Strain identifier

BacDive ID: 8203

Type strain: Yes

Species: Psychrobacter arcticus

Strain Designation: 273-4

Strain history: CIP <- 2008, DSMZ -> C. Bakermans, Center for Microbial Ecol. and NASA Astrobiol. Inst., Michigan, State Univ., USA: strain 273-4

NCBI tax ID(s): 334543 (species)

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General

@ref: 6889

BacDive-ID: 8203

DSM-Number: 17307

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, ovoid-shaped

description: Psychrobacter arcticus 273-4 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from permafrost sediment cores.

NCBI tax id

  • NCBI tax id: 334543
  • Matching level: species

strain history

@refhistory
6889<- C. Bakermans, Center for Microbial Ecol. and NASA Astrobiol. Inst., Michigan State Univ., USA; 273-4 <- T. Vishnivetskaya, Dept. Food Sci., North Carolina State Univ., USA
116479CIP <- 2008, DSMZ -> C. Bakermans, Center for Microbial Ecol. and NASA Astrobiol. Inst., Michigan, State Univ., USA: strain 273-4

doi: 10.13145/bacdive8203.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Moraxellaceae
  • genus: Psychrobacter
  • species: Psychrobacter arcticus
  • full scientific name: Psychrobacter arcticus Bakermans et al. 2006

@ref: 6889

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Psychrobacter

species: Psychrobacter arcticus

full scientific name: Psychrobacter arcticus Bakermans et al. 2006

strain designation: 273-4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31679negative1.62 µm0.73 µmovoid-shapedno
116479negativerod-shapedno

pigmentation

  • @ref: 31679
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6889BACTO 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
41745Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116479CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
116479CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6889positivegrowth20psychrophilic
31679positiveoptimum22psychrophilic
41745positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
31679positivegrowth07-09alkaliphile
31679positiveoptimum07-09

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31679aerobe
116479obligate aerobe

spore formation

  • @ref: 31679
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31679NaClpositivegrowth7.25 %
31679NaClpositiveoptimum7.25 %

observation

  • @ref: 31679
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3167930089acetate+carbon source
3167929987glutamate+carbon source
3167924996lactate+carbon source
3167925017leucine+carbon source
3167915361pyruvate+carbon source
11647917632nitrate+reduction
11647916301nitrite-reduction

metabolite production

  • @ref: 116479
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31679alkaline phosphatase+3.1.3.1
31679catalase+1.11.1.6
31679cytochrome oxidase+1.9.3.1
116479oxidase+
116479catalase+1.11.1.6
116479urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
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
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116479-+---+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6889permafrost sediment coresSiberia, Kolyma lowlandRussiaRUSAsia
116479Siberian permafrostRussian FederationRUSEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Core sample
#Environmental#Terrestrial#Permafrost

taxonmaps

  • @ref: 69479
  • File name: preview.99_279.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_209;98_234;99_279&stattab=map
  • Last taxonomy: Psychrobacter
  • 16S sequence: AY444822
  • Sequence Identity:
  • Total samples: 7634
  • soil counts: 925
  • aquatic counts: 3187
  • animal counts: 3350
  • plant counts: 172

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68891Risk group (German classification)
1164791Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6889
  • description: Psychrobacter arcticus 273-4 small subunit ribosomal RNA (rrn) gene, partial sequence
  • accession: AY444822
  • length: 1504
  • database: ena
  • NCBI tax ID: 259536

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychrobacter arcticus 273-4GCA_000012305completencbi259536
66792Psychrobacter arcticus 273-4259536.19completepatric259536
66792Psychrobacter arcticus 273-4637000226completeimg259536

GC content

  • @ref: 31679
  • GC-content: 42.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno86.806no
flagellatedno92.146yes
gram-positiveno98.351yes
anaerobicno99.021yes
halophileyes73.555yes
spore-formingno97.251yes
thermophileno98.903yes
glucose-utilno75.859no
aerobicyes80.863yes
glucose-fermentno94.151no

