Strain identifier

BacDive ID: 7505

Type strain: Yes

Species: Glaciibacter superstes

Strain history: <- M. Tanaka, Univ. Hokkaido, Japan; AHU1791

NCBI tax ID(s): 1121924 (strain), 501023 (species)

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General

@ref: 15488

BacDive-ID: 7505

DSM-Number: 21135

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive, motile, rod-shaped

description: Glaciibacter superstes DSM 21135 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from ice wedge.

NCBI tax id

NCBI tax idMatching level
1121924strain
501023species

strain history

  • @ref: 15488
  • history: <- M. Tanaka, Univ. Hokkaido, Japan; AHU1791

doi: 10.13145/bacdive7505.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Glaciibacter
  • species: Glaciibacter superstes
  • full scientific name: Glaciibacter superstes Katayama et al. 2009

@ref: 15488

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Glaciibacter

species: Glaciibacter superstes

full scientific name: Glaciibacter superstes Katayama et al. 2009 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28909positive1.1-1.8 µm0.3-0.5 µmrod-shapedyes
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
18342Oyster white (1013)10-14 daysISP 2
18342Oyster white (1013)10-14 daysISP 3
18342Oyster white (1013)10-14 daysISP 4
18342Oyster white (1013)10-14 daysISP 5
18342Beige (1001)10-14 daysISP 6
18342Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18342noISP 2
18342noISP 3
18342noISP 4
18342noISP 5
18342noISP 6
18342noISP 7

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21135_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21135_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21135_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21135_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15488TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18342ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18342ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18342ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18342ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18342ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18342ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
15488positivegrowth15psychrophilic
18342positiveoptimum28mesophilic
28909positiveoptimum20psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 28909
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
28909no
69481no100
69480no99.78

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2890922599arabinose+carbon source
2890917057cellobiose+carbon source
2890928757fructose+carbon source
2890928260galactose+carbon source
2890917234glucose+carbon source
2890917754glycerol+carbon source
2890917306maltose+carbon source
2890929864mannitol+carbon source
2890937684mannose+carbon source
2890926546rhamnose+carbon source
2890933942ribose+carbon source
2890917992sucrose+carbon source
2890917151xylitol+carbon source
2890918222xylose+carbon source
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
28909catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18342-+++--+--++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18342++++++---+----+----

Isolation, sampling and environmental information

isolation

  • @ref: 15488
  • sample type: ice wedge
  • geographic location: Alaska, Fox permafrost tunnel
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Ice

taxonmaps

  • @ref: 69479
  • File name: preview.99_4657.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2315;97_2812;98_3494;99_4657&stattab=map
  • Last taxonomy: Glaciibacter superstes subclade
  • 16S sequence: AB378301
  • Sequence Identity:
  • Total samples: 607
  • soil counts: 217
  • aquatic counts: 163
  • animal counts: 118
  • plant counts: 109

Safety information

risk assessment

  • @ref: 15488
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15488
  • description: Glaciibacter superstes gene for 16S rRNA, partial sequence, strain: AHU1791
  • accession: AB378301
  • length: 1498
  • database: ena
  • NCBI tax ID: 501023

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glaciibacter superstes DSM 21135GCA_000421145scaffoldncbi1121924
66792Glaciibacter superstes DSM 211351121924.6wgspatric1121924
66792Glaciibacter superstes DSM 211352524614536draftimg1121924

GC content

  • @ref: 15488
  • GC-content: 65

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes63.55no
flagellatedno93.884no
gram-positiveyes90.174yes
anaerobicno99.453yes
aerobicyes93.737yes
halophileno91.585no
spore-formingno88.832yes
thermophileno99.015no
glucose-utilyes86.71yes
glucose-fermentno88.162yes

External links

@ref: 15488

culture collection no.: DSM 21135, NBRC 104264, AHU 1791

straininfo link

  • @ref: 76951
  • straininfo: 402872

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19244426Glaciibacter superstes gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge.Katayama T, Kato T, Tanaka M, Douglas TA, Brouchkov A, Fukuda M, Tomita F, Asano KInt J Syst Evol Microbiol10.1099/ijs.0.001354-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Alaska, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Genes, rRNA, *Ice, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny33666687Glaciibacter flavus sp. nov., isolated from a lichen sample.An DF, Jiang LQ, Zhang K, Li GD, Wang XY, Jiang MG, Lang L, Wang LS, Imhoff JF, Jiang CL, Jiang YArch Microbiol10.1007/s00203-021-02247-02021Actinomycetales/chemistry/*classification/cytology/physiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genome, Bacterial/genetics, Lichens/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15488Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21135)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21135
18342Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21135.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
28909Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2534828776041
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
68379Automatically annotated from API Coryne
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76951Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402872.1StrainInfo: A central database for resolving microbial strain identifiers