Acidicapsa acidisoli (DSM 100508, NBRC 111227, SK-11)

Name: Acidicapsa acidisoli (DSM 100508, NBRC 111227, SK-11)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133383

Type strain

Strain Designation SK-11

Culture col. no. DSM 100508 NBRC 111227 SK-11

NCBI tax ID(s) 1615681

Special Collections DSMZ Literature strains

Links

Acidicapsa acidisoli SK-11 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from soil of a deciduous forest.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397255

NBRC 111227,DSM 100508

@ref 20215

Last LPSN update 2025-12-16 10:01:46

Domain Pseudomonadati

Phylum Acidobacteriota

Class Terriglobia

Order Terriglobales

Family Acidobacteriaceae

Genus Acidicapsa

Species Acidicapsa acidisoli

Full scientific name Acidicapsa acidisoli Matsuo et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
25290	negative	1.0-1.4 µm	0.7-1.0 µm	rod-shaped
125439	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
25290	0.4-2.8 mm	white	circular	10 days	modified IS medium (MIS medium)

Culture and growth conditions

Culture medium

@ref	Name	Growth
25290	modified IS medium (MIS medium)
25290	YNG
64146	ACIDICAPSA MEDIUM (GYS MEDIUM) (DSMZ Medium 1671)

Culture temp

@ref	Growth	Type	Temperature (°C)
25290	positive	growth	10-35
25290	positive	optimum	25-30
64146	positive	growth	25

Culture pH

@ref	Ability	Type	PH
25290	positive	optimum	5
25290	positive	growth	4.0-5.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
25290	aerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
25290
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25290	NaCl	positive	growth	0.0-0.4 %
25290	NaCl		optimum	0.0-0.1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
25290	18305 ChEBI	arbutin	+	growth
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
25290	85146 ChEBI	carboxymethylcellulose	-	growth
25290		casamino acids	+	growth
25290	17057 ChEBI	cellobiose	+	growth
25290	17029 ChEBI	chitin	-	growth
25290	17108 ChEBI	D-arabinose	+	growth
25290	15824 ChEBI	D-fructose	+	growth
25290	28847 ChEBI	D-fucose	+	growth
25290	12936 ChEBI	D-galactose	+	growth
25290	18024 ChEBI	D-galacturonic acid	+	growth
25290	17634 ChEBI	D-glucose	+	growth
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
25290	16899 ChEBI	D-mannitol	-	growth
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
25290	16024 ChEBI	D-mannose	+	growth
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
25290	16988 ChEBI	D-ribose	-	growth
25290	17924 ChEBI	D-sorbitol	-	growth
25290	16443 ChEBI	D-tagatose	-	growth
25290	16551 ChEBI	D-trehalose	+	growth
25290	65327 ChEBI	D-xylose	+	growth
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
25290	4853 ChEBI	esculin	-	growth
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
25290	5291 ChEBI	gelatin	-	degradation
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
25290	15443 ChEBI	inulin	+	growth
25290	30849 ChEBI	L-arabinose	+	growth
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
25290	18287 ChEBI	L-fucose	+	growth
25290	62345 ChEBI	L-rhamnose	+	growth
25290	17266 ChEBI	L-sorbose	-	growth
25290	17716 ChEBI	lactose	+	growth
25290	6457 ChEBI	lignin	-	growth
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
25290	17306 ChEBI	maltose	+	growth
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
25290	6731 ChEBI	melezitose	+	growth
25290	28053 ChEBI	melibiose	+	growth
25290	17268 ChEBI	myo-inositol	-	growth
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
25290	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
25290	17309 ChEBI	pectin	+	growth
25290		peptone	+	growth
25290	62969 ChEBI	polygalacturonic acid	-	growth
25290	16634 ChEBI	raffinose	+	growth
25290	15963 ChEBI	ribitol	-	growth
25290	17814 ChEBI	salicin	+	growth
25290	28017 ChEBI	starch	+	growth
25290	17992 ChEBI	sucrose	+	growth
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
25290	32528 ChEBI	turanose	+	growth
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
25290	37166 ChEBI	xylan	+	growth
25290	17151 ChEBI	xylitol	-	growth
25290		yeast extract	+	growth

