Strain identifier

BacDive ID: 2966

Type strain: Yes

Species: Hydrogenophaga pseudoflava

Strain Designation: GA3, GA 3

Strain history: CIP <- 1989, DSMZ, Pseudomonas pseudoflava <- G. Auling: strain GA 3

NCBI tax ID(s): 1349792 (strain), 47421 (species)

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General

@ref: 479

BacDive-ID: 2966

DSM-Number: 1034

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

description: Hydrogenophaga pseudoflava GA3 is an aerobe, chemoorganotroph, mesophilic bacterium that has a nondiffusible yellow pigmentation and was isolated from water samples.

NCBI tax id

NCBI tax idMatching level
47421species
1349792strain

strain history

@refhistory
479<- G. Auling, GA3
67770IAM 14928 <-- DSM 1034 <-- G. Auling GA3.
121988CIP <- 1989, DSMZ, Pseudomonas pseudoflava <- G. Auling: strain GA 3

doi: 10.13145/bacdive2966.20230509.8.1

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 pseudoflava
  • full scientific name: Hydrogenophaga pseudoflava (Auling et al. 1978) Willems et al. 1989

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas pseudoflava

@ref: 479

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Hydrogenophaga

species: Hydrogenophaga pseudoflava

full scientific name: Hydrogenophaga pseudoflava (Auling et al. 1978) Willems et al. 1989

strain designation: GA3, GA 3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23086negative0.6-5.5 µm0.3-0.6 µmrod-shapedyesmonotrichous
69480yes94.321
69480negative99.996

colony morphology

  • @ref: 23086
  • type of hemolysis: gamma

pigmentation

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
479NUTRIENT 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
37136MEDIUM 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)
121988CIP Medium 18yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=18

culture temp

@refgrowthtypetemperaturerange
479positivegrowth35mesophilic
23086positivegrowth30.0mesophilic
23086positivegrowth37.0mesophilic
23086nogrowth42.0thermophilic
37136positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 23086
  • oxygen tolerance: aerobe

nutrition type

@reftype
23086chemoorganotroph
23086chemolithoautotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.994

