Strain identifier

BacDive ID: 158483

Type strain: Yes

Species: Granulicella sibirica

Strain Designation: AF10

Strain history: <- S. Dedysh; Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, RUSSIA; AF10<-I.S, Kulichevskaya

NCBI tax ID(s): 2479048 (species)

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General

@ref: 65159

BacDive-ID: 158483

DSM-Number: 104461

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

description: Granulicella sibirica AF10 is an aerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies and was isolated from organic soil layer in forested tundra.

NCBI tax id

  • NCBI tax id: 2479048
  • Matching level: species

strain history

  • @ref: 65159
  • history: <- S. Dedysh; Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, RUSSIA; AF10<-I.S, Kulichevskaya

doi: 10.13145/bacdive158483.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Terriglobia
  • order: Terriglobales
  • family: Acidobacteriaceae
  • genus: Granulicella
  • species: Granulicella sibirica
  • full scientific name: Granulicella sibirica Oshkin et al. 2019

@ref: 65159

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Granulicella

species: Granulicella sibirica

full scientific name: Granulicella sibirica Oshkin et al. 2019

strain designation: AF10

type strain: yes

Morphology

cell morphology

  • @ref: 67845
  • gram stain: negative
  • cell length: 1.5-5 µm
  • cell width: 0.3-0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 67845
  • colony color: pale-pink
  • colony shape: circular

Culture and growth conditions

culture medium

  • @ref: 65159
  • name: GRANULICELLA MEDIUM (DSMZ Medium 1284)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1284
  • composition: Name: GRANULICELLA MEDIUM (DSMZ Medium 1284; with strain-specific modifications) Composition: Agar 15.0 g/l Glucose 0.5 g/l Casamino acids 0.1 g/l Yeast extract 0.1 g/l NH4NO3 0.1 g/l MgSO4 x 7 H2O 0.04 g/l CaCl2 x 2 H2O 0.02 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
65159positivegrowth25mesophilic
67845positivegrowth2-30

culture pH

@refabilitytypepHPH range
67845positivegrowth3.5-7acidophile
67845positiveoptimum4.5-5

Physiology and metabolism

oxygen tolerance

  • @ref: 67845
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 67845
  • type: chemoorganotroph

observation

  • @ref: 67845
  • observation: Produces copious amounts of EPS. Tends to form large cell conglomerates in old cultures. Colonies have a gummy consistency.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
6784565327D-xylose+builds acid from
6784517634D-glucose+builds acid from
6784517306maltose+builds acid from
6784512936D-galactose+builds acid from
6784515824D-fructose+builds acid from
6784517992sucrose+builds acid from
6784517057cellobiose+builds acid from
6784528053melibiose+builds acid from
6784516024D-mannose+builds acid from
6784517814salicin+builds acid from
6784517716lactose+builds acid from
678456731melezitose+builds acid from
6784559640N-acetylglucosamine+builds acid from
6784516988D-ribose-builds acid from
6784527082trehalose-builds acid from
6784518305arbutin-builds acid from
6784516899D-mannitol-builds acid from
6784517108D-arabinose-builds acid from
6784517924D-sorbitol-builds acid from
6784528847D-fucose-builds acid from
6784517268myo-inositol-builds acid from
6784516634raffinose-builds acid from
6784515963ribitol-builds acid from
6784516813galactitol-builds acid from
6784515443inulin-builds acid from
678456359lactulose+builds acid from
6784579285leucrose+builds acid from
6784563150D-rhamnose+builds acid from
6784524265gluconate+builds acid from
6784530089acetate-builds acid from
6784524996lactate-builds acid from
6784530031succinate-builds acid from
6784524297glucuronate-builds acid from
6784525115malate-builds acid from
6784515361pyruvate-builds acid from
6784517968butyrate-builds acid from
6784530623oxalate-builds acid from
6784517272propionate-builds acid from
6784515740formate-builds acid from
6784529806fumarate-builds acid from
6784516947citrate-builds acid from
6784531011valerate-builds acid from
6784516236ethanol-builds acid from
6784517790methanol-builds acid from
678454853esculin+hydrolysis
678456364laminarin+hydrolysis
678456452lichenin+hydrolysis
6784528017starch+hydrolysis
6784527941pullulan+hydrolysis
6784537166xylan+hydrolysis
6784517309pectin-hydrolysis
6784553311sodium alginate-hydrolysis
6784585146carboxymethylcellulose-hydrolysis
6784562968cellulose-hydrolysis
6784517029chitin-hydrolysis
6784516261chitosan-hydrolysis
678455181fucoidan-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
678456472lincomycinyesyes10 µg (disc)
6784528368novobiocinyesyes30 µg (disc)
678456104kanamycinyesyes30 µg (disc)
6784528971ampicillinyesyes10 µg (disc)
6784517833gentamicinyesyes10 µg (disc)
678457507neomycinyesyes10 µg (disc)
6784517076streptomycinyesyes10 µg (disc)
6784517698chloramphenicolyesyes30 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
67845acid phosphatase+3.1.3.2
67845alkaline phosphatase+3.1.3.1
67845leucine arylamidase+3.4.11.1
67845valine arylamidase+
67845naphthol-AS-BI-phosphohydrolase+
67845alpha-galactosidase+3.2.1.22
67845alpha-glucosidase+3.2.1.20
67845alpha-mannosidase+3.2.1.24
67845alpha-fucosidase+3.2.1.51
67845beta-galactosidase+3.2.1.23
67845beta-glucosidase+3.2.1.21
67845beta-glucuronidase+3.2.1.31
67845N-acetyl-beta-glucosaminidase+3.2.1.52
67845esterase (C 4)-
67845esterase Lipase (C 8)-
67845lipase (C 14)-
67845cystine arylamidase-3.4.11.3
67845trypsin-3.4.21.4
67845alpha-chymotrypsin-3.4.21.1
67845cytochrome oxidase-1.9.3.1
67845urease-3.5.1.5
67845catalase+1.11.1.6
68369cytochrome 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)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
65159-+---++/----++-+++++-+/-