Metabolite production

@ref	Chebi-ID	Metabolite
25290	16136 ChEBI	hydrogen sulfide
25290	35581 ChEBI	indole
68369	35581 ChEBI	indole	from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
25290	acid phosphatase	+	3.1.3.2
25290	alkaline phosphatase	+	3.1.3.1
25290	alpha-chymotrypsin	-	3.4.21.1
25290	alpha-fucosidase	+	3.2.1.51
25290	alpha-galactosidase	+	3.2.1.22
25290	alpha-glucosidase	-	3.2.1.20
25290	alpha-mannosidase	-	3.2.1.24
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
25290	beta-galactosidase	+	3.2.1.23
25290	beta-glucosidase	+	3.2.1.21
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
25290	beta-glucuronidase	+	3.2.1.31
25290	catalase	+	1.11.1.6
25290	cystine arylamidase	+	3.4.11.3
25290	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
25290	esterase (C 4)	+
25290	esterase Lipase (C 8)	+
68369	gelatinase	-		from API 20NE
25290	leucine arylamidase	+	3.4.11.1
25290	lipase (C 14)	-
25290	N-acetyl-beta-glucosaminidase	+	3.2.1.52
25290	naphthol-AS-BI-phosphohydrolase	+
25290	trypsin	+	3.4.21.4
68369	urease	-	3.5.1.5	from API 20NE
25290	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

25290

Fatty acid	Percentage
C15:0 iso	55.4
iso-C17:1ω9c/ 10-methyl-hexadecanoic acid	17.7
C17:0 iso	16.7
C16:0	2.9
C16:1ω7c / C16:1ω6c	2.2
C16:0 iso	1
iso-C15:1H/C13:0 3-OH	0.6
C17:1 iso I / C17:1 anteiso B	0.6
C18:1ω9c	0.5
C18:0	0.5
C17:0	0.5

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
64146	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
25290	soil of a deciduous forest	2013-06-14	Shirakami Natural Science Park of the Shirakami Institute for Environmen- tal Sciences, Hirosaki University, Kawaratai, Nishimeya village, Nakatsugaru District, Aomori	Japan	JPN	Asia	40	140 40/140	IS medium	Nutrient broth (Oxoid) 0.065 g/l, MgSO4x7H2O 1.0 g/l, 2-(N-morpholino)ethanesulfonic acid (MES) 2.0 g/l, cyclo- heximide 0.1 g/l, soil extract, 500 ml/l, gellan gum 8.0 g/l, pH 5.0	60 days	30	serial dilution method
64146	acidic soil of a deciduous forest		Aomori Prefecture, Nakatsugaru District, Nishimera Village, Kawaratai, Shirakami Natural Science Park of the Hirosaki University (N40 30.916, E140 12.894; 346 m elevation above the sea level)	Japan	JPN	Asia	40.5153	140.215 40.5153/140.215

Taxonmaps

69479

Global distribution of 16S sequence LC027464 (>99% sequence identity) for Acidicapsa acidisoli subclade from Microbeatlas

Aquatic Samples	132
Soil Samples	2616
Animal Samples	71
Plant Samples	127
Total Samples	2946

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
64146	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2568562v1 assembly for Acidicapsa acidisoli SK-11	contig	GCA_025685625	1615681.3	8047316530	1615681	72.07

Genome browser: GCA_025685625

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64146	Acidicapsa acidisoli gene for 16S ribosomal RNA, partial sequence	LC027464	1465		1615681

GC content

@ref	GC-content (mol%)	Method
64146	56.9	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: Acidicapsa acidisoli SK-11
NCBI: GCA_025685625

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.20	no
125439	motility	BacteriaNetⓘ	no	76.10	no
125439	gram_stain	BacteriaNetⓘ	negative	96.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidicapsa acidisoli SK-11
NCBI: GCA_025685625.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	89.48	yes
125438	anaerobic	anaerobicⓘ	no	91.75	yes
125438	aerobic	aerobicⓘ	yes	75.76	no
125438	spore-forming	spore-formingⓘ	no	84.17	yes
125438	thermophilic	thermophileⓘ	no	95.72	yes
125438	flagellated	motile2+ⓘ	yes	50.29	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest.	Matsuo H, Kudo C, Li J, Tonouchi A	Int J Syst Evol Microbiol	10.1099/ijsem.0.001688	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 )
#25290	H. K. Matsuo, C.,Li, J.,Tonouchi, A.: Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest. IJSEM 67: 862 - 867 2017 ( DOI 10.1099/ijsem.0.001688 , PubMed 27902281 )
#64146	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100508
#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) .
#68369	Automatically annotated from API 20NE .
#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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Acidicapsa acidisoli (DSM 100508, NBRC 111227, SK-11)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile?

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_025685625

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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Fatty acid profile