Name: Acidisphaera rubrifaciens HS-AP3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 67

Type strain:

Species: Acidisphaera rubrifaciens

Strain Designation: HS-AP3

Culture col. no.: DSM 16009, JCM 10600

Strain history: A. Hiraishi HS-AP3.

NCBI tax ID(s): 50715 (species)

SI-ID 100464

JCM 10600, DSM 16009

Section

Acidisphaera rubrifaciens HS-AP3 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from surface water and sediment from an acidic hot spring.

coccus-shaped
colony-forming
Gram-negative
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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	*Alphaproteobacteria*
	Order	*Rhodospirillales*
	Family	*Acetobacteraceae*
	Genus	*Acidisphaera*
	Species	**Acidisphaera rubrifaciens**
	Full Scientific Name (LPSN)	Acidisphaera rubrifaciens Hiraishi et al. 2000

Information on morphological and physiological properties Morphology

[Ref.: #23249]	Gram stain	negative

[Ref.: #23249]	Cell length	0.8-1.2 µm

[Ref.: #23249]	Cell width	0.7-1.0 µm

[Ref.: #23249]	Cell shape	coccus-shaped

[Ref.: #23249]	Motility	no

[Ref.: #23249]	Colony size	2 mm
[Ref.: #23249]	Colony color	salmon pink to red
[Ref.: #23249]	Colony shape	circular
[Ref.: #23249]	Incubation period	7 days
[Ref.: #23249]	Cultivation medium used	GNYS

[Ref.: #23249]	Pigment production	yes
[Ref.: #23249]	Pigment name	Spirilloxanthin
[Ref.: #23249]	Pigment production	yes
[Ref.: #23249]	Pigment name	carotenoids
[Ref.: #23249]	Pigment production	yes
[Ref.: #23249]	Pigment name	Bacteriochlorophyll a

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6239]

Culture medium

GNYS MEDIUM (DSMZ Medium 1119)

[Ref.: #6239]

Culture medium growth

[Ref.: #6239]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6239]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6239]	growth	30 °C
[Ref.: #23249]	growth	20-40 °C
[Ref.: #23249]	optimum	30-35 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #6239]	Temperature range	mesophilic
[Ref.: #23249]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #23249]			optimum	4.5-5.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23249]

Oxygen tolerance

aerobe

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23249]	acetate ChEBI	-	carbon source
[Ref.: #23249]	benzoate ChEBI	-	carbon source
[Ref.: #23249]	butanol ChEBI	-	carbon source
[Ref.: #23249]	butyrate ChEBI	-	carbon source
[Ref.: #23249]	casamino acids	-	carbon source
[Ref.: #23249]	casein	-	hydrolysis
[Ref.: #23249]	citrate ChEBI	-	carbon source
[Ref.: #23249]	D-xylose ChEBI	+	carbon source
[Ref.: #23249]	ethanol ChEBI	-	carbon source
[Ref.: #23249]	formate ChEBI	-	carbon source
[Ref.: #23249]	fructose ChEBI	-	carbon source
[Ref.: #23249]	fumarate ChEBI	+	carbon source
[Ref.: #23249]	galactose ChEBI	+	carbon source
[Ref.: #23249]	gluconate ChEBI	+	carbon source
[Ref.: #23249]	glucose ChEBI	+	carbon source
[Ref.: #23249]	glycerol ChEBI	+	carbon source
[Ref.: #23249]	L-arabinose ChEBI	-	carbon source
[Ref.: #23249]	lactate ChEBI	+	carbon source
[Ref.: #23249]	lactose ChEBI	-	carbon source
[Ref.: #23249]	malate ChEBI	+	carbon source
[Ref.: #23249]	mannitol ChEBI	+	carbon source
[Ref.: #23249]	mannose ChEBI	-	carbon source
[Ref.: #23249]	methanol ChEBI	-	carbon source
[Ref.: #23249]	myo-inositol ChEBI	-	carbon source
[Ref.: #23249]	nitrate ChEBI	-	reduction
[Ref.: #23249]	peptone	-	carbon source
[Ref.: #23249]	propanol ChEBI	-	carbon source
[Ref.: #23249]	propionate ChEBI	-	carbon source
[Ref.: #23249]	pyruvate ChEBI	+	carbon source
[Ref.: #23249]	sorbitol ChEBI	+	carbon source
[Ref.: #23249]	starch ChEBI	-	hydrolysis
[Ref.: #23249]	succinate ChEBI	+	carbon source
[Ref.: #23249]	sucrose ChEBI	-	carbon source
[Ref.: #23249]	tween 80 ChEBI	-	hydrolysis
[Ref.: #23249]	yeast extract	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #67770]		bacteriochlorophyll a ChEBI	yes
[Ref.: #67770]		carotenoid ChEBI	yes