compound production

@refcompound
479hydrogenase
479poly-ß hydroxyalkanoates
479PHA

halophily

@refsaltgrowthtested relationconcentration
23086NaClpositivegrowth0.5 %
23086NaClnogrowth1.5 %
23086NaClnogrowth3.0 %
23086NaClnogrowth4.5 %
23086NaClnogrowth6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2308632382(R)-mandelate-carbon source
23086165672-aminobenzoate-carbon source
23086168082-dehydro-D-gluconate-carbon source
2308630762salicylate-carbon source
23086309162-oxoglutarate-carbon source
23086307613-aminobenzoate-carbon source
23086879973-aminobutyrate-carbon source
23086178364-aminobenzoate-carbon source
23086174265-dehydro-D-gluconate-carbon source
2308627856acetamide-carbon source
2308622210aconitate-carbon source
2308617128adipate-carbon source
2308615963ribitol-carbon source
2308627613amygdalin-carbon source
2308618305arbutin-carbon source
2308616150benzoate-carbon source
2308616958beta-alanine-carbon source
2308617750betaine-carbon source
2308627689decanoate-carbon source
2308625646octanoate-carbon source
2308630719citraconate-carbon source
2308616919creatine-carbon source
2308617108D-arabinose-carbon source
2308628847D-fucose-carbon source
230866731melezitose-carbon source
2308628053melibiose-carbon source
2308616634raffinose-carbon source
2308616988D-ribose-carbon source
2308616443D-tagatose-carbon source
2308630927D-tartrate-carbon source
2308616296D-tryptophan-carbon source
2308616813galactitol-carbon source
2308617113erythritol-carbon source
230864853esculin-carbon source
2308615862ethylamine-carbon source
2308628066gentiobiose-carbon source
230865417glucosamine-carbon source
2308617859glutaric acid-carbon source
2308615428glycine-carbon source
2308628087glycogen-carbon source
2308632362heptanoate-carbon source
2308618295histamine-carbon source
2308615443inulin-carbon source
2308648944isobutyrate-carbon source
2308630803isophthalate-carbon source
2308648942isovalerate-carbon source
2308617240itaconate-carbon source
2308628683kynurenine-carbon source
2308618403L-arabitol-carbon source
2308616349L-citrulline-carbon source
2308617561L-cysteine-carbon source
2308618287L-fucose-carbon source
2308616643L-methionine-carbon source
2308617266L-sorbose-carbon source
2308665328L-xylose-carbon source
2308618300maleic acid-carbon source
2308615792malonate-carbon source
2308636986mesaconate-carbon source
2308630928meso-tartrate-carbon source
23086320061methyl alpha-D-glucopyranoside-carbon source
2308643943methyl alpha-D-mannoside-carbon source
2308674863methyl beta-D-xylopyranoside-carbon source
23086506227N-acetylglucosamine-carbon source
2308632361nonanoate-carbon source
2308630623oxalate-carbon source
2308618401phenylacetate-carbon source
2308617563phthalate-carbon source
2308617774pimelate-carbon source
2308615611sarcosine-carbon source
2308628017starch-carbon source
2308630043terephthalate-carbon source
2308618123trigonelline-carbon source
2308616765tryptamine-carbon source
2308616199urea-carbon source
2308617151xylitol-carbon source
23086879973-aminobutyrate-growth
230863565cetrimide-growth
2308618287L-fucose-growth
230865291gelatin-hydrolysis
2308629991L-aspartate+carbon source
2308632800(S)-mandelic acid+carbon source
23086283402-aminobutyrate+carbon source
23086194752-aminopentanoic acid+carbon source
23086161933-hydroxybenzoate+carbon source
2308616865gamma-aminobutyric acid+carbon source
23086178794-hydroxybenzoate+carbon source
23086391504-oxopentanoate+carbon source
23086158875-aminovaleric acid+carbon source
2308630089acetate+carbon source
2308678208azelaate+carbon source
2308640538benzylamine+carbon source
2308643799butan-1-amine+carbon source
2308617968butyrate+carbon source
2308627689decanoate+carbon source
2308615570D-alanine+carbon source
2308618333D-arabitol+carbon source
2308617057cellobiose+carbon source
2308615824D-fructose+carbon source
2308612936D-galactose+carbon source
2308617634D-glucose+carbon source
2308615588D-malate+carbon source
2308616024D-mannose+carbon source
2308632528turanose+carbon source
2308665327D-xylose+carbon source
23086370543-hydroxybutyrate+carbon source
2308633871glycerate+carbon source
2308624996lactate+carbon source
2308616000ethanolamine+carbon source
2308629806fumarate+carbon source
2308624265gluconate+carbon source
2308617754glycerol+carbon source
2308629805glycolate+carbon source
2308617268myo-inositol+carbon source
2308648942isovalerate+carbon source
2308616977L-alanine+carbon source
2308630849L-arabinose+carbon source
2308616467L-arginine+carbon source
2308629985L-glutamate+carbon source
2308615971L-histidine+carbon source
2308617191L-isoleucine+carbon source
2308615603L-leucine+carbon source
2308618019L-lysine+carbon source
2308615589L-malate+carbon source
2308618347L-norleucine+carbon source
2308615729L-ornithine+carbon source
2308617295L-phenylalanine+carbon source
2308617203L-proline+carbon source
2308617115L-serine+carbon source
2308616857L-threonine+carbon source
2308616828L-tryptophan+carbon source
2308617895L-tyrosine+carbon source
2308616414L-valine+carbon source
2308617716lactose+carbon source
2308617306maltose+carbon source
2308629864mannitol+carbon source
2308674848pentan-1-amine+carbon source
2308617272propionate+carbon source
2308617148putrescine+carbon source
2308615361pyruvate+carbon source
2308617814salicin+carbon source
2308641865sebacic acid+carbon source
2308630911sorbitol+carbon source
2308615746spermine+carbon source
230869300suberic acid+carbon source
2308630031succinate+carbon source
2308617992sucrose+carbon source
2308627082trehalose+carbon source
2308631011valerate+carbon source
23086158875-aminovaleric acid+growth
2308678208azelaate+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
2308629805glycolate+growth
2308630849L-arabinose+growth
2308615971L-histidine+growth
2308617716lactose+growth
2308617306maltose+growth
2308629864mannitol+growth
2308630911sorbitol+growth
2308617992sucrose+growth
230864853esculin+hydrolysis
2308653426tween 80+hydrolysis
2308617632nitrate+reduction
2308616301nitrite+reduction

antibiotic resistance

  • @ref: 23086
  • ChEBI: 17334
  • metabolite: penicillin
  • is antibiotic: yes
  • is resistant: no
  • resistance conc.: 10 µg (disc)

