Strain identifier

BacDive ID: 24776

Type strain: Yes

Species: Aridibacter famidurans

Strain Designation: A22/HD/4H, A22_HD_4H

Strain history: <- B. Fösel, Leibniz-Institut DSMZ GmbH, Germany; A22/HD/4H <- B. Fösel, LMU, Munich

NCBI tax ID(s): 1384638 (species)

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General

@ref: 21336

BacDive-ID: 24776

DSM-Number: 26555

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

description: Aridibacter famidurans A22/HD/4H is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from clayey sand soil from a subtropical pasture.

NCBI tax id

  • NCBI tax id: 1384638
  • Matching level: species

strain history

  • @ref: 21336
  • history: <- B. Fösel, Leibniz-Institut DSMZ GmbH, Germany; A22/HD/4H <- B. Fösel, LMU, Munich

doi: 10.13145/bacdive24776.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Blastocatellia
  • order: Blastocatellales
  • family: Blastocatellaceae
  • genus: Aridibacter
  • species: Aridibacter famidurans
  • full scientific name: Aridibacter famidurans Huber et al. 2014

@ref: 21336

domain: Bacteria

phylum: Acidobacteria

class: Blastocatellia

order: Blastocatellales

family: Blastocatellaceae

genus: Aridibacter

species: Aridibacter famidurans

full scientific name: Aridibacter famidurans Huber et al. 2014

strain designation: A22/HD/4H, A22_HD_4H

type strain: yes

Morphology

cell morphology

  • @ref: 21408
  • gram stain: negative
  • cell length: 2.75 µm
  • cell width: 0.9 µm
  • cell shape: rod-shaped

colony morphology

@refincubation periodcolony sizecolony colorcolony shapemedium used
213363-7 days
214087 days0.15 mmpink, translucent, in initial state - yellow, with increased density - bright pinkcircular convex with entire margins, rod - firm aggregation even during shakingagar solidified soil solution equivalent (Angle et al. 1991) SSE/HD 1:10 pH 8 (Foesel et al., 2013). buffered by HEPPS 10 mM
21408liquid soil solution equivalent (Angle et.al. 1991) SSE/HD 1:10 pH 8 (Foesel et al., 2013). buffered by HEPPS 10 mM

Culture and growth conditions

culture medium

@refnamecompositiongrowthlink
21408liquid SSE/HD 1 : 10 mediumliquid SSE/HD 1 : 10 medium
21408agar solidified soil solution equivalent (Angle et al. 1991) SSE/HD 1:10 pH 8 (Foesel et al., 2013). buffered by HEPPS 10 mM
21408liquid soil solution equivalent (Angle et.al. 1991) SSE/HD 1:10 pH 8 (Foesel et al., 2013). buffered by HEPPS 10 mM
21336SSE/HD1:10 (DSMZ Medium 1426)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 wateryeshttps://mediadive.dsmz.de/medium/1426

culture temp

@refgrowthtypetemperaturerange
21336positivegrowth28mesophilic
21408positivemaximum44thermophilic
21408positiveminimum15psychrophilic
21408positiveoptimum27mesophilic

culture pH

@refabilitytypepHPH range
21408positivemaximum9.5alkaliphile
21408positiveminimum4acidophile
21408positiveoptimum7.4