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

[Ref.: #6239]	Sample type/isolated from	surface water and sediment from an acidic hot spring
[Ref.: #6239]	Geographic location (country and/or sea, region)	Kanagawa Prefecture, Hakone
[Ref.: #6239]	Country	Japan
[Ref.: #6239]	Country ISO 3 Code	JPN
[Ref.: #6239]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Hot spring water
[Ref.: #67770]	Geographic location (country and/or sea, region)	Hakone, Kanagawa Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Surface water
#Environmental	#Aquatic	#Thermal spring
#Condition	#Acidic	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence D86512 (>99% sequence identity) for Acidisphaera rubrifaciens subclade from Microbeatlas

Aquatic Samples	658
Soil Samples	3255
Animal Samples	249
Plant Samples	402
Total Samples	4564

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6239]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #6239]	Acidisphaera rubrifaciens rrn gene for 16S rRNA	D86512	1451	ENA	50715 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Acidisphaera rubrifaciens HS-AP3	GCA_000964365	scaffold	GenBank	1231350 tax ID
[Ref.: #66792]	Acidisphaera rubrifaciens HS-AP3	1231350.12	wgs	PATRIC	1231350 tax ID	*

[Ref.: #23249]	GC-content	69.1-69.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	69.3 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Acidisphaera rubrifaciens HS-AP3 PATRIC: 1231350.12
[Ref.: #69480]	motile	yes	65.345	yes
[Ref.: #69480]	gram-positive	no	97.93	yes
[Ref.: #69480]	anaerobic	no	95.859	yes
[Ref.: #69480]	aerobic	yes	90.572	yes
[Ref.: #69480]	halophile	no	89.403	no
[Ref.: #69480]	spore-forming	no	92.827	no
[Ref.: #69480]	thermophile	no	95.514	no
[Ref.: #69480]	glucose-util	yes	74.066	no
[Ref.: #69480]	flagellated	no	92.372	yes
[Ref.: #69480]	glucose-ferment	no	94.061	no

Availability in culture collections External links

[Ref.: #6239]

Culture collection no.

DSM 16009, JCM 10600

[Ref.: #69751]

SI-ID 100464

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Acidibrevibacterium fodinaquatile gen. nov., sp. nov., isolated from acidic mine drainage.	Muhadesi JB, Huang Y, Wang BJ, Jiang CY, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003618	2019	*
Phylogeny	Rhodovastum atsumiense gen. nov., sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil.	Okamura K, Hisada T, Kanbe T, Hiraishi A	J Gen Appl Microbiol	10.2323/jgam.55.43	2009	*
Phylogeny	Acidisphaera rubrifaciens gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from acidic environments.	Hiraishi A, Matsuzawa Y, Kanbe T, Wakao N	Int J Syst Evol Microbiol	10.1099/00207713-50-4-1539	2000	*

References

#6239

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16009

#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 )

#23249

A Hiraishi, Y Matsuzawa, T Kanbe, N Wakao: Acidisphaera rubrifaciens gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from acidic environments.. IJSEM 50: 1539 - 1546 2000 ( DOI 10.1099/00207713-50-4-1539 , PubMed 10939661 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69751

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID100464.1 )

* These data were automatically processed and therefore are not curated

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