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
65159-----+-+-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
65159organic soil layer in forested tundraWest Siberia, Nadym region (65° 36' 51.6'' N, 72° 43' 35.5'' E)RussiaRUSAsia65.614372.7265
67845soil sample from an acidic (pH 4.1-4.5) organic soil layerforested tundra, Nadym regionSiberiaAsia65.614372.7265modified DSM mdeium No. 1284per litre distilled water): 0.6 g glucose, 0.1 g yeast extract, 0.1 g casamino acids, 0.1 g NH4NO3, 0.04 g MgSO 4 x 7H2O, 0.02 g CaCl2 x 2H2O. The medium was solidified with 10 g l-1 phytagel. The medium pH was adjusted to 4.0-5.0 with 20-50 mg alginic acid l-1.4 weeks20

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Climate#Cold#Tundra

Sequence information

16S sequences

  • @ref: 67845
  • description: Granulicella sibirica strain AF10 16S ribosomal RNA gene, partial sequence
  • accession: MK053657
  • length: 1496
  • database: ena
  • NCBI tax ID: 2479048

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Granulicella sibirica AF102880944282draftimg2479048
67845Granulicella sibirica AF10GCA_004115155contigncbi2479048

GC content

  • @ref: 67845
  • GC-content: 59.8
  • method: genome sequence analysis

External links

@ref: 65159

culture collection no.: DSM 104461, VKM B-3276

straininfo link

  • @ref: 111278
  • straininfo: 401345

literature

  • topic: Phylogeny
  • Pubmed-ID: 30775959
  • title: Granulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia.
  • authors: Oshkin IY, Kulichevskaya IS, Rijpstra WIC, Sinninghe Damste JS, Rakitin AL, Ravin NV, Dedysh SN
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003290
  • year: 2019
  • mesh: Acidobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Siberia, *Soil Microbiology, *Tundra
  • topic2: Transcriptome

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
65159Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104461Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104461)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67845Igor Y. Oshkin, Irina S. Kulichevskaya, W. Irene C. Rijpstra, Jaap S. Sinninghe Damsté, Andrey L. Rakitin, Nikolai V. Ravin, Svetlana N. DedyshGranulicella sibirica sp. nov., a psychrotolerant acidobacterium isolated from an organic soil layer in forested tundra, West Siberia10.1099/ijsem.0.003290IJSEM 69: 1195-1201 2019
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
111278Reimer, 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-ID401345.1