Strain identifier

BacDive ID: 24777

Type strain: Yes

Species: Aridibacter kavangonensis

Strain Designation: Ac_23_E3

Strain history: <- P. Wüst, Leibniz-Institut DSMZ GmbH, Germany; Ac_23_E3

NCBI tax ID(s): 1384639 (species)

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General

@ref: 21337

BacDive-ID: 24777

DSM-Number: 26558

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

description: Aridibacter kavangonensis Ac_23_E3 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from sandy subtropical savannah soil .

NCBI tax id

  • NCBI tax id: 1384639
  • Matching level: species

strain history

  • @ref: 21337
  • history: <- P. Wüst, Leibniz-Institut DSMZ GmbH, Germany; Ac_23_E3

doi: 10.13145/bacdive24777.20230509.8.1

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 kavangonensis
  • full scientific name: Aridibacter kavangonensis Huber et al. 2014

@ref: 21337

domain: Bacteria

phylum: Acidobacteria

class: Blastocatellia

order: Blastocatellales

family: Blastocatellaceae

genus: Aridibacter

species: Aridibacter kavangonensis

full scientific name: Aridibacter kavangonensis Huber et al. 2014

strain designation: Ac_23_E3

type strain: yes

Morphology

cell morphology

  • @ref: 21408
  • gram stain: negative
  • cell length: 2.75 µm
  • cell width: 0.65 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refincubation periodcolony sizecolony colorcolony shapemedium used
213378-14 days
214087 days0.25 mmwhite pinkish hue, translucentcircular, convex with enitre marginsagar solidified soil solution equivalent (Angle et.al. 1991) SSE/HD 1:10 pH 8 (Foesel et al., 2013). buffered by HEPPS 10 mM
21408whiteliquid 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

@refnamegrowthlinkcomposition
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
21337SSE/HD1:10 (DSMZ Medium 1426)yeshttps://mediadive.dsmz.de/medium/1426Name: 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
21337positivegrowth28mesophilic
21408positivemaximum47thermophilic
21408positiveminimum12psychrophilic
21408positiveoptimum26.5mesophilic

culture pH

@refabilitytypepHPH range
21408positivemaximum10alkaliphile
21408positiveminimum3.5acidophile
21408positiveoptimum6.75

