384
  • database: ena
  • NCBI tax ID: 335476

GC content

@refGC-contentmethod
692762.5
2308962.5high performance liquid chromatography (HPLC)

External links

@ref: 6927

culture collection no.: DSM 17735, CIP 109586, NRRL B-41369

straininfo link

  • @ref: 72505
  • straininfo: 297298

literature

  • topic: Phylogeny
  • Pubmed-ID: 17329795
  • title: Polaromonas hydrogenivorans sp. nov., a psychrotolerant hydrogen-oxidizing bacterium from Alaskan soil.
  • authors: Sizova M, Panikov N
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64350-0
  • year: 2007
  • mesh: Alaska, Betaproteobacteria/*classification/genetics/isolation & purification/*metabolism, Cold Temperature, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Hydrogen/metabolism, Molecular Sequence Data, Oxidation-Reduction, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6927Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17735)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17735
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
23089Maria Sizova,Nicolai Panikov10.1099/ijs.0.64350-0Polaromonas hydrogenivorans sp. nov., a psychrotolerant hydrogen-oxidizing bacterium from Alaskan soilIJSEM 57: 616-619 200717329795
68369Automatically annotated from API 20NE
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
72505Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297298.1StrainInfo: A central database for resolving microbial strain identifiers
120002Curators of the CIPCollection of Institut Pasteur (CIP 109586)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109586