External links

@ref: 6889

culture collection no.: DSM 17307, CIP 109905, VKM B-2377

straininfo link

  • @ref: 77606
  • straininfo: 297302

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738105Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost.Bakermans C, Ayala-Del-Rio HL, Ponder MA, Vishnivetskaya T, Gilichinsky D, Thomashow MF, Tiedje JMInt J Syst Evol Microbiol10.1099/ijs.0.64043-02006Cold Climate, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Psychrobacter/*classification/genetics/isolation & purification, SiberiaGenetics
Metabolism18335164Metabolic activity of Siberian permafrost isolates, Psychrobacter arcticus and Exiguobacterium sibiricum, at low water activities.Ponder MA, Thomashow MF, Tiedje JMExtremophiles10.1007/s00792-008-0151-02008Cell Membrane/metabolism, Cold Temperature, Electron Transport, Ice, Leucine/chemistry, Microscopy, Electron, Transmission/methods, Models, Biological, Oxazines/pharmacology, Permeability, Phylogeny, Psychrobacter/*metabolism, Salts/pharmacology, Siberia, Temperature, Time Factors, Xanthenes/pharmacologyPhylogeny
18818866Development and use of genetic system to identify genes required for efficient low-temperature growth of Psychrobacter arcticus 273-4.Bakermans C, Sloup RE, Zarka DG, Tiedje JM, Thomashow MFExtremophiles10.1007/s00792-008-0193-32008Adaptation, Physiological, *Cold Temperature, Electroporation, *Genes, Bacterial, Genetic Vectors, Membrane Fluidity, Plasmids, Psychrobacter/genetics/*growth & development/physiology, Reverse Transcriptase Polymerase Chain Reaction
Metabolism19168616Psychrobacter arcticus 273-4 uses resource efficiency and molecular motion adaptations for subzero temperature growth.Bergholz PW, Bakermans C, Tiedje JMJ Bacteriol10.1128/JB.01377-082009Adaptation, Physiological, Bacterial Proteins/genetics/metabolism, Cold Temperature, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Psychrobacter/enzymology/genetics/growth & development/*physiologyEnzymology
Genetics20154119The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth.Ayala-del-Rio HL, Chain PS, Grzymski JJ, Ponder MA, Ivanova N, Bergholz PW, Di Bartolo G, Hauser L, Land M, Bakermans C, Rodrigues D, Klappenbach J, Zarka D, Larimer F, Richardson P, Murray A, Thomashow M, Tiedje JMAppl Environ Microbiol10.1128/AEM.02101-092010Cold Temperature, DNA, Bacterial/*chemistry/*genetics, Freezing, *Genome, Bacterial, Molecular Sequence Data, Psychrobacter/*genetics/isolation & purification/physiology, Sequence Analysis, DNA, Siberia, Soil MicrobiologyTranscriptome
Enzymology21445265Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein.Das D, Herve M, Feuerhelm J, Farr CL, Chiu HJ, Elsliger MA, Knuth MW, Klock HE, Miller MD, Godzik A, Lesley SA, Deacon AM, Mengin-Lecreulx D, Wilson IAPLoS One10.1371/journal.pone.00176242011Amino Acid Sequence, Cell Wall/enzymology, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Peptide Synthases/chemistry/*metabolism, Protein Conformation, Psychrobacter/*enzymology, Sequence Homology, Amino Acid, Structure-Activity Relationship, Substrate SpecificityGenetics
Biotechnology22364438Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production.Shi S, Valle-Rodriguez JO, Khoomrung S, Siewers V, Nielsen JBiotechnol Biofuels10.1186/1754-6834-5-72012
Metabolism23082745Toward understanding life under subzero conditions: the significance of exploring psychrophilic "cold-shock" proteins.Kuhn EAstrobiology10.1089/ast.2012.08582012Adaptation, Physiological, Amino Acid Sequence, Cold Shock Proteins and Peptides/genetics/*metabolism, *Cold Temperature, Escherichia coli/enzymology/genetics/metabolism, Escherichia coli Proteins/genetics/metabolism, Freezing, Molecular Chaperones/genetics/metabolism, Molecular Sequence Data, Psychrobacter/enzymology/genetics/metabolism, RNA Helicases/genetics/metabolismEnzymology
Enzymology23603675Biofilm formation by Psychrobacter arcticus and the role of a large adhesin in attachment to surfaces.Hinsa-Leasure SM, Koid C, Tiedje JM, Schultzhaus JNAppl Environ Microbiol10.1128/AEM.00867-132013Adhesins, Bacterial/*physiology, Biofilms/*growth & development, Cloning, Molecular, DNA Primers/genetics, DNA Transposable Elements/genetics, Microscopy, Fluorescence, Microscopy, Phase-Contrast, Mutagenesis, Open Reading Frames/genetics, Psychrobacter/genetics/*growth & development, Real-Time Polymerase Chain Reaction, Siberia, Silicon Dioxide/chemistry, *Soil Microbiology, Surface Properties
