Acidicapsa ligni (DSM 25248, LMG 26244, NCCB 100371)

Name: Acidicapsa ligni (DSM 25248, LMG 26244, NCCB 100371)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 143

Type strain

Strain Designation WH120

Culture col. no. DSM 25248 LMG 26244 NCCB 100371 VKM B-2677 WH120

NCBI tax ID(s) 542300

Special Collections DSMZ Literature strains

History <- LMG; LMG 26244 <- W de Boer, Centre for Terrest. Ecology; WH120

Links

Acidicapsa ligni WH120 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from decaying wood colonized by Hypholoma fasciculare in a temperate broadleaf forest.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400954

LMG 26244,NCCB 100371,DSM 25248

@ref 20215

Last LPSN update 2026-02-09 11:17:48

Domain Bacteria

Phylum Acidobacteriota

Class Terriglobia

Order Terriglobales

Family Acidobacteriaceae

Genus Acidicapsa

Species Acidicapsa ligni

Full scientific name Acidicapsa ligni Kulichevskaya et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
23352	negative	1.0-2.0 µm	0.5-0.8 µm	rod-shaped
125439	negative					99.5

Colony morphology

@ref	Incubation period	Colony color
17958	3-7 days
23352		colourless

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17958	SSE/HD1:10 (DSMZ Medium 1426)		Medium recipe at MediaDive	Name: SSE/HD 1:10 MEDIUM (DSMZ Medium 1426) Composition: MES 1.95 g/l Peptone 0.5 g/l CaSO4 x 2 H2O 0.4303 g/l MgSO4 x 7 H2O 0.3695 g/l Yeast extract 0.25 g/l Na NO3 0.212 g/l CaCl2 x 2 H2O 0.1469 g/l Ca(NO3)2 x 4 H2O 0.118 g/l MgCl2 x 6 H2O 0.1018 g/l Glucose 0.1 g/l (NH4)2SO4 0.09915 g/l NH4Cl 0.05345 g/l K2SO4 0.0435 g/l FeSO4 x 7 H2O 0.00555 g/l KH2PO4 0.00340213 g/l HCl 0.0025 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 Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Pyridoxine hydrochloride 1e-05 g/l H3BO3 6e-06 g/l Lipoic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17958	positive	growth	25	mesophilic
23352	positive	maximum	33	mesophilic
23352	positive	minimum	10	psychrophilic
23352	positive	optimum	22-28

Culture pH

@ref	Ability	Type	PH	PH range
23352	positive	maximum	6.4
23352	positive	minimum	3.5	acidophile
23352	positive	optimum	4.0-4.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23352	aerobe
125439	obligate aerobe	99.8

Spore formation

@ref	Spore formation	Confidence
125439		93.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23352	NaCl	positive	growth	<2.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
23352	58187 ChEBI	alginate	-	carbon source
23352	18305 ChEBI	arbutin	-	hydrolysis
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
23352	16150 ChEBI	benzoate	-	carbon source
23352	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
23352		casein	-	hydrolysis
23352	57704 ChEBI	cationic chitosan	-	hydrolysis
23352	17057 ChEBI	cellobiose	+	carbon source
23352	62968 ChEBI	cellulose	-	hydrolysis
23352	17029 ChEBI	chitin	-	hydrolysis
23352	16947 ChEBI	citrate	-	carbon source
23352	17108 ChEBI	D-arabinose	+	carbon source
23352	15824 ChEBI	D-fructose	+	carbon source
23352	28847 ChEBI	D-fucose	-	carbon source
23352	12936 ChEBI	D-galactose	+	carbon source
23352	18024 ChEBI	D-galacturonic acid	-	carbon source
23352	17634 ChEBI	D-glucose	+	carbon source
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
23352	15748 ChEBI	D-glucuronate	-	carbon source
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
23352	16024 ChEBI	D-mannose	+	carbon source
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
23352	63150 ChEBI	D-rhamnose	+	carbon source
23352	16988 ChEBI	D-ribose	+	carbon source
23352	17317 ChEBI	D-sorbose	-	carbon source
23352	65327 ChEBI	D-xylose	+	carbon source
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
23352	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
23352	16236 ChEBI	ethanol	-	carbon source
23352	5181 ChEBI	fucoidan	-	hydrolysis
23352	29806 ChEBI	fumarate	-	carbon source
23352	16813 ChEBI	galactitol	+	carbon source
23352	5291 ChEBI	gelatin	+	hydrolysis
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
23352	17754 ChEBI	glycerol	-	carbon source
23352	17120 ChEBI	hexanoate	-	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
23352	24996 ChEBI	lactate	+	carbon source
23352	17716 ChEBI	lactose	+	carbon source
23352	6359 ChEBI	lactulose	+	carbon source
23352	6364 ChEBI	laminarin	-	hydrolysis
23352	25115 ChEBI	malate	-	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
23352	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
23352	29864 ChEBI	mannitol	-	carbon source
23352	6731 ChEBI	melezitose	+	energy source
23352	28053 ChEBI	melibiose	+	carbon source
23352	17790 ChEBI	methanol	-	carbon source
23352	506227 ChEBI	N-acetylglucosamine	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
23352	30623 ChEBI	oxalate	+	carbon source
23352	16452 ChEBI	oxaloacetate	-	carbon source
23352	17309 ChEBI	pectin	-	hydrolysis
23352	17272 ChEBI	propionate	-	carbon source
23352	27941 ChEBI	pullulan	-	hydrolysis
23352	15361 ChEBI	pyruvate	-	carbon source
23352	16634 ChEBI	raffinose	+	carbon source
23352	17814 ChEBI	salicin	+	carbon source
23352	30911 ChEBI	sorbitol	-	carbon source
23352	28017 ChEBI	starch	-	hydrolysis
23352	30031 ChEBI	succinate	-	carbon source
23352	17992 ChEBI	sucrose	+	carbon source
23352	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
23352	37166 ChEBI	xylan	+	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite	Resistance conc.	Sensitivity conc.
23352	28971	ampicillin	10 µg (disc)
23352	17698	chloramphenicol	30 µg (disc)
23352	17833	gentamicin	10 µg (disc)
23352	6104	kanamycin	30 µg (disc)
23352	6472	lincomycin	10 µg (disc)
23352	7507	neomycin	10 µg (disc)
23352	28368	novobiocin	30 µg (disc)
23352	28368	novobiocin		30 µg (disc)
23352	17076	streptomycin	10 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
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
23352	acid phosphatase	+	3.1.3.2
23352	alkaline phosphatase	+	3.1.3.1
23352	alpha-chymotrypsin	+	3.4.21.1
23352	alpha-chymotrypsin	-	3.4.21.1
23352	alpha-fucosidase	+	3.2.1.51
23352	alpha-galactosidase	+	3.2.1.22
23352	alpha-glucosidase	+	3.2.1.20
23352	alpha-mannosidase	+	3.2.1.24
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
23352	beta-galactosidase	+	3.2.1.23
23352	beta-glucosidase	+	3.2.1.21
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
23352	beta-glucuronidase	+	3.2.1.31
17958	catalase	+	1.11.1.6
23352	catalase	+	1.11.1.6
23352	cystine arylamidase	+	3.4.11.3
23352	cytochrome oxidase	-	1.9.3.1
17958	cytochrome-c oxidase	-	1.9.3.1
23352	esterase	+
68369	gelatinase	-		from API 20NE
23352	leucine arylamidase	+	3.4.11.1
23352	lipase	-
23352	N-acetyl-beta-glucosaminidase	+	3.2.1.52
23352	naphthol-AS-BI-phosphohydrolase	+
68369	urease	-	3.5.1.5	from API 20NE
23352	valine arylamidase	+

