Strain identifier
BacDive ID: 140763
Type strain:
Species: Hydrogenophaga soli
Strain Designation: S10
Strain history: T. Seo; Dongguk Univ., South Korea; S10.
NCBI tax ID(s): 2025714 (species)
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
43541 | positive | growth | 8-37 | |
43541 | positive | optimum | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
43541 | positive | growth | 6-8 |
43541 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 43541
- oxygen tolerance: obligate aerobe
spore formation
- @ref: 43541
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration | halophily level |
---|---|---|---|---|---|
43541 | NaCl | positive | growth | 0 %(w/v) | |
43541 | NaCl | positive | optimum | 0 %(w/v) | non-halophilic |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43541 | 30089 | acetate | - | assimilation |
43541 | 17128 | adipate | - | assimilation |
43541 | 27613 | amygdalin | - | assimilation |
43541 | 18305 | arbutin | - | assimilation |
43541 | 27689 | decanoate | - | assimilation |
43541 | 17057 | cellobiose | - | assimilation |
43541 | 16947 | citrate | - | assimilation |
43541 | 15963 | ribitol | - | assimilation |
43541 | 18333 | D-arabitol | - | assimilation |
43541 | 16899 | D-mannitol | - | assimilation |
43541 | 16988 | D-ribose | - | assimilation |
43541 | 17924 | D-sorbitol | - | assimilation |
43541 | 16443 | D-tagatose | - | assimilation |
43541 | 16551 | D-trehalose | - | assimilation |
43541 | 16813 | galactitol | - | assimilation |
43541 | 17113 | erythritol | - | assimilation |
43541 | 28066 | gentiobiose | - | assimilation |
43541 | 24265 | gluconate | - | assimilation |
43541 | 28087 | glycogen | - | assimilation |
43541 | 15443 | inulin | - | assimilation |
43541 | 17240 | itaconate | - | assimilation |
43541 | 30849 | L-arabinose | - | assimilation |
43541 | 18403 | L-arabitol | - | assimilation |
43541 | 15589 | L-malate | - | assimilation |
43541 | 62345 | L-rhamnose | - | assimilation |
43541 | 17115 | L-serine | - | assimilation |
43541 | 17266 | L-sorbose | - | assimilation |
43541 | 65328 | L-xylose | - | assimilation |
43541 | 17716 | lactose | - | assimilation |
43541 | 17306 | maltose | - | assimilation |
43541 | 6731 | melezitose | - | assimilation |
43541 | 28053 | melibiose | - | assimilation |
43541 | 320061 | methyl alpha-D-glucopyranoside | - | assimilation |
43541 | 43943 | methyl alpha-D-mannoside | - | assimilation |
43541 | 74863 | methyl beta-D-xylopyranoside | - | assimilation |
43541 | 17268 | myo-inositol | - | assimilation |
43541 | 506227 | N-acetylglucosamine | - | assimilation |
43541 | 18401 | phenylacetate | - | assimilation |
43541 | 32032 | potassium gluconate | - | assimilation |
43541 | 17272 | propionate | - | assimilation |
43541 | 16634 | raffinose | - | assimilation |
43541 | 17814 | salicin | - | assimilation |
43541 | 62983 | sodium malonate | - | assimilation |
43541 | 28017 | starch | - | assimilation |
43541 | 9300 | suberic acid | - | assimilation |
43541 | 17992 | sucrose | - | assimilation |
43541 | 32528 | turanose | - | assimilation |
43541 | 31011 | valerate | - | assimilation |
43541 | 17151 | xylitol | - | assimilation |
43541 | 28066 | gentiobiose | - | fermentation |
43541 | 24265 | gluconate | - | fermentation |
43541 | 17234 | glucose | - | fermentation |
43541 | 17268 | myo-inositol | - | fermentation |
43541 | 5291 | gelatin | - | hydrolysis |
43541 | 16808 | 2-dehydro-D-gluconate | + | assimilation |
43541 | 17879 | 4-hydroxybenzoate | + | assimilation |
43541 | 58143 | 5-dehydro-D-gluconate | + | assimilation |
43541 | 16947 | citrate | + | assimilation |
