Strain identifier

BacDive ID: 2965

Type strain: Yes

Species: Hydrogenophaga palleronii

Strain Designation: 362

Strain history: CIP <- 1989, DSM <- R.Y. Stanier: strain 362, Pseudomonas palleronii <- D. Davis: strain 1-6-1

NCBI tax ID(s): 1349791 (strain), 65655 (species)

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General

@ref: 2046

BacDive-ID: 2965

DSM-Number: 63

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

description: Hydrogenophaga palleronii 362 is an aerobe, chemoorganotroph, mesophilic bacterium that has a nondiffusible yellow pigmentation and was isolated from water enriched for hydrogen bacteria.

NCBI tax id

NCBI tax idMatching level
65655species
1349791strain

strain history

@refhistory
2046<- IMG <- R.Y. Stanier, 362 <- N.J. Palleroni
67770IAM 14930 <-- DSM 63 <-- IMG <-- R. Y. Stanier 362 <-- N. J. Palleroni.
121511CIP <- 1989, DSM <- R.Y. Stanier: strain 362, Pseudomonas palleronii <- D. Davis: strain 1-6-1

doi: 10.13145/bacdive2965.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Hydrogenophaga
  • species: Hydrogenophaga palleronii
  • full scientific name: Hydrogenophaga palleronii (Davis 1970) Willems et al. 1989

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas palleronii

@ref: 2046

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Hydrogenophaga

species: Hydrogenophaga palleronii

full scientific name: Hydrogenophaga palleronii (Davis 1970) Willems et al. 1989

strain designation: 362

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23086negative0.6-5.5 µm0.3-0.6 µmrod-shapedyesmonotrichous
69480yes96.623
69480negative99.997

pigmentation

  • @ref: 23086
  • production: yes
  • color: nondiffusible yellow

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2046MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)yeshttps://mediadive.dsmz.de/medium/81Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
2046NUTRIENT 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
35525MEDIUM 18 - for Hydrogenophaga, Vogesella and Pseudomonas generayesDistilled water make up to (1000.000 ml);Sodium chloride (3.000 g);Agar(12.000 g);Yeast extract (3.000 g);Peptone (0.600 g)
121511CIP Medium 18yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=18

culture temp

@refgrowthtypetemperaturerange
2046positivegrowth30mesophilic
35525positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 23086
  • oxygen tolerance: aerobe

nutrition type

@reftype
23086chemoorganotroph
23086chemolithoautotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.956

compound production

  • @ref: 2046
  • compound: polyhydroxyalkanoic acids

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23086309162-oxoglutarate-carbon source
2308630089acetate-carbon source
2308622210aconitate-carbon source
2308616947citrate-carbon source
2308630924L-tartrate-carbon source
23086879973-aminobutyrate-growth
23086158875-aminovaleric acid-growth
2308643799butan-1-amine-growth
2308618333D-arabitol-growth
2308617057cellobiose-growth
2308615824D-fructose-growth
2308612936D-galactose-growth
2308616024D-mannose-growth
2308632528turanose-growth
2308665327D-xylose-growth
2308616000ethanolamine-growth
2308630849L-arabinose-growth
2308618287L-fucose-growth
2308615971L-histidine-growth
2308617716lactose-growth
2308617306maltose-growth
2308629864mannitol-growth
2308630911sorbitol-growth
2308617992sucrose-growth
2308617632nitrate-reduction
2308616301nitrite-reduction
2308615570D-alanine+carbon source
2308648942isovalerate+carbon source
2308617240itaconate+carbon source
2308616977L-alanine+carbon source
2308617191L-isoleucine+carbon source
2308615603L-leucine+carbon source
2308618347L-norleucine+carbon source
2308617295L-phenylalanine+carbon source
2308636405norleucine+carbon source
2308617774pimelate+carbon source
2308641865sebacic acid+carbon source
2308630043terephthalate+carbon source
2308631011valerate+carbon source
2308678208azelaate+growth
2308629805glycolate+growth

enzymes

  • @ref: 23086
  • value: cytochrome oxidase
  • activity: +
  • ec: 1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample type
23086water enriched for hydrogen bacteria
2046water
67770Atmosphere of 6% O2
121511Environment, Water enriched for isolation of hydrogen bacteria

