Strain identifier

BacDive ID: 140763

Type strain: Yes

Species: Hydrogenophaga soli

Strain Designation: S10

Strain history: T. Seo; Dongguk Univ., South Korea; S10.

NCBI tax ID(s): 2025714 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 8.1 (current version)

General

@ref: 43541

BacDive-ID: 140763

keywords: 16S sequence, Bacteria, obligate aerobe, Gram-negative, motile, rod-shaped, colony-forming

description: Hydrogenophaga soli S10 is an obligate aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from soil sample collected in a rice field.

NCBI tax id

  • NCBI tax id: 2025714
  • Matching level: species

strain history

  • @ref: 67770
  • history: T. Seo; Dongguk Univ., South Korea; S10.

doi: 10.13145/bacdive140763.20230509.8.1

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 soli
  • full scientific name: Hydrogenophaga soli Yang et al. 2017

@ref: 43541

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Hydrogenophaga

species: Hydrogenophaga soli

strain designation: S10

type strain: yes

Morphology

cell morphology

  • @ref: 43541
  • gram stain: negative
  • cell length: 0.9-1.8 µm
  • cell width: 0.7-0.9 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous

colony morphology

  • @ref: 43541
  • colony color: transparent to white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 43541
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43541positivegrowth8-37
43541positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
43541positivegrowth6-8
43541positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43541
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 43541
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43541NaClpositivegrowth0 %(w/v)
43541NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4354130089acetate-assimilation
4354117128adipate-assimilation
4354127613amygdalin-assimilation
4354118305arbutin-assimilation
4354127689decanoate-assimilation
4354117057cellobiose-assimilation
4354116947citrate-assimilation
4354115963ribitol-assimilation
4354118333D-arabitol-assimilation
4354116899D-mannitol-assimilation
4354116988D-ribose-assimilation
4354117924D-sorbitol-assimilation
4354116443D-tagatose-assimilation
4354116551D-trehalose-assimilation
4354116813galactitol-assimilation
4354117113erythritol-assimilation
4354128066gentiobiose-assimilation
4354124265gluconate-assimilation
4354128087glycogen-assimilation
4354115443inulin-assimilation
4354117240itaconate-assimilation
4354130849L-arabinose-assimilation
4354118403L-arabitol-assimilation
4354115589L-malate-assimilation
4354162345L-rhamnose-assimilation
4354117115L-serine-assimilation
4354117266L-sorbose-assimilation
4354165328L-xylose-assimilation
4354117716lactose-assimilation
4354117306maltose-assimilation
435416731melezitose-assimilation
4354128053melibiose-assimilation
43541320061methyl alpha-D-glucopyranoside-assimilation
4354143943methyl alpha-D-mannoside-assimilation
4354174863methyl beta-D-xylopyranoside-assimilation
4354117268myo-inositol-assimilation
43541506227N-acetylglucosamine-assimilation
4354118401phenylacetate-assimilation
4354132032potassium gluconate-assimilation
4354117272propionate-assimilation
4354116634raffinose-assimilation
4354117814salicin-assimilation
4354162983sodium malonate-assimilation
4354128017starch-assimilation
435419300suberic acid-assimilation
4354117992sucrose-assimilation
4354132528turanose-assimilation
4354131011valerate-assimilation
4354117151xylitol-assimilation
4354128066gentiobiose-fermentation
4354124265gluconate-fermentation
4354117234glucose-fermentation
4354117268myo-inositol-fermentation
435415291gelatin-hydrolysis
43541168082-dehydro-D-gluconate+assimilation
43541178794-hydroxybenzoate+assimilation
43541581435-dehydro-D-gluconate+assimilation
4354116947citrate+assimilation
4354117108D-arabinose+assimilation
4354115824D-fructose+assimilation
4354128847D-fucose+assimilation
4354112936D-galactose+assimilation
4354117634D-glucose+assimilation
4354162318D-lyxose+assimilation
4354116024D-mannose+assimilation
4354165327D-xylose+assimilation
43541370543-hydroxybutyrate+assimilation
4354124996lactate+assimilation
435414853esculin+assimilation
4354117754glycerol+assimilation
4354128087glycogen+assimilation
4354116977L-alanine+assimilation
4354130849L-arabinose+assimilation
4354118287L-fucose+assimilation
4354115971L-histidine+assimilation
4354117203L-proline+assimilation
43541168082-dehydro-D-gluconate+fermentation
4354117108D-arabinose+fermentation
4354115824D-fructose+fermentation
4354128847D-fucose+fermentation
4354112936D-galactose+fermentation
4354162318D-lyxose+fermentation
4354116024D-mannose+fermentation
4354165327D-xylose+fermentation
4354130849L-arabinose+fermentation
4354118287L-fucose+fermentation
435414853esculin+hydrolysis
4354117632nitrate+reduction

metabolite production

  • @ref: 43541
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
43541catalase+1.11.1.6
43541cytochrome oxidase+1.9.3.1
43541esterase (C 4)+
43541esterase Lipase (C 8)+
43541lipase (C 14)+
43541valine arylamidase+
43541cystine arylamidase+3.4.11.3
43541acid phosphatase+3.1.3.2
43541naphthol-AS-BI-phosphohydrolase+
43541alpha-galactosidase+3.2.1.22
43541alkaline phosphatase-3.1.3.1
43541leucine arylamidase-3.4.11.1
43541trypsin-3.4.21.4
43541alpha-chymotrypsin-3.4.21.1
43541beta-galactosidase-3.2.1.23
43541beta-glucuronidase-3.2.1.31
43541alpha-glucosidase-3.2.1.20
43541beta-glucosidase-3.2.1.21
43541N-acetyl-beta-glucosaminidase-3.2.1.52
43541alpha-mannosidase-3.2.1.24
43541alpha-fucosidase-3.2.1.51
43541arginine dihydrolase-3.5.3.6
43541urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43541C15:0 anteiso16.4
    43541C15:1 anteiso1.5
    43541C16:1ω5c6.9
    43541C16:1ω7c / C16:1ω6c13.6
    43541C17:1I / anteiso-C17:1B10.7
    43541C14:0 iso1.8
    43541C15:0 iso18.2
    43541C15:0 iso 3OH2.1
    43541C15:1 iso G9
    43541C16:0 iso4.5
    43541C16:0 iso 3OH2.3
    43541C16:1 iso H6.7
    43541C17:0 iso1.1
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar plates
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.01
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43541soil sample collected in a rice fieldGoyang, Gyeonggi ProvinceRepublic of KoreaKORAsia37.674126.806
67770Soil in a rice field in GoyangRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

Sequence information

16S sequences

  • @ref: 43541
  • description: 16S rRNA gene sequence
  • accession: KX636167
  • database: nuccore

GC content

@refGC-contentmethod
4354168.2Thermal denaturation, fluorometry
6777068.2thermal denaturation, midpoint method (Tm)

External links

@ref: 43541

culture collection no.: KCTC 52520, JCM 31711

literature

  • topic: Phylogeny
  • Pubmed-ID: 28920826
  • title: Hydrogenophaga soli sp. nov., isolated from rice field soil.
  • authors: Yang D, Cha S, Choi J, Seo T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002277
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Oryza, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
43541Dahye Yang, Seho Cha, Jiwon Choi, Taegun SeoHydrogenophaga soli sp. nov., isolated from rice field soil10.1099/ijsem.0.002277IJSEM 67: 4200-4204 201728920826
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/