Physiology and metabolism

spore formation

  • @ref: 20215
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
21408NaClpositivemaximum1 %
21408NaClpositiveminimum0 %
21408NaClpositiveoptimum0.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2140826546rhamnose+
2140818222xylose+
2140828800N-acetylgalactosamine+
2140836241protocatechuate+
21408casamino acids+
21408casein hydrolysate+
21408peptone+
21408yeast extract+
2140817057cellobiose+/-
2140817196L-asparagine+/-
2140822599arabinose-
2140833946erythrose-
2140823958erythrulose-
2140828757fructose-
2140833984fucose-
2140828260galactose-
2140817234glucose-
2140817716lactose-
2140825097lyxose-
2140817306maltose-
2140837684mannose-
214086731melezitose-
2140816634raffinose-
2140827922sorbose-
2140817992sucrose-
2140827082trehalose-
214085417glucosamine-
2140859640N-acetylglucosamine-
2140815688acetoin-
2140815963ribitol-
2140816813galactitol-
2140822605arabinitol-
2140829864mannitol-
2140817268myo-inositol-
2140830911sorbitol-
2140817151xylitol-
2140816449alanine-
2140829016arginine-
2140835391aspartate-
2140815356cysteine-
2140829987glutamate-
2140815428glycine-
2140827570histidine-
2140824741hydroxyproline-
2140824898isoleucine-
2140825017leucine-
2140825094lysine-
2140816811methionine-
2140818257ornithine-
2140828044phenylalanine-
2140826271proline-
2140826986threonine-
2140827897tryptophan-
2140818186tyrosine-
2140827266valine-
2140817128adipate-
2140830089acetate-
2140822651ascorbate-
2140816150benzoate-
21408trimethoxybenzoate-
2140817968butyrate-
21408645522-hydroxybutyrate-
214088295beta-hydroxybutyrate-
21408167244-hydroxybutyrate-
2140848944isobutyrate-
2140817120hexanoate-
2140825646octanoate-
2140816947citrate-
2140816087isocitrate-
2140815740formate-
2140835899crotonate-
2140829806fumarate-
2140824265gluconate-
2140824297glucuronate-
214082-oxogluconate-
2140829805glycolate-
2140836655glyoxylate-
2140848942isovalerate-
21408391504-oxopentanoate-
2140824996lactate-
2140825115malate-
2140818300maleic acid-
2140815792malonate-
2140832544nicotinate-
2140816452oxaloacetate-
2140817272propionate-
2140815361pyruvate-
2140836208shikimate-
2140830031succinate-
21408132950tartrate-
21408286442-oxopentanoate-
21408butanol-
214081,2-butandiol-
214082,3-butanediol-
2140816236ethanol-
2140829362ethylene-
2140813643glycol-
2140817754glycerol-
2140817790methanol-
2140828831propanol-
21408169971,2-propandiol-
21408rumen extract-
214086364laminarin-
2140853426tween 80-
21408esculin hydrolysate+
214084-nitrophenyl beta-D-galactopyranoside hydrolysate+
214085291gelatin hydrolyzed+
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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
21336catalase+1.11.1.6
21336cytochrome-c oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21408-+-++++-++++---+++--
21336-+-+/--+++/-+-+/----+-++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21336-----+-+------------
21336-----+-+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
21336clayey sand soil from a subtropical pastureErichsfelde (21° 38' 15.8'' S 16° 52' 03.9'' E, 1497 m above sea level)NamibiaNAMAfrica
21408soil sample, subtropical savannah soil, clayey sand soil pH 7.4 - 8.2, 1497m above sea levelErichsfelde (21° 38' 15.8'' S 16° 52' 03.9'' E, 1497 m above sea level)NamibiaNAMAfrica2009-00-00-21.637716.8678liquid SSE/HD 1 : 10 mediumsoil solution equivalent (Angle et al. 1991) SSE/HD 1:10 pH 8 (Foesel et al., 2013). buffered by HEPPS 10 mM6 weeks20pure culture was gained by prolonged (about 1 year) stravation of an enrichment culture in pure SSE pH 8 - isolation by plating on SSE/HD 1 : 10 solidified with purified agar (15 g/l Oxoid)

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Soil
#Climate#Temperate#Subtropical

taxonmaps

  • @ref: 69479
  • File name: preview.99_102139.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_737;96_14812;97_18089;98_69678;99_102139&stattab=map
  • Last taxonomy: Aridibacter famidurans
  • 16S sequence: KF245634
  • Sequence Identity:
  • Total samples: 42
  • soil counts: 33
  • aquatic counts: 3
  • animal counts: 4
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
214081
213361Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21336
  • description: Aridibacter famidurans strain A22_HD_4H 16S ribosomal RNA gene, partial sequence
  • accession: KF245634
  • length: 1478
  • database: ena
  • NCBI tax ID: 1384638

GC content

  • @ref: 21336
  • GC-content: 53.2
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 21336

culture collection no.: DSM 26555, LMG 27985

straininfo link

  • @ref: 88601
  • straininfo: 391685

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24573163Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil.Huber KJ, Wust PK, Rohde M, Overmann J, Foesel BUInt J Syst Evol Microbiol10.1099/ijs.0.060236-02014Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Namibia, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28945537Aridibacter nitratireducens sp. nov., a member of the family Blastocatellaceae, class Blastocatellia, isolated from an African soil.Huber KJ, Geppert AM, Gross U, Luckner M, Wanner G, Cooper P, Abakah J, Janssen I, Overmann JInt J Syst Evol Microbiol10.1099/ijsem.0.0023182017Acidobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ghana, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
21336Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26555Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26555)
21408Huber K.J. , Wüst P. , Rohde M. , Overmann J., Foesel B. U.,Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil10.1099/ijs.0.060236-0IJSEM 64: 1866-1875 201424573163
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88601Reimer, 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 identifiers10.60712/SI-ID391685.1