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
17958	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Fungi	#Mushroom
#Host	#Plants	#Decomposing plant
#Host Body Product	#Plant	#Timber
#Climate	#Temperate	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
17958	decaying wood colonized by Hypholoma fasciculare in a temperate broadleaf forest	Hypholoma fasciculare	close to Doorwerth village, Wolfheze nature reserve	Netherlands	NLD	Europe
23352	natural birch wood sample, Hypholoma fasciculare

Taxonmaps

69479

Global distribution of 16S sequence EU780204 (>99% sequence identity) for Acidicapsa ligni subclade from Microbeatlas

Aquatic Samples	19
Soil Samples	158
Animal Samples	7
Plant Samples	60
Total Samples	244

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17958	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	Score
66792	ASM2568565v1 assembly for Acidicapsa ligni WH120	contig	GCA_025685655	542300.4	542300	69.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17958	Acidicapsa ligni strain WH120 16S ribosomal RNA gene, partial sequence	EU780204	1401		542300

GC content

@ref	GC-content (mol%)	Method
17958	51.7	thermal denaturation, midpoint method (Tm)
23352	51.7	Thermal denaturation, fluorometry

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidicapsa ligni WH120
NCBI: GCA_025685655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.90	no
125439	motility	BacteriaNetⓘ	no	72.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	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: Acidicapsa ligni WH120
NCBI: GCA_025685655.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	88.79	no
125438	anaerobic	anaerobicⓘ	no	91.08	no
125438	aerobic	aerobicⓘ	yes	75.32	no
125438	spore-forming	spore-formingⓘ	no	79.76	no
125438	thermophilic	thermophileⓘ	no	92.55	no
125438	flagellated	motile2+ⓘ	no	58.15	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey.	Aytar P, Kay CM, Mutlu MB, Cabuk A, Johnson DB.	Environ Sci Pollut Res Int	10.1007/s11356-014-3789-4	2015
Phylogeny	The Evolution of Ecological Diversity in Acidobacteria.	Sikorski J, Baumgartner V, Birkhofer K, Boeddinghaus RS, Bunk B, Fischer M, Fosel BU, Friedrich MW, Goker M, Holzel N, Huang S, Huber KJ, Kandeler E, Klaus VH, Kleinebecker T, Marhan S, von Mering C, Oelmann Y, Prati D, Regan KM, Richter-Heitmann T, Rodrigues JFM, Schmitt B, Schoning I, Schrumpf M, Schurig E, Solly EF, Wolters V, Overmann J.	Front Microbiol	10.3389/fmicb.2022.715637	2022
Phylogeny	Bacterial Community Succession in Pine-Wood Decomposition.	Kielak AM, Scheublin TR, Mendes LW, van Veen JA, Kuramae EE.	Front Microbiol	10.3389/fmicb.2016.00231	2016
Phylogeny	Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae.	Foesel BU, Mayer S, Luckner M, Wanner G, Rohde M, Overmann J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.000700	2016
Phylogeny	Acidicapsa dinghuensis sp. nov., a novel acidobacterium isolated from forest soil.	Ou-Yang TN, Xia F, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002846	2018
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
Phylogeny	Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation.	Garcia-Fraile P, Benada O, Cajthaml T, Baldrian P, Llado S	Appl Environ Microbiol	10.1128/AEM.03353-15	2015
Phylogeny	Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood.	Kulichevskaya IS, Kostina LA, Valaskova V, Rijpstra WIC, Sinninghe Damste JS, de Boer W, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.034819-0	2011

References

#17958	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25248
#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 )
#23352	Irina S. Kulichevskaya, Lilia A. Kostina, Vendula Valásková, W. Irene C. Rijpstra, Jaap S. Sinninghe Damsté, Wietse de Boer, Svetlana N. Dedysh: Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood. IJSEM 62: 1512 - 1520 2012 ( DOI 10.1099/ijs.0.034819-0 , PubMed 21856984 )
#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 ligni (DSM 25248, LMG 26244, NCCB 100371)

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

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_025685655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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