Name: Acidicapsa ligni WH120
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 143

Type strain:

Species: Acidicapsa ligni

Strain Designation: WH120

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

Strain history: <- LMG; LMG 26244 <- W de Boer, Centre for Terrest. Ecology; WH120

NCBI tax ID(s): 542300 (species)

SI-ID 400954

DSM 25248

Section

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

Gram-negative
rod-shaped
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	*Acidobacteriota*
	Class	*Terriglobia*
	Order	*Terriglobales*
	Family	*Acidobacteriaceae*
	Genus	*Acidicapsa*
	Species	**Acidicapsa ligni**
	Full Scientific Name (LPSN)	Acidicapsa ligni Kulichevskaya et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #23352]	Gram stain	negative

[Ref.: #23352]	Cell length	1.0-2.0 µm

[Ref.: #23352]	Cell width	0.5-0.8 µm

[Ref.: #23352]	Cell shape	rod-shaped

[Ref.: #23352]	Motility	no

[Ref.: #23352]	Colony color	colourless

[Ref.: #17958]	Incubation period	3-7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17958]

Culture medium

SSE/HD1:10 (DSMZ Medium 1426)

[Ref.: #17958]

Culture medium growth

[Ref.: #17958]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17958]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17958]	growth	25 °C
[Ref.: #23352]	maximum	33 °C
[Ref.: #23352]	minimum	10 °C
[Ref.: #23352]	optimum	22-28 °C

[Ref.: #17958]	Temperature range	mesophilic
[Ref.: #23352]	Temperature range	mesophilic
[Ref.: #23352]	Temperature range	psychrophilic

		pH
[Ref.: #23352]	maximum	6.4
[Ref.: #23352]	minimum	3.5
[Ref.: #23352]	optimum	4.0-4.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23352]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23352]		NaCl		growth	<2.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #23352]	alginate ChEBI	-	carbon source
[Ref.: #23352]	arbutin ChEBI	-	hydrolysis
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #23352]	benzoate ChEBI	-	carbon source
[Ref.: #23352]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #23352]	casein	-	hydrolysis
[Ref.: #23352]	cationic chitosan ChEBI	-	hydrolysis
[Ref.: #23352]	cellobiose ChEBI	+	carbon source
[Ref.: #23352]	cellulose ChEBI	-	hydrolysis
[Ref.: #23352]	chitin ChEBI	-	hydrolysis
[Ref.: #23352]	citrate ChEBI	-	carbon source
[Ref.: #23352]	D-arabinose ChEBI	+	carbon source
[Ref.: #23352]	D-fructose ChEBI	+	carbon source
[Ref.: #23352]	D-fucose ChEBI	-	carbon source
[Ref.: #23352]	D-galactose ChEBI	+	carbon source
[Ref.: #23352]	D-galacturonic acid ChEBI	-	carbon source
[Ref.: #23352]	D-glucose ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #23352]	D-glucuronate ChEBI	-	carbon source
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #23352]	D-mannose ChEBI	+	carbon source
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #23352]	D-rhamnose ChEBI	+	carbon source
[Ref.: #23352]	D-ribose ChEBI	+	carbon source
[Ref.: #23352]	D-sorbose ChEBI	-	carbon source
[Ref.: #23352]	D-xylose ChEBI	+	carbon source
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #23352]	esculin ChEBI	-	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #23352]	ethanol ChEBI	-	carbon source
[Ref.: #23352]	fucoidan ChEBI	-	hydrolysis
[Ref.: #23352]	fumarate ChEBI	-	carbon source
[Ref.: #23352]	galactitol ChEBI	+	carbon source
[Ref.: #23352]	gelatin ChEBI	+	hydrolysis
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #23352]	glycerol ChEBI	-	carbon source
[Ref.: #23352]	hexanoate ChEBI	-	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #23352]	lactate ChEBI	+	carbon source
[Ref.: #23352]	lactose ChEBI	+	carbon source
[Ref.: #23352]	lactulose ChEBI	+	carbon source
[Ref.: #23352]	laminarin ChEBI	-	hydrolysis
[Ref.: #23352]	malate ChEBI	-	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #23352]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #23352]	mannitol ChEBI	-	carbon source
[Ref.: #23352]	melezitose ChEBI	+	energy source
[Ref.: #23352]	melibiose ChEBI	+	carbon source
[Ref.: #23352]	methanol ChEBI	-	carbon source
[Ref.: #23352]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #23352]	oxalate ChEBI	+	carbon source
[Ref.: #23352]	oxaloacetate ChEBI	-	carbon source
[Ref.: #23352]	pectin ChEBI	-	hydrolysis
[Ref.: #23352]	propionate ChEBI	-	carbon source
[Ref.: #23352]	pullulan ChEBI	-	hydrolysis
[Ref.: #23352]	pyruvate ChEBI	-	carbon source
[Ref.: #23352]	raffinose ChEBI	+	carbon source
[Ref.: #23352]	salicin ChEBI	+	carbon source
[Ref.: #23352]	sorbitol ChEBI	-	carbon source
[Ref.: #23352]	starch ChEBI	-	hydrolysis
[Ref.: #23352]	succinate ChEBI	-	carbon source
[Ref.: #23352]	sucrose ChEBI	+	carbon source
[Ref.: #23352]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #23352]	xylan ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #23352]	ampicillin ChEBI				yes	10	µg (disc)
[Ref.: #23352]	chloramphenicol ChEBI				yes	30	µg (disc)
[Ref.: #23352]	gentamicin ChEBI				yes	10	µg (disc)
[Ref.: #23352]	kanamycin ChEBI				yes	30	µg (disc)
[Ref.: #23352]	lincomycin ChEBI				yes	10	µg (disc)
[Ref.: #23352]	neomycin ChEBI				yes	10	µg (disc)
[Ref.: #23352]	novobiocin ChEBI				yes	30	µg (disc)
[Ref.: #23352]	novobiocin ChEBI	yes	30	µg (disc)
[Ref.: #23352]	streptomycin ChEBI				yes	10	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #23352]	acid phosphatase	+	3.1.3.2
[Ref.: #23352]	alkaline phosphatase	+	3.1.3.1
[Ref.: #23352]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #23352]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #23352]	alpha-fucosidase	+	3.2.1.51
[Ref.: #23352]	alpha-galactosidase	+	3.2.1.22
[Ref.: #23352]	alpha-glucosidase	+	3.2.1.20
[Ref.: #23352]	alpha-mannosidase	+	3.2.1.24
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #23352]	beta-galactosidase	+	3.2.1.23
[Ref.: #23352]	beta-glucosidase	+	3.2.1.21
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #23352]	beta-glucuronidase	+	3.2.1.31
[Ref.: #17958]	catalase	+	1.11.1.6
[Ref.: #23352]	catalase	+	1.11.1.6
[Ref.: #23352]	cystine arylamidase	+	3.4.11.3
[Ref.: #23352]	cytochrome oxidase	-	1.9.3.1
[Ref.: #17958]	cytochrome-c oxidase	-	1.9.3.1
[Ref.: #23352]	esterase	+
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #23352]	leucine arylamidase	+	3.4.11.1
[Ref.: #23352]	lipase	-
[Ref.: #23352]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #23352]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #23352]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #17958]	23891	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