Physiology and metabolism

spore formation

  • @ref: 21408
  • spore formation: no

halophily

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

metabolite utilization

@refmetaboliteutilization activityChebi-IDkind of utilization tested
21408casamino acids+
21408casein hydrolysate+
21408cellulose+62968
21408fumarate+29806
21408isovalerate+48942
21408laminarin+6364
21408N-acetylgalactosamine+28800
21408peptone+
21408protocatechuate+36241
21408rhamnose+26546
21408yeast extract+
21408chitin+/-17029
21408glutamine+/-28300
21408lactose+/-17716
21408L-asparagine+/-17196
21408starch+/-28017
21408trimethoxybenzoate+/-
21408arabinose-22599
21408erythrose-33946
21408erythrulose-23958
21408fructose-28757
21408fucose-33984
21408galactose-28260
21408glucose-17234
21408lyxose-25097
21408mannose-37684
21408melezitose-6731
21408raffinose-16634
21408sorbose-27922
21408sucrose-17992
21408trehalose-27082
21408xylose-18222
21408glucosamine-5417
21408N-acetylglucosamine-59640
21408acetoin-15688
21408ribitol-15963
21408galactitol-16813
21408arabinitol-22605
21408mannitol-29864
21408myo-inositol-17268
21408sorbitol-30911
21408xylitol-17151
21408alanine-16449
21408arginine-29016
21408aspartate-35391
21408cysteine-15356
21408glutamate-29987
21408glycine-15428
21408histidine-27570
21408hydroxyproline-24741
21408isoleucine-24898
21408lysine-25094
21408methionine-16811
21408ornithine-18257
21408phenylalanine-28044
21408proline-26271
21408threonine-26986
21408tryptophan-27897
21408tyrosine-18186
21408valine-27266
21408adipate-17128
21408acetate-30089
21408ascorbate-22651
21408benzoate-16150
21408butyrate-17968
214082-hydroxybutyrate-64552
21408beta-hydroxybutyrate-8295
214084-hydroxybutyrate-16724
21408isobutyrate-48944
21408hexanoate-17120
21408octanoate-25646
21408citrate-16947
21408isocitrate-16087
21408crotonate-35899
21408formate-15740
21408fumarate-29806
21408gluconate-24265
214082-oxogluconate-
21408glucuronate-24297
214082-oxoglutarate-
21408glycolate-29805
21408glyoxylate-36655
214084-oxopentanoate-39150
21408lactate-24996
21408malate-25115
21408maleic acid-18300
21408malonate-15792
21408nicotinate-32544
21408oxaloacetate-16452
21408propionate-17272
21408pyruvate-15361
21408shikimate-36208
21408succinate-30031
21408tartrate-132950
214082-oxopentanoate-28644
21408butanol-
214081,2-butandiol-
214082,3-butanediol-
21408ethanol-16236
21408ethylene-29362
21408glycol-13643
21408glycerol-17754
21408methanol-17790
21408propanol-28831
214081,2-propandiol-16997
21408rumen extract-
21408tween 80-53426
21408maltose+17306
21408cellobiose-17057
68369malate-25115assimilation
68369adipate-17128assimilation
68369decanoate-27689assimilation
68369gluconate-24265assimilation
68369maltose-17306assimilation
68369N-acetylglucosamine-59640assimilation
68369D-mannitol-16899assimilation
68369D-mannose-16024assimilation
68369L-arabinose-30849assimilation
68369D-glucose-17634assimilation
68369esculin+4853hydrolysis
68369urea-16199hydrolysis
68369arginine-29016hydrolysis
68369D-glucose-17634fermentation
68369tryptophan-27897energy source
68369nitrate-17632reduction

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
21337catalase+1.11.1.6
21337cytochrome-c oxidase+1.9.3.1
68369cytochrome oxidase-1.9.3.1
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)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase-3.2.1.20
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-+-+-++-++++--+-++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21408-----+-+-------------
21337-----++/-+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
21337sandy subtropical savannah soil (17° 53' 37.93'' S 20° 14' 50.71'' E, 1069 m above sea level)Kavango region, MashareNamibiaNAMAfrica
21408subtropical savannah soils ,sandy fallow pH 7.3 - 8.2, 1069 m above sea levelKavango region, MashareNamibiaNAMAfrica2011-00-00-17.893920.2474liquid soil solution equvivalentliquid soil solution equvivalent (Angle et.al. 1991) SSE/HD 1:10 pH 8 (Foesel et al., 2013). buffered by HEPPS 10 mM6 weeks25isolated by constantly streaking out on SSE/HD 1 : 10 solidified with purified agar (15 g/l Oxoid) starting from an enrichnent culture

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_102138.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_737;96_14812;97_18089;98_69678;99_102138&stattab=map
  • Last taxonomy: Aridibacter kavangonensis
  • 16S sequence: KF245633
  • Sequence Identity:
  • Total samples: 143
  • soil counts: 101
  • aquatic counts: 9
  • animal counts: 13
  • plant counts: 20

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
214081
213371Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21337
  • description: Aridibacter kavangonensis strain Ac_23_E3 16S ribosomal RNA gene, partial sequence
  • accession: KF245633
  • length: 1484
  • database: ena
  • NCBI tax ID: 1384639

GC content

  • @ref: 21337
  • GC-content: 52.6
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 21337

culture collection no.: DSM 26558, LMG 27597

straininfo link

  • @ref: 88602
  • straininfo: 388706

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
21337Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26558Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26558)
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/
88602Reimer, 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-ID388706.1