Acidisphaera rubrifaciens (DSM 16009, JCM 10600, HS-AP3)

Name: Acidisphaera rubrifaciens (DSM 16009, JCM 10600, HS-AP3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 67

Type strain

Strain Designation HS-AP3

Culture col. no. DSM 16009 JCM 10600 HS-AP3

NCBI tax ID(s) 50715

Special Collections DSMZ JCM Literature strains

Links

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

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

Name and taxonomic classification

SI-ID 100464

JCM 10600,DSM 16009

@ref 20215

Last LPSN update 2025-12-16 09:46:46

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodospirillales

Family Acetobacteraceae

Genus Acidisphaera

Species Acidisphaera rubrifaciens

Full scientific name Acidisphaera rubrifaciens Hiraishi et al. 2000

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
23249	negative	0.8-1.2 µm	0.7-1.0 µm	coccus-shaped
125438	negative					96.468

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23249	2 mm	salmon pink to red	circular	7 days	GNYS

Pigmentation

@ref	Production	Name
23249		Spirilloxanthin
23249		carotenoids
23249		Bacteriochlorophyll a

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6239	GNYS MEDIUM (DSMZ Medium 1119)		Medium recipe at MediaDive	Name: GNYS MEDIUM (DSMZ Medium 1119) Composition: Agar 18.0 g/l Sodium gluconate 3.0 g/l Yeast extract 1.0 g/l (NH4)2SO4 1.0 g/l KH2PO4 1.0 g/l MgCl2 x 6 H2O 0.2 g/l NaCl 0.2 g/l CaCl2 x 2 H2O 0.05 g/l Na2-EDTA 0.0052 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l H3BO3 6.2e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l CuCl2 x 2 H2O 1.7e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6239	positive	growth	30	mesophilic
23249	positive	growth	20-40
23249	positive	optimum	30-35	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
23249	positive	optimum	4.5-5.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23249	aerobe
125439	obligate aerobe	99.8

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23249	30089 ChEBI	acetate	-	carbon source
23249	16150 ChEBI	benzoate	-	carbon source
23249	28885 ChEBI	butanol	-	carbon source
23249	17968 ChEBI	butyrate	-	carbon source
23249		casamino acids	-	carbon source
23249		casein	-	hydrolysis
23249	16947 ChEBI	citrate	-	carbon source
23249	65327 ChEBI	D-xylose	+	carbon source
23249	16236 ChEBI	ethanol	-	carbon source
23249	15740 ChEBI	formate	-	carbon source
23249	28757 ChEBI	fructose	-	carbon source
23249	29806 ChEBI	fumarate	+	carbon source
23249	28260 ChEBI	galactose	+	carbon source
23249	24265 ChEBI	gluconate	+	carbon source
23249	17234 ChEBI	glucose	+	carbon source
23249	17754 ChEBI	glycerol	+	carbon source
23249	30849 ChEBI	L-arabinose	-	carbon source
23249	24996 ChEBI	lactate	+	carbon source
23249	17716 ChEBI	lactose	-	carbon source
23249	25115 ChEBI	malate	+	carbon source
23249	29864 ChEBI	mannitol	+	carbon source
23249	37684 ChEBI	mannose	-	carbon source
23249	17790 ChEBI	methanol	-	carbon source
23249	17268 ChEBI	myo-inositol	-	carbon source
23249	17632 ChEBI	nitrate	-	reduction
23249		peptone	-	carbon source
23249	28831 ChEBI	propanol	-	carbon source
23249	17272 ChEBI	propionate	-	carbon source
23249	15361 ChEBI	pyruvate	+	carbon source
23249	30911 ChEBI	sorbitol	+	carbon source
23249	28017 ChEBI	starch	-	hydrolysis
23249	30031 ChEBI	succinate	+	carbon source
23249	17992 ChEBI	sucrose	-	carbon source
23249	53426 ChEBI	tween 80	-	hydrolysis
23249		yeast extract	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
67770	30033 ChEBI	bacteriochlorophyll a
67770	23044 ChEBI	carotenoid

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Surface water
#Environmental	#Aquatic	#Thermal spring
#Condition	#Acidic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6239	surface water and sediment from an acidic hot spring	Kanagawa Prefecture, Hakone	Japan	JPN	Asia
67770	Hot spring water	Hakone, Kanagawa Pref.	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6239	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID
67770	ASM96436v1 assembly for Acidisphaera rubrifaciens HS-AP3	scaffold	GCA_000964365	1231350.15	1231350
66792	Acidisphaera rubrifaciens HS-AP3	contig		1231350.12	1231350

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6239	Acidisphaera rubrifaciens rrn gene for 16S rRNA	D86512	1451		50715

GC content

@ref	GC-content (mol%)	Method
23249	69.1-69.8	high performance liquid chromatography (HPLC)
67770	69.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidisphaera rubrifaciens HS-AP3
NCBI: GCA_000964365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	87.40	no
125439	motility	BacteriaNetⓘ	yes	55.90	no
125439	gram_stain	BacteriaNetⓘ	negative	88.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidisphaera rubrifaciens HS-AP3
PATRIC: 1231350.12

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.47	yes
125438	anaerobic	anaerobicⓘ	no	90.24	yes
125438	spore-forming	spore-formingⓘ	no	88.72	no
125438	aerobic	aerobicⓘ	yes	79.55	yes
125438	thermophilic	thermophileⓘ	no	94.30	yes
125438	flagellated	motile2+ⓘ	yes	68.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome Sequence of the Acidophilic Nonsulfur Purple Photosynthetic Alphaproteobacterium Rhodovastum atsumiense, a Divergent Member of the Acetobacteraceae Family.	Montano Salama D, Meyer TE, Kyndt JA.	Microbiol Resour Announc	10.1128/mra.01541-19	2020
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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Acidisphaera rubrifaciens (DSM 16009, JCM 10600, HS-AP3)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Metabolite production

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000964365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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