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Host#Microbial#Bacteria

taxonmaps

  • @ref: 69479
  • File name: preview.99_6558.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_872;97_2609;98_3233;99_6558&stattab=map
  • Last taxonomy: Hydrogenophaga
  • 16S sequence: AF078769
  • Sequence Identity:
  • Total samples: 1
  • aquatic counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
20461Risk group (German classification)
1215111Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Hydrogenophaga palleronii 16S ribosomal RNA gene, partial sequenceAF0787691510ena65655
20218Hydrogenophaga palleronii 16S ribosomal RNA gene, complete sequenceAF0190731481ena65655
20218Hydrogenophaga palleronii gene for 16S rRNA, partial sequence, strain: NBRC 102513AB6818471454ena65655

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hydrogenophaga palleronii NBRC 1025131349791.3wgspatric1349791
66792Hydrogenophaga palleronii NBRC 1025132681813002draftimg1349791
67770Hydrogenophaga palleronii NBRC 102513GCA_001571225contigncbi1349791

GC content

@refGC-contentmethod
2308667.0thermal denaturation, midpoint method (Tm)
204666.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.586no
gram-positiveno98.819no
anaerobicno97.601no
halophileno93.064no
spore-formingno96.369no
glucose-utilno59.358no
thermophileno98.792yes
flagellatedyes80.326yes
aerobicyes96.284no
glucose-fermentno90.901no

External links

@ref: 2046

culture collection no.: DSM 63, ATCC 17724, Stanier 362, JCM 21412, BCRC 13886, CCM 4454, CCUG 1780, CCUG 20334, CECT 4107, CFBP 2445, CIP 103304, IAM 14930, LMG 2366, NBRC 102513, VKM B-1328

straininfo link

  • @ref: 72487
  • straininfo: 92268

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21282897Hydrogenophaga temperata sp. nov., a betaproteobacterium isolated from compost in Korea.Kim YJ, Kim MK, Weon HY, Kim HB, Yang DCJ Gen Appl Microbiol10.2323/jgam.56.4192010*Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny31661044Hydrogenophaga borbori sp. nov., isolated from activated sludge.Choi GM, Lee SY, Kim SY, Wee JH, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0037872020Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, UbiquinoneTranscriptome
Phylogeny33688800Hydrogenophaga aromaticivorans sp. nov., isolated from a para-xylene-degrading enrichment culture, capable of degrading benzene, meta- and para-xylene.Banerjee S, Tancsics A, Toth E, Revesz F, Boka K, Kriszt BInt J Syst Evol Microbiol10.1099/ijsem.0.0047432021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2046Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 63)https://www.dsmz.de/collection/catalogue/details/culture/DSM-63
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23086A. Willems,J. Busse,M. Goor,B. Pot,E. Falsen,E. Jantzen,B. Hoste,M. Gillis,K. Kersters,G. Auling,J. De Ley10.1099/00207713-39-3-319Hydrogenophaga, a New Genus of Hydrogen-Oxidizing Bacteria That Includes Hydrogenophaga flava comb. nov. (Formerly Pseudomonas flava), Hydrogenophaga palleronii (Formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (Formerly Pseudomonas pseudoflava and 'Pseudomonas carboxydoflava'), and Hydrogenophaga taeniospiralis (Formerly Pseudomonas taeniospiralis)IJSEM 39: 319-333 1989
35525Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15086
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/
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
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
72487Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92268.1StrainInfo: A central database for resolving microbial strain identifiers
121511Curators of the CIPCollection of Institut Pasteur (CIP 103304)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103304