43541 | 17108 | D-arabinose | + | assimilation |
43541 | 15824 | D-fructose | + | assimilation |
43541 | 28847 | D-fucose | + | assimilation |
43541 | 12936 | D-galactose | + | assimilation |
43541 | 17634 | D-glucose | + | assimilation |
43541 | 62318 | D-lyxose | + | assimilation |
43541 | 16024 | D-mannose | + | assimilation |
43541 | 65327 | D-xylose | + | assimilation |
43541 | 37054 | 3-hydroxybutyrate | + | assimilation |
43541 | 24996 | lactate | + | assimilation |
43541 | 4853 | esculin | + | assimilation |
43541 | 17754 | glycerol | + | assimilation |
43541 | 28087 | glycogen | + | assimilation |
43541 | 16977 | L-alanine | + | assimilation |
43541 | 30849 | L-arabinose | + | assimilation |
43541 | 18287 | L-fucose | + | assimilation |
43541 | 15971 | L-histidine | + | assimilation |
43541 | 17203 | L-proline | + | assimilation |
43541 | 16808 | 2-dehydro-D-gluconate | + | fermentation |
43541 | 17108 | D-arabinose | + | fermentation |
43541 | 15824 | D-fructose | + | fermentation |
43541 | 28847 | D-fucose | + | fermentation |
43541 | 12936 | D-galactose | + | fermentation |
43541 | 62318 | D-lyxose | + | fermentation |
43541 | 16024 | D-mannose | + | fermentation |
43541 | 65327 | D-xylose | + | fermentation |
43541 | 30849 | L-arabinose | + | fermentation |
43541 | 18287 | L-fucose | + | fermentation |
43541 | 4853 | esculin | + | hydrolysis |
43541 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 43541
- Chebi-ID: 35581
- metabolite: indole
- production: yes
enzymes
@ref | value | activity | ec |
---|---|---|---|
43541 | catalase | + | 1.11.1.6 |
43541 | cytochrome oxidase | + | 1.9.3.1 |
43541 | esterase (C 4) | + | |
43541 | esterase Lipase (C 8) | + | |
43541 | lipase (C 14) | + | |
43541 | valine arylamidase | + | |
43541 | cystine arylamidase | + | 3.4.11.3 |
43541 | acid phosphatase | + | 3.1.3.2 |
43541 | naphthol-AS-BI-phosphohydrolase | + | |
43541 | alpha-galactosidase | + | 3.2.1.22 |
43541 | alkaline phosphatase | - | 3.1.3.1 |
43541 | leucine arylamidase | - | 3.4.11.1 |
43541 | trypsin | - | 3.4.21.4 |
43541 | alpha-chymotrypsin | - | 3.4.21.1 |
43541 | beta-galactosidase | - | 3.2.1.23 |
43541 | beta-glucuronidase | - | 3.2.1.31 |
43541 | alpha-glucosidase | - | 3.2.1.20 |
43541 | beta-glucosidase | - | 3.2.1.21 |
43541 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43541 | alpha-mannosidase | - | 3.2.1.24 |
43541 | alpha-fucosidase | - | 3.2.1.51 |
43541 | arginine dihydrolase | - | 3.5.3.6 |
43541 | urease | - | 3.5.1.5 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43541 C15:0 anteiso 16.4 43541 C15:1 anteiso 1.5 43541 C16:1ω5c 6.9 43541 C16:1ω7c / C16:1ω6c 13.6 43541 C17:1I / anteiso-C17:1B 10.7 43541 C14:0 iso 1.8 43541 C15:0 iso 18.2 43541 C15:0 iso 3OH 2.1 43541 C15:1 iso G 9 43541 C16:0 iso 4.5 43541 C16:0 iso 3OH 2.3 43541 C16:1 iso H 6.7 43541 C17:0 iso 1.1 - 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
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
43541 | soil sample collected in a rice field | Goyang, Gyeonggi Province | Republic of Korea | KOR | Asia | 37.674 | 126.806 |
67770 | Soil in a rice field in Goyang | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | GC-content | method |
---|---|---|
43541 | 68.2 | Thermal denaturation, fluorometry |
67770 | 68.2 | thermal 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
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
43541 | Dahye Yang, Seho Cha, Jiwon Choi, Taegun Seo | Hydrogenophaga soli sp. nov., isolated from rice field soil | 10.1099/ijsem.0.002277 | IJSEM 67: 4200-4204 2017 | 28920826 |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ |