Name: Hydrogenophaga soli S10
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140763

Type strain:

Species: Hydrogenophaga soli

Strain Designation: S10

Culture col. no.: KCTC 52520, JCM 31711

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

NCBI tax ID(s): 2025714 (species)

Section

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.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Hydrogenophaga*
	Species	**Hydrogenophaga soli**
	Full Scientific Name (LPSN)	Hydrogenophaga soli Yang et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43541]	Gram stain	negative

[Ref.: #43541]	Cell length	0.9-1.8 µm

[Ref.: #43541]	Cell width	0.7-0.9 µm

[Ref.: #43541]	Cell shape	rod-shaped

[Ref.: #43541]	Motility	yes

[Ref.: #43541]	Flagellum arrangement	monotrichous

[Ref.: #43541]	Colony color	transparent to white
[Ref.: #43541]	Colony shape	circular
[Ref.: #43541]	Incubation period	2 days
[Ref.: #43541]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

		Temperature
[Ref.: #43541]	growth	8-37 °C
[Ref.: #43541]	optimum	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #43541]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43541]			optimum	7
[Ref.: #43541]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

obligate aerobe

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Ability of spore formation

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Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43541]		NaCl		growth	0	%(w/v)
[Ref.: #43541]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43541]	2-dehydro-D-gluconate ChEBI	+	assimilation
[Ref.: #43541]	2-dehydro-D-gluconate ChEBI	+	fermentation
[Ref.: #43541]	3-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #43541]	4-hydroxybenzoate ChEBI	+	assimilation
[Ref.: #43541]	5-dehydro-D-gluconate ChEBI	+	assimilation
[Ref.: #43541]	acetate ChEBI	-	assimilation
[Ref.: #43541]	adipate ChEBI	-	assimilation
[Ref.: #43541]	amygdalin ChEBI	-	assimilation
[Ref.: #43541]	arbutin ChEBI	-	assimilation
[Ref.: #43541]	cellobiose ChEBI	-	assimilation
[Ref.: #43541]	citrate ChEBI	-	assimilation
[Ref.: #43541]	citrate ChEBI	+	assimilation
[Ref.: #43541]	D-arabinose ChEBI	+	assimilation
[Ref.: #43541]	D-arabinose ChEBI	+	fermentation
[Ref.: #43541]	D-arabitol ChEBI	-	assimilation
[Ref.: #43541]	D-fructose ChEBI	+	assimilation
[Ref.: #43541]	D-fructose ChEBI	+	fermentation
[Ref.: #43541]	D-fucose ChEBI	+	assimilation
[Ref.: #43541]	D-fucose ChEBI	+	fermentation
[Ref.: #43541]	D-galactose ChEBI	+	assimilation
[Ref.: #43541]	D-galactose ChEBI	+	fermentation
[Ref.: #43541]	D-glucose ChEBI	+	assimilation
[Ref.: #43541]	D-lyxose ChEBI	+	assimilation
[Ref.: #43541]	D-lyxose ChEBI	+	fermentation
[Ref.: #43541]	D-mannitol ChEBI	-	assimilation
[Ref.: #43541]	D-mannose ChEBI	+	assimilation
[Ref.: #43541]	D-mannose ChEBI	+	fermentation
[Ref.: #43541]	D-ribose ChEBI	-	assimilation
[Ref.: #43541]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43541]	D-tagatose ChEBI	-	assimilation
[Ref.: #43541]	D-trehalose ChEBI	-	assimilation
[Ref.: #43541]	D-xylose ChEBI	+	assimilation
[Ref.: #43541]	D-xylose ChEBI	+	fermentation
[Ref.: #43541]	decanoate ChEBI	-	assimilation
[Ref.: #43541]	erythritol ChEBI	-	assimilation
[Ref.: #43541]	esculin ChEBI	+	assimilation
[Ref.: #43541]	esculin ChEBI	+	hydrolysis
[Ref.: #43541]	galactitol ChEBI	-	assimilation
[Ref.: #43541]	gelatin ChEBI	-	hydrolysis
[Ref.: #43541]	gentiobiose ChEBI	-	assimilation
[Ref.: #43541]	gentiobiose ChEBI	-	fermentation
[Ref.: #43541]	gluconate ChEBI	-	assimilation
[Ref.: #43541]	gluconate ChEBI	-	fermentation
[Ref.: #43541]	glucose ChEBI	-	fermentation
[Ref.: #43541]	glycerol ChEBI	+	assimilation
[Ref.: #43541]	glycogen ChEBI	-	assimilation
[Ref.: #43541]	glycogen ChEBI	+	assimilation
[Ref.: #43541]	inulin ChEBI	-	assimilation
[Ref.: #43541]	itaconate ChEBI	-	assimilation
[Ref.: #43541]	L-alanine ChEBI	+	assimilation
[Ref.: #43541]	L-arabinose ChEBI	-	assimilation
[Ref.: #43541]	L-arabinose ChEBI	+	assimilation
[Ref.: #43541]	L-arabinose ChEBI	+	fermentation
[Ref.: #43541]	L-arabitol ChEBI	-	assimilation
[Ref.: #43541]	L-fucose ChEBI	+	assimilation
[Ref.: #43541]	L-fucose ChEBI	+	fermentation
[Ref.: #43541]	L-histidine ChEBI	+	assimilation
[Ref.: #43541]	L-malate ChEBI	-	assimilation
[Ref.: #43541]	L-proline ChEBI	+	assimilation
[Ref.: #43541]	L-rhamnose ChEBI	-	assimilation
[Ref.: #43541]	L-serine ChEBI	-	assimilation
[Ref.: #43541]	L-sorbose ChEBI	-	assimilation
[Ref.: #43541]	L-xylose ChEBI	-	assimilation
[Ref.: #43541]	lactate ChEBI	+	assimilation
[Ref.: #43541]	lactose ChEBI	-	assimilation
[Ref.: #43541]	maltose ChEBI	-	assimilation
[Ref.: #43541]	melezitose ChEBI	-	assimilation
[Ref.: #43541]	melibiose ChEBI	-	assimilation
[Ref.: #43541]	methyl alpha-D-glucopyranoside ChEBI	-	assimilation
[Ref.: #43541]	methyl alpha-D-mannoside ChEBI	-	assimilation
[Ref.: #43541]	methyl beta-D-xylopyranoside ChEBI	-	assimilation
[Ref.: #43541]	myo-inositol ChEBI	-	assimilation
[Ref.: #43541]	myo-inositol ChEBI	-	fermentation
[Ref.: #43541]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43541]	nitrate ChEBI	+	reduction
[Ref.: #43541]	phenylacetate ChEBI	-	assimilation
[Ref.: #43541]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43541]	propionate ChEBI	-	assimilation
[Ref.: #43541]	raffinose ChEBI	-	assimilation
[Ref.: #43541]	ribitol ChEBI	-	assimilation
[Ref.: #43541]	salicin ChEBI	-	assimilation
[Ref.: #43541]	sodium malonate ChEBI	-	assimilation
[Ref.: #43541]	starch ChEBI	-	assimilation
[Ref.: #43541]	suberic acid ChEBI	-	assimilation
[Ref.: #43541]	sucrose ChEBI	-	assimilation
[Ref.: #43541]	turanose ChEBI	-	assimilation
[Ref.: #43541]	valerate ChEBI	-	assimilation
[Ref.: #43541]	xylitol ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43541]		indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #43541]	acid phosphatase	+	3.1.3.2
[Ref.: #43541]	alkaline phosphatase	-	3.1.3.1
[Ref.: #43541]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43541]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43541]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43541]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43541]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43541]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43541]	beta-galactosidase	-	3.2.1.23
[Ref.: #43541]	beta-glucosidase	-	3.2.1.21
[Ref.: #43541]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43541]	catalase	+	1.11.1.6
[Ref.: #43541]	cystine arylamidase	+	3.4.11.3
[Ref.: #43541]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43541]	esterase (C 4)	+
[Ref.: #43541]	esterase Lipase (C 8)	+
[Ref.: #43541]	leucine arylamidase	-	3.4.11.1
[Ref.: #43541]	lipase (C 14)	+
[Ref.: #43541]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43541]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43541]	trypsin	-	3.4.21.4
[Ref.: #43541]	urease	-	3.5.1.5
[Ref.: #43541]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43541]

Fatty acid	Percentage
C15:0 iso	18.2
C15:0 anteiso	16.4
C16:1ω7c / C16:1ω6c	13.6
C17:1I / anteiso-C17:1B	10.7
C15:1 iso G	9
C16:1ω5c	6.9
C16:1 iso H	6.7
C16:0 iso	4.5
C16:0 iso 3OH	2.3
C15:0 iso 3OH	2.1
C14:0 iso	1.8
C15:1 anteiso	1.5
C17:0 iso	1.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #43541]	Sample type/isolated from	soil sample collected in a rice field
[Ref.: #43541]	Geographic location (country and/or sea, region)	Goyang, Gyeonggi Province
[Ref.: #43541]	Country	Republic of Korea
[Ref.: #43541]	Country ISO 3 Code	KOR
[Ref.: #43541]	Continent	Asia
[Ref.: #43541]	Geographic location	37.6740°/126.8060°

[Ref.: #67770]	Sample type/isolated from	Soil in a rice field in Goyang
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #43541]	16S rRNA gene sequence	KX636167		GenBank

[Ref.: #43541]	GC-content	68.2 mol%	Thermal denaturation, fluorometry
[Ref.: #67770]	GC-content	68.2 mol%	thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #43541]

Culture collection no.

KCTC 52520, JCM 31711

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hydrogenophaga soli sp. nov., isolated from rice field soil.	Yang D, Cha S, Choi J, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.002277	2017	*

References

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#43541

Dahye Yang, Seho Cha, Jiwon Choi, Taegun Seo: Hydrogenophaga soli sp. nov., isolated from rice field soil. IJSEM 67: 4200 - 4204 2017 ( DOI 10.1099/ijsem.0.002277 , PubMed 28920826 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
* These data were automatically processed and therefore are not curated

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