enzymes

@refvalueactivityec
23086acid phosphatase-3.1.3.2
23086alpha-chymotrypsin-3.4.21.1
23086alpha-fucosidase-3.2.1.51
23086alpha-galactosidase-3.2.1.22
23086alpha-mannosidase-3.2.1.24
23086amylase-
23086arginine dihydrolase-3.5.3.6
23086beta-galactosidase+3.2.1.23
23086beta-galactosidase-3.2.1.23
23086beta-glucuronidase-3.2.1.31
23086catalase-1.11.1.6
23086cystine arylamidase-3.4.11.3
23086cytochrome oxidase+1.9.3.1
23086esterase (C 4)+
23086esterase lipase (C 8)+
23086leucine arylamidase+3.4.11.1
23086lysine decarboxylase-4.1.1.18
23086N-acetyl-beta-glucosaminidase-3.2.1.52
23086naphthol-AS-BI-phosphohydrolase-
23086ornithine decarboxylase-4.1.1.17
23086trypsin-3.4.21.4
23086valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
479water samplesGöttingen, River WeendeGermanyDEUEurope
23086soil, mud and water by enrichment for hydrogen bacteria
46016Water,riverGöttingen, River WeendeGermanyDEUEurope
67770River waterGöttingenGermanyDEUEurope
121988Environment, Water, riverGöttingenGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Terrestrial#Soil
#Host#Microbial#Bacteria
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1523.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_872;97_1019;98_1202;99_1523&stattab=map
  • Last taxonomy: Hydrogenophaga
  • 16S sequence: AF078770
  • Sequence Identity:
  • Total samples: 737
  • soil counts: 9
  • aquatic counts: 295
  • animal counts: 23
  • plant counts: 410

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
4791Risk group (German classification)
1219881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Hydrogenophaga pseudoflava 16S ribosomal RNA gene, partial sequenceAF0787701513ena47421
20218Hydrogenophaga pseudoflava 16S rRNA gene, strain DSM 1034AJ4203271469ena47421
20218Hydrogenophaga pseudoflava gene for 16S rRNA, partial sequence, strain: NBRC 102511AB6818451454ena47421

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hydrogenophaga pseudoflava NBRC 1025111349792.3wgspatric1349792
66792Hydrogenophaga pseudoflava NBRC 1025112731957687draftimg1349792
67770Hydrogenophaga pseudoflava NBRC 102511 NBRC 102511GCA_001592285contigncbi1349792

GC content

@refGC-contentmethod
2308666.0thermal denaturation, midpoint method (Tm)
47966.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.675yes
gram-positiveno99.245no
anaerobicno96.894yes
halophileno97.311no
spore-formingno95.103no
glucose-utilyes58.104no
thermophileno97.487no
flagellatedyes88.365yes
aerobicyes85.928yes
glucose-fermentno90.862no

External links

@ref: 479

culture collection no.: DSM 1034, ATCC 33668, CCUG 13799, LMG 5945, JCM 21410, BCRC 13892, CCM 4455, CFBP 2439, CIP 103270, IAM 14928, KACC 10200, NBRC 102511

straininfo link

  • @ref: 72488
  • straininfo: 3016

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
22767883The Importance of Accurate Microorganism Identification in Microbial Challenge Tests of Membrane Filters. Part II. The Comparison of Hydrogenophaga pseudoflava ATTC 33668 and Curvibacter sp. ATCC 700892 by Microbial Challenge Tests with Membrane Filters.Haake G, Kaesler-Neumann I, Hennig H, Meltzer TH, Jornitz MWPDA J Pharm Sci Technol10.5731/pdajpst.2012.008762012Colony Count, Microbial, Comamonadaceae, *Filtration, Microbial Sensitivity Tests, Micropore Filters, Sterilization, *Ultrafiltration
Metabolism23201074Polyhydroxyalkanoate biosynthesis by Hydrogenophaga pseudoflava DSM1034 from structurally unrelated carbon sources.Povolo S, Romanelli MG, Basaglia M, Ilieva VI, Corti A, Morelli A, Chiellini E, Casella SN Biotechnol10.1016/j.nbt.2012.11.0192012Carbon/metabolism, Comamonadaceae/growth & development/*metabolism, *Food Industry, *Industrial Waste, Magnetic Resonance Spectroscopy, Polyhydroxyalkanoates/*biosynthesis, Sucrose/metabolism/pharmacologyBiotechnology
Phylogeny26154498Hydrogenophaga luteola sp. nov. isolated from reed pond water.Du J, Yang JE, Singh H, Akter S, Won K, Yin CS, Jin FX, Yi THAntonie Van Leeuwenhoek10.1007/s10482-015-0525-02015Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Comamonadaceae/*classification/genetics/*isolation & purification/physiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Ponds/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
479Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1034)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1034
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
37136Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15049
46016Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 13799)https://www.ccug.se/strain?id=13799
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
72488Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3016.1StrainInfo: A central database for resolving microbial strain identifiers
121988Curators of the CIPCollection of Institut Pasteur (CIP 103270)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103270