Strain identifier

BacDive ID: 2968

Type strain: Yes

Species: Hydrogenophaga taeniospiralis

Strain Designation: 2K1

Strain history: CIP <- 2000, CCM <- LMG <- DSMZ <- IMG <- L. Lalucat: strain 2K1

NCBI tax ID(s): 1281780 (strain), 65656 (species)

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General

@ref: 716

BacDive-ID: 2968

DSM-Number: 2082

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

description: Hydrogenophaga taeniospiralis 2K1 is an aerobe, chemoorganotroph, mesophilic bacterium that has a nondiffusible yellow pigmentation and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1281780strain
65656species

strain history

@refhistory
716<- IMG <- L. Lalucat, 2K1
67770IAM 14929 <-- DSM 2082 <-- IMG <-- L. Lalucat 2K1.
123412CIP <- 2000, CCM <- LMG <- DSMZ <- IMG <- L. Lalucat: strain 2K1

doi: 10.13145/bacdive2968.20230509.8.1

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 taeniospiralis
  • full scientific name: Hydrogenophaga taeniospiralis (Lalucat et al. 1982) Willems et al. 1989

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas taeniospiralis

@ref: 716

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Hydrogenophaga

species: Hydrogenophaga taeniospiralis

full scientific name: Hydrogenophaga taeniospiralis (Lalucat et al. 1982) Willems et al. 1989

strain designation: 2K1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
23086negative0.6-5.5 µm0.3-0.6 µmrod-shapedyesmonotrichous
123412negativerod-shapedyes

colony morphology

  • @ref: 23086
  • type of hemolysis: gamma

pigmentation

@refproductioncolorname
23086yesnondiffusible yellow
123412noPyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
716MINERAL 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
716NUTRIENT 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
39561MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
123412CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
716positivegrowth30mesophilic
23086nogrowth37.0mesophilic
23086positivegrowth30.0mesophilic
23086nogrowth42.0thermophilic
39561positivegrowth30mesophilic
67770positivegrowth30mesophilic
123412positivegrowth25-37mesophilic
123412nogrowth5psychrophilic
123412nogrowth10psychrophilic
123412nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 23086
  • oxygen tolerance: aerobe

nutrition type

@reftype
23086chemoorganotroph
23086chemolithoautotroph

halophily

@refsaltgrowthtested relationconcentration
23086NaClnogrowth0.5 %
23086NaClnogrowth1.5 %
23086NaClnogrowth3.0 %
23086NaClnogrowth4.5 %
23086NaClnogrowth6.5 %
123412NaClpositivegrowth0 %
123412NaClnogrowth2 %
123412NaClnogrowth4 %
123412NaClnogrowth6 %
123412NaClnogrowth8 %
123412NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2308632382(R)-mandelate-carbon source
23086165672-aminobenzoate-carbon source
23086283402-aminobutyrate-carbon source
23086194752-aminopentanoic acid-carbon source
23086168082-dehydro-D-gluconate-carbon source
2308630762salicylate-carbon source
23086307613-aminobenzoate-carbon source
23086161933-hydroxybenzoate-carbon source
23086178364-aminobenzoate-carbon source
23086178794-hydroxybenzoate-carbon source
23086174265-dehydro-D-gluconate-carbon source
2308627856acetamide-carbon source
2308630089acetate-carbon source
2308622210aconitate-carbon source
2308617128adipate-carbon source
2308615963ribitol-carbon source
2308627613amygdalin-carbon source
2308618305arbutin-carbon source
2308616150benzoate-carbon source
2308640538benzylamine-carbon source
2308616958beta-alanine-carbon source
2308617750betaine-carbon source
2308627689decanoate-carbon source
2308625646octanoate-carbon source
2308630719citraconate-carbon source
2308616947citrate-carbon source
2308616919creatine-carbon source
2308615570D-alanine-carbon source
2308617108D-arabinose-carbon source
2308628847D-fucose-carbon source
2308662318D-lyxose-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
2308632528turanose-carbon source
2308616813galactitol-carbon source
2308617113erythritol-carbon source
230864853esculin-carbon source
2308615862ethylamine-carbon source
2308628066gentiobiose-carbon source
230865417glucosamine-carbon source
2308615428glycine-carbon source
2308628087glycogen-carbon source
2308629805glycolate-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
2308616977L-alanine-carbon source
2308618403L-arabitol-carbon source
2308616349L-citrulline-carbon source
2308617561L-cysteine-carbon source
2308615971L-histidine-carbon source
2308618019L-lysine-carbon source
2308616643L-methionine-carbon source
2308618347L-norleucine-carbon source
2308617115L-serine-carbon source
2308617266L-sorbose-carbon source
2308630924L-tartrate-carbon source
2308616857L-threonine-carbon source
2308616414L-valine-carbon source
2308665328L-xylose-carbon source
2308617716lactose-carbon source
2308618300maleic acid-carbon source
2308615792malonate-carbon source
2308617306maltose-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
2308636405norleucine-carbon source
2308630623oxalate-carbon source
2308674848pentan-1-amine-carbon source
2308618401phenylacetate-carbon source
2308617563phthalate-carbon source
2308617774pimelate-carbon source
2308617272propionate-carbon source
2308617814salicin-carbon source
2308615611sarcosine-carbon source
2308628017starch-carbon source
2308630043terephthalate-carbon source
2308627082trehalose-carbon source
2308618123trigonelline-carbon source
2308616765tryptamine-carbon source
2308616199urea-carbon source
2308631011valerate-carbon source
2308617151xylitol-carbon source
23086879973-aminobutyrate-growth
230863565cetrimide-growth
2308632528turanose-growth
2308629805glycolate-growth
2308618287L-fucose-growth
2308615971L-histidine-growth
2308617716lactose-growth
2308617306maltose-growth
2308627856acetamide-hydrolysis
2308629991L-aspartate+carbon source
2308632800(S)-mandelic acid+carbon source
23086309162-oxoglutarate+carbon source
23086879973-aminobutyrate+carbon source
2308616865gamma-aminobutyric acid+carbon source
23086391504-oxopentanoate+carbon source
23086158875-aminovaleric acid+carbon source
2308678208azelaate+carbon source
2308643799butan-1-amine+carbon source
2308617968butyrate+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
2308665327D-xylose+carbon source
23086370543-hydroxybutyrate+carbon source
2308633871glycerate+carbon source
2308624996lactate+carbon source
2308616000ethanolamine+carbon source
2308629806fumarate+carbon source
2308624265gluconate+carbon source
2308617859glutaric acid+carbon source
2308617754glycerol+carbon source
2308617268myo-inositol+carbon source
2308630849L-arabinose+carbon source
2308616467L-arginine+carbon source
2308618287L-fucose+carbon source
2308629985L-glutamate+carbon source
2308617191L-isoleucine+carbon source
2308615603L-leucine+carbon source
2308615589L-malate+carbon source
2308615729L-ornithine+carbon source
2308617295L-phenylalanine+carbon source
2308617203L-proline+carbon source
2308662345L-rhamnose+carbon source
2308616828L-tryptophan+carbon source
2308617895L-tyrosine+carbon source
2308629864mannitol+carbon source
2308617148putrescine+carbon source
2308615361pyruvate+carbon source
2308641865sebacic acid+carbon source
2308630911sorbitol+carbon source
2308615746spermine+carbon source
230869300suberic acid+carbon source
2308630031succinate+carbon source
2308617992sucrose+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
2308665327D-xylose+growth
2308616000ethanolamine+growth
2308630849L-arabinose+growth
2308629864mannitol+growth
2308630911sorbitol+growth
2308617992sucrose+growth
230864853esculin+hydrolysis
2308653426tween 80+hydrolysis
2308617632nitrate+reduction
2308616301nitrite+reduction
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
12341216947citrate-carbon source
1234124853esculin+hydrolysis
12341217632nitrate+reduction
12341216301nitrite+reduction
12341217632nitrate+respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitive
2308617334penicillinyesno10 µg (disc)
1234120129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesyesno

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12341235581indoleno

metabolite tests

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

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-glucosidase-3.2.1.20
23086alpha-mannosidase-3.2.1.24
23086arginine dihydrolase-3.5.3.6
23086beta-galactosidase-3.2.1.23
23086beta-glucosidase+3.2.1.21
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
23086lipase (C 14)-
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
23086urease+3.5.1.5
23086valine arylamidase-
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
68382beta-glucuronidase-3.2.1.31
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)+
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123412oxidase+
123412beta-galactosidase+3.2.1.23
123412alcohol dehydrogenase-1.1.1.1
123412gelatinase+/-
123412amylase-
123412DNase-
123412caseinase-3.4.21.50
123412catalase-1.11.1.6
123412tween esterase-
123412lecithinase-
123412lipase-
123412lysine decarboxylase-4.1.1.18
123412ornithine decarboxylase-4.1.1.17
123412protease-
123412tryptophan deaminase-
123412urease+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
46387--++-+----------+---
123412-+++-+----++++-++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
46387+----+-+++-+--+--+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123412+++-+--+--+----+----++-++-+----+++-++-----------+++---++-++-+-+-+------+++-+---++++++---+++++++--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
716soilnear BarcelonaSpainESPEurope
46387Soilnear BarcelonaSpainESPEurope
67770SoilSpainESPEurope
123412Environment, SoilSpainESPEurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6546.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_872;97_2609;98_4833;99_6546&stattab=map
  • Last taxonomy: Hydrogenophaga
  • 16S sequence: AF078768
  • Sequence Identity:
  • Total samples: 572
  • soil counts: 12
  • aquatic counts: 515
  • animal counts: 29
  • plant counts: 16

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
7161Risk group (German classification)
1234121Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Hydrogenophaga taeniospiralis 16S ribosomal RNA gene, partial sequenceAF0787681514ena1281780
20218Hydrogenophaga taeniospiralis gene for 16S rRNA, partial sequence, strain: NBRC 102512AB6818461458ena1281780

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hydrogenophaga taeniospiralis NBRC 1025121349793.3wgspatric1281780
66792Hydrogenophaga taeniospiralis NBRC 1025122731957688draftimg1349793
67770Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512GCA_001592305contigncbi1281780

GC content

@refGC-contentmethod
2308665.0thermal denaturation, midpoint method (Tm)
71660.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.873no
gram-positiveno99.089yes
anaerobicno97.688no
halophileno91.393no
spore-formingno94.069no
glucose-utilyes81.895yes
thermophileno98.601no
flagellatedyes86.015yes
aerobicyes90.239yes
glucose-fermentno88.797yes

External links

@ref: 716

culture collection no.: DSM 2082, ATCC 49743, CCUG 15921, LMG 7170, JCM 21411, CIP 106727, IAM 14929, KCTC 12153, NBRC 102512, CCM 4458

straininfo link

  • @ref: 72490
  • straininfo: 14284

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
716Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2082)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2082
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
39561Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18890
46387Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15921)https://www.ccug.se/strain?id=15921
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/
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
72490Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14284.1StrainInfo: A central database for resolving microbial strain identifiers
123412Curators of the CIPCollection of Institut Pasteur (CIP 106727)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106727