Strain identifier

BacDive ID: 82

Type strain: Yes

Species: Acidisoma sibiricum

Strain Designation: TPB606

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; TPB606 <- T. A. Pankratov

NCBI tax ID(s): 512383 (species)

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General

@ref: 9076

BacDive-ID: 82

DSM-Number: 21000

keywords: 16S sequence, Bacteria, obligate aerobe, chemoorganotroph, psychrophilic, Gram-negative, coccus-shaped, colony-forming

description: Acidisoma sibiricum TPB606 is an obligate aerobe, chemoorganotroph, psychrophilic bacterium that forms circular colonies and was isolated from Sphagnum peat.

NCBI tax id

  • NCBI tax id: 512383
  • Matching level: species

strain history

  • @ref: 9076
  • history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; TPB606 <- T. A. Pankratov

doi: 10.13145/bacdive82.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Acidisoma
  • species: Acidisoma sibiricum
  • full scientific name: Acidisoma sibiricum Belova et al. 2009

@ref: 9076

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Acidisoma

species: Acidisoma sibiricum

full scientific name: Acidisoma sibiricum Belova et al. 2009

strain designation: TPB606

type strain: yes

Morphology

cell morphology

  • @ref: 22964
  • gram stain: negative
  • cell length: 1.4-3.1 µm
  • cell width: 0.7-1.2 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 22964
  • colony size: 2.0-5.0 mm
  • colony color: pinkish
  • colony shape: circular
  • incubation period: 14 days

Culture and growth conditions

culture medium

  • @ref: 9076
  • name: ACIDOSOMA MEDIUM (DSMZ Medium 1220)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1220
  • composition: Name: ACIDOSOMA MEDIUM (DSMZ Medium 1220) Composition: Agar 15.0 g/l Na gluconate 0.5 g/l (NH4)2SO4 0.25 g/l KH2PO4 0.1 g/l Yeast extract 0.1 g/l CaCl2 x 2 H2O 0.05 g/l MgSO4 x 7 H2O 0.02 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l CuCl2 x 5 H2O 0.0001 g/l Na2MoO4 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
9076positivegrowth20psychrophilic
22964positivegrowth2.0-30.0
22964positiveoptimum20.0-25.0

culture pH

@refabilitytypepHPH range
22964positivegrowth3.7-7.6acidophile
22964positiveoptimum5.0-6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 22964
  • oxygen tolerance: obligate aerobe

nutrition type

  • @ref: 22964
  • type: chemoorganotroph

spore formation

  • @ref: 22964
  • spore formation: no

halophily

  • @ref: 22964
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: >2.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2296430089acetate-growth
2296416449alanine-growth
2296416150benzoate-growth
2296428885butanol-growth
2296417968butyrate-growth
2296416947citrate-growth
2296415748D-glucuronate-growth
2296416236ethanol-growth
2296415740formate-growth
2296429806fumarate-growth
2296417120hexanoate-growth
2296424996lactate-growth
2296425017leucine-growth
2296425115malate-growth
2296417306maltose-growth
2296430623oxalate-growth
2296428831propanol-growth
2296417272propionate-growth
2296416634raffinose-growth
2296430031succinate-growth
2296458187alginate-hydrolysis
2296485146carboxymethylcellulose-hydrolysis
2296437397chondroitin sulfate-hydrolysis
2296417309pectin-hydrolysis
2296427941pullulan-hydrolysis
2296417632nitrate-reduction
2296422599arabinose+carbon source
22964casamino acids+carbon source
2296418024D-galacturonic acid+carbon source
2296416813galactitol+carbon source
2296428757fructose+carbon source
2296428260galactose+carbon source
2296424265gluconate+carbon source
2296417234glucose+carbon source
2296417754glycerol+carbon source
2296417196L-asparagine+carbon source
2296429864mannitol+carbon source
2296417268myo-inositol+carbon source
22964peptone+carbon source
2296415361pyruvate+carbon source
2296430911sorbitol+carbon source
2296427922sorbose+carbon source
2296418222xylose+carbon source
22964yeast extract+carbon source
229644853esculin+hydrolysis
2296428304heparin+hydrolysis
2296428017starch+hydrolysis
2296437166xylan+hydrolysis
2296428938ammonium+nitrogen source
2296428300glutamine+nitrogen source
2296427570histidine+nitrogen source
2296416811methionine+nitrogen source
2296417632nitrate+nitrogen source
2296426271proline+nitrogen source
2296416199urea+nitrogen source
22964yeast extract+nitrogen source
2296435391aspartate+/-growth
2296417057cellobiose+/-growth
2296417716lactose+/-growth
2296437684mannose+/-growth
2296417992sucrose+/-growth
2296427082trehalose+/-growth
229645181fucoidan+/-hydrolysis
229646364laminarin+/-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2296428971ampicillinyesyes
2296417698chloramphenicolyesyes
229646472lincomycinyesyes
229647507neomycinyesyes
2296428368novobiocinyesyes
2296417076streptomycinyesyes
2296417833gentamicinyesyes
229646104kanamycinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2296430033bacteriochlorophyll alphano
229648295beta-hydroxybutyrateyes

