Strain identifier

BacDive ID: 452

Type strain: Yes

Species: Paraglaciecola mesophila

Strain history: CIP <- 2004, DSMZ <- L. A. Romanenko, Russian Academy Sciences, Vladivostok, Russia

NCBI tax ID(s): 1128912 (strain), 197222 (species)

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General

@ref: 5677

BacDive-ID: 452

DSM-Number: 15026

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

description: Paraglaciecola mesophila DSM 15026 is a mesophilic, Gram-negative, motile bacterium that was isolated from liquor of ascidian Halocynthia aurantium.

NCBI tax id

NCBI tax idMatching level
1128912strain
197222species

strain history

@refhistory
5677<- E. Stackebrandt <- L. A. Romanenko
120910CIP <- 2004, DSMZ <- L. A. Romanenko, Russian Academy Sciences, Vladivostok, Russia

doi: 10.13145/bacdive452.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Paraglaciecola
  • species: Paraglaciecola mesophila
  • full scientific name: Paraglaciecola mesophila (Romanenko et al. 2003) Shivaji and Reddy 2014

  • synonyms

    • @ref: 20215
    • synonym: Glaciecola mesophila

@ref: 5677

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Paraglaciecola

species: Paraglaciecola mesophila

full scientific name: Paraglaciecola mesophila (Romanenko et al. 2003) Shivaji and Reddy 2014

type strain: yes

Morphology

cell morphology

  • @ref: 120910
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5677BACTO 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
36577Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120910CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
120910CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5677positivegrowth25mesophilic
36577positivegrowth25mesophilic
120910positivegrowth5-30

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
120910NaClpositivegrowth2-6 %
120910NaClnogrowth0 %
120910NaClnogrowth8 %
120910NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1209104853esculin-hydrolysis
12091017632nitrate-reduction
12091016301nitrite-reduction
120910132112sodium thiosulfate-builds gas from

metabolite production

  • @ref: 120910
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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
120910oxidase-
120910beta-galactosidase+3.2.1.23
120910alcohol dehydrogenase-1.1.1.1
120910gelatinase+/-
120910amylase+
120910caseinase+3.4.21.50
120910catalase+1.11.1.6
120910tween esterase+
120910lecithinase-
120910lipase+
120910lysine decarboxylase-4.1.1.18
120910ornithine decarboxylase-4.1.1.17
120910protease+
120910tryptophan deaminase-
120910urease-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
120910-+++-+--+-+++++++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
5677liquor of ascidian Halocynthia aurantiumHalocynthia aurantiumTroista Bay, Peter the Great BayRussiaRUSAsia
120910Liquor of ascidian Halocynthia aurantiumRussian FederationRUSEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Tunicata
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_1068.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_98;96_345;97_456;98_525;99_1068&stattab=map
  • Last taxonomy: Paraglaciecola
  • 16S sequence: AJ488501
  • Sequence Identity:
  • Total samples: 12250
  • soil counts: 201
  • aquatic counts: 6393
  • animal counts: 5596
  • plant counts: 60

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56771Risk group (German classification)
1209101Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5677
  • description: Glaciecola sp. KMM 241 partial 16S rRNA gene, strain KMM 241
  • accession: AJ488501
  • length: 1499
  • database: ena
  • NCBI tax ID: 1128912

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraglaciecola mesophila KMM 241GCA_000315015contigncbi1128912
66792Glaciecola mesophila KMM 2411128912.3wgspatric1128912
66792Paraglaciecola mesophila KMM 2412531839187draftimg1128912

GC content

  • @ref: 5677
  • GC-content: 44.6-44.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.717no
flagellatedyes84.34no
gram-positiveno98.989no
anaerobicno98.09no
aerobicyes83.008no
halophileyes66.702no
spore-formingno96.885no
glucose-utilyes94.428no
thermophileno99.608yes
glucose-fermentno78.697no

External links

@ref: 5677

culture collection no.: DSM 15026, CIP 108360, KMM 241, LMG 22017

straininfo link

  • @ref: 70131
  • straininfo: 88313

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807181Glaciecola mesophila sp. nov., a novel marine agar-digesting bacterium.Romanenko LA, Zhukova NV, Rohde M, Lysenko AM, Mikhailov VV, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.02469-02003Agar/*metabolism, Alteromonadaceae/*classification/*genetics/isolation & purification/physiology, Animals, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Urochordata/*microbiologyGenetics
Phylogeny17473239Glaciecola agarilytica sp. nov., an agar-digesting marine bacterium from the East Sea, Korea.Yong JJ, Park SJ, Kim HJ, Rhee SKInt J Syst Evol Microbiol10.1099/ijs.0.64723-02007Agar/metabolism, Alteromonadaceae/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Carbon/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, TemperatureMetabolism
Enzymology19506861Gene cloning, expression and characterization of a new cold-active and salt-tolerant endo-beta-1,4-xylanase from marine Glaciecola mesophila KMM 241.Guo B, Chen XL, Sun CY, Zhou BC, Zhang YZAppl Microbiol Biotechnol10.1007/s00253-009-2056-y2009Alteromonadaceae/*enzymology/genetics, Amino Acid Sequence, Cloning, Molecular, Cold Temperature, DNA, Bacterial/genetics, Escherichia coli/metabolism, Genes, Bacterial, Molecular Sequence Data, Recombinant Proteins/biosynthesis, Salt Tolerance, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Substrate Specificity, Water Microbiology, *Xylan Endo-1,3-beta-Xylosidase/genetics/metabolismMetabolism
Enzymology23567318Gene cloning, expression and characterization of a novel xylanase from the marine bacterium, Glaciecola mesophila KMM241.Guo B, Li PY, Yue YS, Zhao HL, Dong S, Song XY, Sun CY, Zhang WX, Chen XL, Zhang XY, Zhou BC, Zhang YZMar Drugs10.3390/md110411732013Alteromonadaceae/*enzymology/genetics, *Cloning, Molecular, Endo-1,4-beta Xylanases/genetics/isolation & purification/*metabolism, Escherichia coli/*enzymology/genetics, Gene Expression Regulation, Bacterial, Hydrogen-Ion Concentration, Salt Tolerance, Temperature, beta-Glucosidase/genetics/isolation & purification/*metabolismPhylogeny
Phylogeny24981324Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov., isolated from the Southern Ocean.Shivaji S, Reddy GSInt J Syst Evol Microbiol10.1099/ijs.0.065409-02014Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny30217847A New Group of Modular Xylanases in Glycoside Hydrolase Family 8 from Marine Bacteria.Chen XL, Zhao F, Yue YS, Zhang XY, Zhang YZ, Li PYAppl Environ Microbiol10.1128/AEM.01785-182018Amino Acid Motifs, Amino Acid Sequence, Bacteria/classification/*enzymology/genetics/*isolation & purification, Bacterial Proteins/chemistry/genetics/*metabolism, Catalytic Domain, Glycoside Hydrolases/chemistry/genetics/*metabolism, *Multigene Family, Phylogeny, Seawater/*microbiology, Xylans/metabolismMetabolism
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
Phylogeny32687464Paraglaciecola marina sp. nov., isolated from marine alga (Sargassum natans (L.) Gaillon).Wang Y, Zhang Y, Liu T, Zhu X, Ma J, Su X, Kang J, Guo CInt J Syst Evol Microbiol10.1099/ijsem.0.0041322020Alteromonadaceae/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sargassum/*microbiology, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
5677Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15026)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15026
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
36577Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5974
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
70131Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88313.1StrainInfo: A central database for resolving microbial strain identifiers
120910Curators of the CIPCollection of Institut Pasteur (CIP 108360)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108360