Enzymology23826991Branched-chain 2-keto acid decarboxylases derived from Psychrobacter.Wei J, Timler JG, Knutson CM, Barney BMFEMS Microbiol Lett10.1111/1574-6968.122082013Alcohol Dehydrogenase, Amino Acids, Branched-Chain/*metabolism, Bacterial Proteins/chemistry/genetics/*metabolism, Carboxy-Lyases/chemistry/genetics/*metabolism, Hydrogen-Ion Concentration, Kinetics, Psychrobacter/*enzymology/genetics, TemperatureMetabolism
Metabolism24077718DNA double-strand break repair at--15{degrees}C.Dieser M, Battista JR, Christner BCAppl Environ Microbiol10.1128/AEM.02845-132013Cold Temperature, DNA Breaks, Double-Stranded/*radiation effects, *DNA Repair, Psychrobacter/*metabolism/*radiation effects, Radiation, Ionizing
Phylogeny26204948Structural Investigation of the Oligosaccharide Portion Isolated from the Lipooligosaccharide of the Permafrost Psychrophile Psychrobacter arcticus 273-4.Casillo A, Parrilli E, Filomena S, Lindner B, Lanzetta R, Parrilli M, Tutino ML, Corsaro MMMar Drugs10.3390/md130745392015Lipopolysaccharides/*chemistry/isolation & purification, Magnetic Resonance Spectroscopy, Molecular Structure, Oligosaccharides/*chemistry/isolation & purification, Permafrost/*microbiology, Psychrobacter/*chemistryEnzymology
Phylogeny26827927Psychrobacter glaciei sp. nov., isolated from the ice core of an Arctic glacier.Zeng YX, Yu Y, Liu Y, Li HRInt J Syst Evol Microbiol10.1099/ijsem.0.0009392016Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Psychrobacter/*classification/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Svalbard, Ubiquinone/chemistryGenetics
Enzymology29807140Biochemical characterization of ParI, an orphan C5-DNA methyltransferase from Psychrobacter arcticus 273-4.Grgic M, Williamson A, Kjaereng Bjerga GE, Altermark B, Leiros IProtein Expr Purif10.1016/j.pep.2018.05.0122018*Bacterial Proteins/biosynthesis/chemistry/genetics/isolation & purification, *DNA (Cytosine-5-)-Methyltransferases/biosynthesis/chemistry/genetics/isolation & purification, Enzyme Stability, Hot Temperature, Psychrobacter/*enzymology/genetics, Recombinant Proteins/biosynthesis/chemistry/genetics/isolation & purificationPhylogeny
Metabolism30128707Lipid A structural characterization from the LPS of the Siberian psychro-tolerant Psychrobacter arcticus 273-4 grown at low temperature.Casillo A, Ziaco M, Lindner B, Parrilli E, Schwudke D, Holgado A, Beyaert R, Lanzetta R, Tutino ML, Corsaro MMExtremophiles10.1007/s00792-018-1051-62018Acclimatization, *Cold Temperature, Lipid A/*chemistry, Psychrobacter/*chemistry/metabolism
Enzymology31309337Cell-wall associated polysaccharide from the psychrotolerant bacterium Psychrobacter arcticus 273-4: isolation, purification and structural elucidation.Casillo A, Ricciardelli A, Parrilli E, Tutino ML, Corsaro MMExtremophiles10.1007/s00792-019-01113-82019Cell Wall, Magnetic Resonance Spectroscopy, Polysaccharides, *PsychrobacterPhylogeny
33729771Physicochemical Approach to Understanding the Structure, Conformation, and Activity of Mannan Polysaccharides.Casillo A, Fabozzi A, Russo Krauss I, Parrilli E, Biggs CI, Gibson MI, Lanzetta R, Appavou MS, Radulescu A, Tutino ML, Paduano L, Corsaro MMBiomacromolecules10.1021/acs.biomac.0c016592021Bacterial Adhesion, *Mannans, Polysaccharides, *Psychrobacter

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6889Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17307)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17307
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
31679Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2795628776041
41745Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7702
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
77606Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297302.1StrainInfo: A central database for resolving microbial strain identifiers
116479Curators of the CIPCollection of Institut Pasteur (CIP 109905)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109905