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

[Ref.: #17958]	Sample type/isolated from	decaying wood colonized by Hypholoma fasciculare in a temperate broadleaf forest
[Ref.: #17958]	Host species	Hypholoma fasciculare
[Ref.: #17958]	Geographic location (country and/or sea, region)	close to Doorwerth village, Wolfheze nature reserve
[Ref.: #17958]	Country	Netherlands
[Ref.: #17958]	Country ISO 3 Code	NLD
[Ref.: #17958]	Continent	Europe

[Ref.: #23352]	Sample type/isolated from	natural birch wood sample, Hypholoma fasciculare
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #17958]

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.: #17958]	Acidicapsa ligni strain WH120 16S ribosomal RNA gene, partial sequence	EU780204	1401	ENA	542300 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Acidicapsa ligni WH120	GCA_025685655	contig	GenBank	542300 tax ID	*

[Ref.: #17958]	GC-content	51.7 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #23352]	GC-content	51.7 mol%	Thermal denaturation, fluorometry

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Acidicapsa ligni WH120 NCBI: GCA_025685655.1
[Ref.: #69480]	motile	no	57.776	no
[Ref.: #69480]	flagellated	no	92.52	yes
[Ref.: #69480]	gram-positive	no	97.242	no
[Ref.: #69480]	anaerobic	no	98.903	no
[Ref.: #69480]	aerobic	yes	85.239	no
[Ref.: #69480]	halophile	no	96.08	no
[Ref.: #69480]	spore-forming	no	88.9	no
[Ref.: #69480]	glucose-ferment	no	90.94	yes
[Ref.: #69480]	thermophile	no	96.307	no
[Ref.: #69480]	glucose-util	yes	78.154	no

Availability in culture collections External links

[Ref.: #17958]

Culture collection no.

DSM 25248, LMG 26244, NCCB 100371, VKM B-2677

[Ref.: #69826]

SI-ID 400954

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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) .

#69826

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-ID400954.1 )

* These data were automatically processed and therefore are not curated

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