Strain identifier

BacDive ID: 5631

Type strain: Yes

Species: Psychroserpens burtonensis

Strain history: CIP <- 1998, ACAM <- 1985, AJ. McGuire, Tasmania Univ., Australia <- P. Franzmann

NCBI tax ID(s): 1123037 (strain), 49278 (species)

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General

@ref: 4643

BacDive-ID: 5631

DSM-Number: 12212

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

description: Psychroserpens burtonensis DSM 12212 is a psychrophilic, Gram-negative bacterium that was isolated from water.

NCBI tax id

NCBI tax idMatching level
1123037strain
49278species

strain history

@refhistory
4643<- ACAM <- A. McQuize <- P. D. Franzmann, Antarctic Division
117078CIP <- 1998, ACAM <- 1985, AJ. McGuire, Tasmania Univ., Australia <- P. Franzmann

doi: 10.13145/bacdive5631.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Psychroserpens
  • species: Psychroserpens burtonensis
  • full scientific name: Psychroserpens burtonensis Bowman et al. 1997

@ref: 4643

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Psychroserpens

species: Psychroserpens burtonensis

full scientific name: Psychroserpens burtonensis Bowman et al. 1997 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.972
117078negativerod-shapedno

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_12212_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_12212_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_12212_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_12212_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_12212_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4643BACTO 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
36203Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
117078CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
4643positivegrowth10-15psychrophilic
36203positivegrowth15psychrophilic
117078positivegrowth15-30
117078nogrowth5psychrophilic
117078nogrowth37mesophilic
117078nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.983

halophily

@refsaltgrowthtested relationconcentration
117078NaClnogrowth0 %
117078NaClnogrowth2 %
117078NaClnogrowth4 %
117078NaClnogrowth6 %
117078NaClnogrowth8 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1170784853esculin-hydrolysis
11707817632nitrate-reduction
11707816301nitrite-reduction

metabolite production

  • @ref: 117078
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11707815688acetoin-
11707817234glucose-

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
117078oxidase+
117078beta-galactosidase-3.2.1.23
117078alcohol dehydrogenase-1.1.1.1
117078gelatinase+
117078amylase-
117078DNase+
117078caseinase+3.4.21.50
117078catalase+1.11.1.6
117078tween esterase+
117078gamma-glutamyltransferase-2.3.2.2
117078lecithinase+
117078lipase-
117078lysine decarboxylase-4.1.1.18
117078ornithine decarboxylase-4.1.1.17
117078phenylalanine ammonia-lyase+4.3.1.24
117078tryptophan deaminase-
117078urease-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
117078-++--+++++++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
4643waterButon Lake, 10.4m depth, Vestfold HillsAustralia and Oceania
117078Environment, Water samplesBurton lakeAntarcticaAntarcticaATA1984

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_72229.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_3138;97_38928;98_50620;99_72229&stattab=map
  • Last taxonomy: Psychroserpens burtonensis subclade
  • 16S sequence: NR_029190
  • Sequence Identity:
  • Total samples: 97
  • soil counts: 16
  • aquatic counts: 77
  • animal counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
46431Risk group (German classification)
1170781Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Psychroserpens burtonensis ACAM188 16s ribosomal RNA gene, partial sequenceU629131484ena49278
4643Psychroserpens burtonensis strain ACAM 188 16S ribosomal RNA, partial sequenceNR_0291901484nuccore49278

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychroserpens burtonensis DSM 12212GCA_000425305scaffoldncbi1123037
66792Psychroserpens burtonensis DSM 122121123037.4wgspatric1123037
66792Psychroserpens burtonensis DSM 122122524023130draftimg1123037

GC content

  • @ref: 4643
  • GC-content: 33.4
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno87.353no
flagellatedno96.013no
gram-positiveno98.115no
anaerobicno98.555no
aerobicyes88.961no
halophileno65.141no
spore-formingno94.675no
thermophileno99.771yes
glucose-utilyes83.007no
glucose-fermentno90.626no

External links

@ref: 4643

culture collection no.: DSM 12212, ACAM 188, ATCC 700359, CIP 105822

straininfo link

  • @ref: 75114
  • straininfo: 43891

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9226898Psychroserpens burtonensis gen. nov., sp. nov., and Gelidibacter algens gen. nov., sp. nov., psychrophilic bacteria isolated from antarctic lacustrine and sea ice habitats.Bowman JP, McCammon SA, Brown JL, Nichols PD, McMeekin TAInt J Syst Bacteriol10.1099/00207713-47-3-6701997Antarctic Regions, Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Gram-Negative Bacteria/*classification/genetics/isolation & purification, Molecular Sequence Data, Oceans and Seas, Phenotype, Phylogeny, Seawater/*microbiologyGenetics
Phylogeny22544799Psychroserpens damuponensis sp. nov., isolated from seawater.Lee DH, Cho SJ, Kim SM, Lee SBInt J Syst Evol Microbiol10.1099/ijs.0.041632-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny35461400Psychroserpens luteolus sp. nov., isolated from Gelidium, reclassification of Ichthyenterobacterium magnum as Psychroserpens magnus comb. nov., Flavihalobacter algicola as Psychroserpens algicola comb. nov., Arcticiflavibacter luteus as Psychroserpens luteus comb. nov.Ping XY, Wang K, Zhang JY, Wang SX, Du ZJ, Mu DSArch Microbiol10.1007/s00203-022-02895-w2022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae, *Gammaproteobacteria/genetics, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhodophyta, Seawater/microbiology, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4643Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12212)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12212
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
36203Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17884
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 life 35: 676-683 201728604660
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
75114Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43891.1StrainInfo: A central database for resolving microbial strain identifiers
117078Curators of the CIPCollection of Institut Pasteur (CIP 105822)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105822