Strain identifier

BacDive ID: 143

Type strain: Yes

Species: Acidicapsa ligni

Strain Designation: WH120

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

NCBI tax ID(s): 542300 (species)

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General

@ref: 17958

BacDive-ID: 143

DSM-Number: 25248

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: 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.

NCBI tax id

  • NCBI tax id: 542300
  • Matching level: species

strain history

  • @ref: 17958
  • history: <- LMG; LMG 26244 <- W de Boer, Centre for Terrest. Ecology; WH120

doi: 10.13145/bacdive143.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Terriglobia
  • order: Terriglobales
  • family: Acidobacteriaceae
  • genus: Acidicapsa
  • species: Acidicapsa ligni
  • full scientific name: Acidicapsa ligni Kulichevskaya et al. 2012

@ref: 17958

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Acidicapsa

species: Acidicapsa ligni

full scientific name: Acidicapsa ligni Kulichevskaya et al. 2012

strain designation: WH120

type strain: yes

Morphology

cell morphology

  • @ref: 23352
  • gram stain: negative
  • cell length: 1.0-2.0 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refincubation periodcolony color
179583-7 days
23352colourless

Culture and growth conditions

culture medium

  • @ref: 17958
  • name: SSE/HD1:10 (DSMZ Medium 1426)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1426
  • composition: 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

@refgrowthtypetemperaturerange
17958positivegrowth25mesophilic
23352positivemaximum33mesophilic
23352positiveminimum10psychrophilic
23352positiveoptimum22-28

culture pH

@refabilitytypepHPH range
23352positiveminimum3.5acidophile
23352positivemaximum6.4
23352positiveoptimum4.0-4.5

Physiology and metabolism

oxygen tolerance

  • @ref: 23352
  • oxygen tolerance: aerobe

halophily

  • @ref: 23352
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2335258187alginate-carbon source
2335216150benzoate-carbon source
2335216947citrate-carbon source
2335228847D-fucose-carbon source
2335218024D-galacturonic acid-carbon source
2335215748D-glucuronate-carbon source
2335217317D-sorbose-carbon source
2335216236ethanol-carbon source
2335229806fumarate-carbon source
2335217754glycerol-carbon source
2335217120hexanoate-carbon source
2335225115malate-carbon source
2335229864mannitol-carbon source
2335217790methanol-carbon source
2335216452oxaloacetate-carbon source
2335217272propionate-carbon source
2335215361pyruvate-carbon source
2335230911sorbitol-carbon source
2335230031succinate-carbon source
2335218305arbutin-hydrolysis
2335285146carboxymethylcellulose-hydrolysis
23352casein-hydrolysis
2335257704cationic chitosan-hydrolysis
2335262968cellulose-hydrolysis
2335217029chitin-hydrolysis
233524853esculin-hydrolysis
233525181fucoidan-hydrolysis
233526364laminarin-hydrolysis
2335217309pectin-hydrolysis
2335227941pullulan-hydrolysis
2335228017starch-hydrolysis
2335217057cellobiose+carbon source
2335217108D-arabinose+carbon source
2335215824D-fructose+carbon source
2335212936D-galactose+carbon source
2335217634D-glucose+carbon source
2335216024D-mannose+carbon source
2335263150D-rhamnose+carbon source
2335216988D-ribose+carbon source
2335265327D-xylose+carbon source
2335216813galactitol+carbon source
2335224996lactate+carbon source
2335217716lactose+carbon source
233526359lactulose+carbon source
2335217306maltose+carbon source
2335228053melibiose+carbon source
23352506227N-acetylglucosamine+carbon source
2335230623oxalate+carbon source
2335216634raffinose+carbon source
2335217814salicin+carbon source
2335217992sucrose+carbon source
2335227082trehalose+carbon source
233526731melezitose+energy source
233525291gelatin+hydrolysis
2335237166xylan+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
2335228971ampicillinyesyes10 µg (disc)
2335217833gentamicinyesyes10 µg (disc)
233526472lincomycinyesyes10 µg (disc)
233527507neomycinyesyes10 µg (disc)
2335217076streptomycinyesyes10 µg (disc)
2335217698chloramphenicolyesyes30 µg (disc)
233526104kanamycinyesyes30 µg (disc)
2335228368novobiocinyesyes30 µg (disc)
2335228368novobiocinyesyes30 µg (disc)

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
17958-----+-+------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
17958decaying wood colonized by Hypholoma fasciculare in a temperate broadleaf forestHypholoma fasciculareclose to Doorwerth village, Wolfheze nature reserveNetherlandsNLDEurope
23352natural birch wood sample, Hypholoma fasciculare

isolation source categories

Cat1Cat2Cat3
#Host#Fungi#Mushroom
#Host#Plants#Decomposing plant
#Host Body Product#Plant#Timber
#Climate#Temperate

taxonmaps

  • @ref: 69479
  • File name: preview.99_30394.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_236;96_11435;97_18179;98_22615;99_30394&stattab=map
  • Last taxonomy: Acidicapsa ligni subclade
  • 16S sequence: EU780204
  • Sequence Identity:
  • Total samples: 244
  • soil counts: 158
  • aquatic counts: 19
  • animal counts: 7
  • plant counts: 60

Safety information

risk assessment

  • @ref: 17958
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17958
  • description: Acidicapsa ligni strain WH120 16S ribosomal RNA gene, partial sequence
  • accession: EU780204
  • length: 1401
  • database: ena
  • NCBI tax ID: 542300

Genome sequences

  • @ref: 66792
  • description: Acidicapsa ligni WH120
  • accession: GCA_025685655
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 542300

GC content

@refGC-contentmethod
1795851.7thermal denaturation, midpoint method (Tm)
2335251.7Thermal denaturation, fluorometry

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno57.776no
flagellatedno92.52yes
gram-positiveno97.242no
anaerobicno98.903no
aerobicyes85.239no
halophileno96.08no
spore-formingno88.9no
glucose-fermentno90.94yes
thermophileno96.307no
glucose-utilyes78.154no

External links

@ref: 17958

culture collection no.: DSM 25248, LMG 26244, NCCB 100371, VKM B-2677

straininfo link

  • @ref: 69826
  • straininfo: 400954

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21856984Acidicapsa 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 SNInt J Syst Evol Microbiol10.1099/ijs.0.034819-02011Acidobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphagnopsida/*microbiology, Temperature, Wood/*microbiologyGenetics
Phylogeny26546425Terracidiphilus 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 SAppl Environ Microbiol10.1128/AEM.03353-152015Acidobacteria/genetics/*isolation & purification/*metabolism, Biodegradation, Environmental, Biotransformation, Forests, Molecular Sequence Data, Phylogeny, Plants/metabolism/microbiology, *Soil MicrobiologyMetabolism
Phylogeny27902281Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest.Matsuo H, Kudo C, Li J, Tonouchi AInt J Syst Evol Microbiol10.1099/ijsem.0.0016882017Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Japan, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29873630Acidicapsa dinghuensis sp. nov., a novel acidobacterium isolated from forest soil.Ou-Yang TN, Xia F, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0028462018Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17958Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25248)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25248
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
23352Irina S. Kulichevskaya, Lilia A. Kostina, Vendula Valásková, W. Irene C. Rijpstra, Jaap S. Sinninghe Damsté, Wietse de Boer, Svetlana N. Dedysh10.1099/ijs.0.034819-0Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying woodIJSEM 62: 1512-1520 201221856984
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69826Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400954.1StrainInfo: A central database for resolving microbial strain identifiers