enzymes

@refvalueactivityec
22964acid phosphatase+3.1.3.2
22964alkaline phosphatase+3.1.3.1
22964alpha-chymotrypsin-3.4.21.1
22964alpha-fucosidase-3.2.1.51
22964alpha-galactosidase-3.2.1.22
22964alpha-glucosidase-3.2.1.20
22964alpha-mannosidase-3.2.1.24
22964beta-galactosidase-3.2.1.23
22964beta-glucosidase-3.2.1.21
22964beta-glucuronidase-3.2.1.31
22964catalase+1.11.1.6
22964cystine arylamidase+3.4.11.3
22964cytochrome oxidase+1.9.3.1
22964esterase+
22964esterase lipase (C 8)+
22964leucine arylamidase+3.4.11.1
22964lipase (C 14)-
22964N-acetyl-beta-glucosaminidase-3.2.1.52
22964naphthol-AS-BI-phosphohydrolase-
22964phosphatidate phosphatase+3.1.3.4
22964trypsin-3.4.21.4
22964urease+3.5.1.5
22964valine arylamidase+

Isolation, sampling and environmental information

isolation

  • @ref: 9076
  • sample type: Sphagnum peat
  • host species: Sphagnum
  • geographic location: western Siberia, Tomsk region, peat bog Bakchar
  • country: Russia
  • origin.country: RUS
  • continent: Asia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Peat moss

Safety information

risk assessment

  • @ref: 9076
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 9076
  • description: Acidisoma sibiricum partial 16S rRNA gene, type strain TPB606
  • accession: AM947653
  • length: 1430
  • database: ena
  • NCBI tax ID: 512383

GC content

@refGC-contentmethod
907660.5thermal denaturation, midpoint method (Tm)
907667.8

External links

@ref: 9076

culture collection no.: DSM 21000, VKM B-2487

straininfo link

  • @ref: 69765
  • straininfo: 402735

literature

  • topic: Phylogeny
  • Pubmed-ID: 19620354
  • title: Acidisoma tundrae gen. nov., sp. nov. and Acidisoma sibiricum sp. nov., two acidophilic, psychrotolerant members of the Alphaproteobacteria from acidic northern wetlands.
  • authors: Belova SE, Pankratov TA, Detkova EN, Kaparullina EN, Dedysh SN
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.009209-0
  • year: 2009
  • mesh: Acetobacteraceae/*classification/*isolation & purification, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cold Temperature, Cytoplasmic Granules/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Hydrogen-Ion Concentration, Hydroxybutyrates/analysis, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polyesters/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siberia, *Wetlands
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9076Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21000)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21000
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
22964Svetlana E. Belova,Timofei A. Pankratov,Ekaterina N. Detkova,Elena N. Kaparullina,Svetlana N. Dedysh10.1099/ijs.0.009209-0Acidisoma tundrae gen. nov., sp. nov. and Acidisoma sibiricum sp. nov., two acidophilic, psychrotolerant members of the Alphaproteobacteria from acidic northern wetlandsIJSEM 59: 2283-2290 200919620354
69765Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402735.1StrainInfo: A central database for resolving microbial strain identifiers