Strain identifier

BacDive ID: 451

Type strain: Yes

Species: Glaciecola pallidula

Strain Designation: ICO29, C12ST5

Strain history: CIP <- 1998, ACAM <- 1997, G. Bowman: strain ICO29 <- D. Nichols: strain C12ST5

NCBI tax ID(s): 1121922 (strain), 56807 (species)

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General

@ref: 5267

BacDive-ID: 451

DSM-Number: 14239

keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, slightly halophilic, chemoheterotroph, psychrophilic, Gram-negative, motile, rod-shaped

description: Glaciecola pallidula ICO29 is a facultative aerobe, slightly halophilic, chemoheterotroph bacterium that was isolated from sea ice.

NCBI tax id

NCBI tax idMatching level
56807species
1121922strain

strain history

@refhistory
5267<- J. P. Bowman
121512CIP <- 1998, ACAM <- 1997, G. Bowman: strain ICO29 <- D. Nichols: strain C12ST5

doi: 10.13145/bacdive451.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Glaciecola
  • species: Glaciecola pallidula
  • full scientific name: Glaciecola pallidula Bowman et al. 1998

@ref: 5267

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Glaciecola

species: Glaciecola pallidula

full scientific name: Glaciecola pallidula Bowman et al. 1998

strain designation: ICO29, C12ST5

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilitycell lengthcell widthconfidence
23291negativerod-shapedyes
232911-5 µm0.2-0.4 µm
69480yes92.824
69480negative99.983
121512negativerod-shapedyes

colony morphology

@refcolony sizeincubation periodcolony colorcolony shape
232913-5 mm14 days
23291pale pinkcircular

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5267BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
36585Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121512CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5267positivegrowth2-15psychrophilic
23291positivemaximum18-20psychrophilic
23291positiveoptimum10-15psychrophilic
23291psychrophilic
36585positivegrowth10psychrophilic
121512positivegrowth5-18psychrophilic
121512nogrowth22psychrophilic
121512nogrowth25mesophilic
121512nogrowth30mesophilic
121512nogrowth37mesophilic
121512nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 23291
  • oxygen tolerance: facultative aerobe

nutrition type

  • @ref: 23291
  • type: chemoheterotroph

spore formation

@refspore formationconfidence
23291no
69481no100
69480no99.995

halophily

  • @ref: 23291
  • halophily level: slightly halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2329129806fumarate-assimilation
2329117203L-proline-assimilation
2329117895L-tyrosine-assimilation
23291yeast extract-required for growth
2329130089acetate+carbon source
2329124996lactate+carbon source
2329117754glycerol+carbon source
2329114336glycerol 1-phosphate+carbon source
2329128087glycogen+carbon source
2329129985L-glutamate+carbon source
2329116452oxaloacetate+carbon source
2329115361pyruvate+carbon source
2329130089acetate+energy source
2329124996lactate+energy source
2329117754glycerol+energy source
2329114336glycerol 1-phosphate+energy source
2329128087glycogen+energy source
2329129985L-glutamate+energy source
2329116452oxaloacetate+energy source
2329115361pyruvate+energy source
2329153426tween 80+hydrolysis
2329112936D-galactose+/-builds acid from
2329117634D-glucose+/-builds acid from
2329128053melibiose+/-builds acid from
2329117754glycerol+/-builds acid from
2329117306maltose+/-builds acid from
2329117968butyrate+/-carbon source
2329128017starch+/-degradation
2329117968butyrate+/-energy source
1215124853esculin-hydrolysis
12151217632nitrate-reduction
12151216301nitrite-reduction

metabolite production

  • @ref: 121512
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
232916-phospho-beta-galactosidase+3.2.1.85
23291alkaline phosphatase+3.1.3.1
23291alpha-galactosidase+3.2.1.22
23291catalase+1.11.1.6
23291cytochrome oxidase+1.9.3.1
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
121512oxidase+
121512beta-galactosidase+3.2.1.23
121512alcohol dehydrogenase-1.1.1.1
121512gelatinase-
121512amylase-
121512caseinase-3.4.21.50
121512catalase+1.11.1.6
121512tween esterase+
121512lecithinase-
121512lipase-
121512lysine decarboxylase-4.1.1.18
121512ornithine decarboxylase-4.1.1.17
121512protease-
121512tryptophan deaminase-
121512urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121512-+++-+--++++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
5267sea iceTaynaya BayAustralia and Oceania
23291Antarctic sea-ice diatom assemblages
121512Environment, Sea iceAntarcticaAntarcticaATA1994

isolation source categories

Cat1Cat2Cat3
#Host#Algae
#Climate#Cold#Polar
#Environmental#Aquatic#Ice
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_7889.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_98;96_1394;97_1661;98_3881;99_7889&stattab=map
  • Last taxonomy: Glaciecola pallidula subclade
  • 16S sequence: U85854
  • Sequence Identity:
  • Total samples: 1635
  • soil counts: 26
  • aquatic counts: 1533
  • animal counts: 74
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
52671Risk group (German classification)
1215121Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Glaciecola pallidula ACAM 615T 16S ribosomal RNA gene, partial sequenceU858541475ena1121922
20218Glaciecola pallidula partial 16S rRNA gene, type strain DSM 14239TFR7461071522ena1121922

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glaciecola pallidula DSM 14239 = ACAM 615GCA_000428905scaffoldncbi1121922
66792Glaciecola pallidula DSM 14239 = ACAM 615GCA_000315035contigncbi1121922
66792Glaciecola pallidula DSM 14239 = ACAM 6151121922.3wgspatric1121922
66792Glaciecola pallidula DSM 142392531839186draftimg1121922
66792Glaciecola pallidula DSM 142392524023167draftimg1121922

GC content

  • @ref: 23291
  • GC-content: 40.00
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.988yes
flagellatedyes81.605no
gram-positiveno98.888yes
anaerobicno98.367yes
aerobicyes79.225yes
halophileyes65.963no
spore-formingno96.1yes
glucose-utilyes81.368no
thermophileno99.756no
glucose-fermentno86.94no

External links

@ref: 5267

culture collection no.: DSM 14239, ACAM 615, CIP 105819

straininfo link

  • @ref: 70130
  • straininfo: 46254

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957118Glaciecola nitratireducens sp. nov., isolated from seawater.Baik KS, Park YD, Seong CN, Kim EM, Bae KS, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.64330-02006Alteromonadaceae/classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/*analysis, Seawater/*microbiology, *Water MicrobiologyGenetics
Phylogeny30608230Glaciecola amylolytica sp. nov., an amylase-producing bacterium isolated from seawater.Xiao YK, Yan ZF, Kim Y, Lee HM, Trinh H, Yang JE, Won KH, Yi TH, Kook MInt J Syst Evol Microbiol10.1099/ijsem.0.0032222019Alteromonadaceae/*classification/isolation & purification, Amylases, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5267Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14239)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14239
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23291JOHN P. BOWMAN, SHAREE A. McCAMMON, JANELLE L. BROWN, TOM A. McMEEKIN10.1099/00207713-48-4-1213Glaciecola punicea gen. nov., sp. nov. and Glaciecola pallidula gen. nov., sp. nov.: psychrophilic bacteria from Antarctic sea-ice habitatsIJSEM 48: 1213-1222 1998
36585Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17881
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)
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
70130Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46254.1StrainInfo: A central database for resolving microbial strain identifiers
121512Curators of the CIPCollection of Institut Pasteur (CIP 105819)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105819