Strain identifier

BacDive ID: 13674

Type strain: Yes

Species: Loktanella fryxellensis

Strain Designation: R-7670

Strain history: CIP <- 2004, S. Van Trappen, Ghent Univ., Ghent, Belgium <- J. Mergaert, Ghent Univ., Ghent, Belgium: strain R-7670

NCBI tax ID(s): 245187 (species)

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General

@ref: 6329

BacDive-ID: 13674

DSM-Number: 16213

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

description: Loktanella fryxellensis R-7670 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from microbial mat.

NCBI tax id

  • NCBI tax id: 245187
  • Matching level: species

strain history

@refhistory
6329<- D. Janssens, LMG <- J. Mergaert, Univ. Ghent, Belgium; R-7670
67770IAM 15180 <-- LMG 22007 <-- J. Mergaert R-7670.
119473CIP <- 2004, S. Van Trappen, Ghent Univ., Ghent, Belgium <- J. Mergaert, Ghent Univ., Ghent, Belgium: strain R-7670

doi: 10.13145/bacdive13674.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Loktanella
  • species: Loktanella fryxellensis
  • full scientific name: Loktanella fryxellensis Van Trappen et al. 2004

@ref: 6329

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Loktanella

species: Loktanella fryxellensis

full scientific name: Loktanella fryxellensis Van Trappen et al. 2004

strain designation: R-7670

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30155negative2.5 µm1 µmrod-shapedno
69480negative99.984
119473negativerod-shapedyes

pigmentation

  • @ref: 30155
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6329BACTO 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
37381Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119473CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6329positivegrowth20psychrophilic
30155positivegrowth5.0-30
30155positiveoptimum25mesophilic
37381positivegrowth25mesophilic
67770positivegrowth20psychrophilic
119473positivegrowth5-25psychrophilic
119473nogrowth30mesophilic
119473nogrowth37mesophilic
119473nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30155
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30155no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
30155NaClpositivegrowth0.0-5.0 %
30155NaClpositiveoptimum2.5 %
119473NaClnogrowth0 %
119473NaClnogrowth2 %
119473NaClnogrowth4 %
119473NaClnogrowth6 %
119473NaClnogrowth8 %
119473NaClnogrowth10 %

observation

  • @ref: 30155
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3015553426tween 80+carbon source
301554853esculin+hydrolysis
11947316947citrate-carbon source
1194734853esculin+hydrolysis
11947317632nitrate-reduction
11947316301nitrite-reduction

metabolite production

  • @ref: 119473
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11947315688acetoin-
11947317234glucose+

enzymes

@refvalueactivityec
30155acid phosphatase+3.1.3.2
30155alkaline phosphatase+3.1.3.1
30155catalase+1.11.1.6
30155cytochrome oxidase+1.9.3.1
119473oxidase+
119473beta-galactosidase+3.2.1.23
119473alcohol dehydrogenase-1.1.1.1
119473gelatinase+/-
119473amylase+
119473DNase-
119473caseinase-3.4.21.50
119473catalase+1.11.1.6
119473tween esterase+
119473gamma-glutamyltransferase+2.3.2.2
119473lecithinase-
119473lipase-
119473lysine decarboxylase-4.1.1.18
119473ornithine decarboxylase-4.1.1.17
119473phenylalanine ammonia-lyase-4.3.1.24
119473tryptophan deaminase-
119473urease+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
119473-+++-+----++++-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
6329microbial matLake Fryxell, Dry ValleysAustralia and Oceania
67770Microbial mat from Lake FryxellMcMurdo Dry ValleysAntarcticaAntarcticaATA
119473Microbial materialFryxell lake, McMurdo dry valleysAntarcticaAntarcticaATA1999

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Microbial community
  • Cat3: #Microbial mat

taxonmaps

  • @ref: 69479
  • File name: preview.99_53995.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2693;97_4702;98_6048;99_53995&stattab=map
  • Last taxonomy: Loktanella fryxellensis
  • 16S sequence: AJ582225
  • Sequence Identity:
  • Total samples: 1481
  • soil counts: 170
  • aquatic counts: 1203
  • animal counts: 76
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63291Risk group (German classification)
1194731Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Loktanella fryxellensis strain LMG22007 16S ribosomal RNA gene, partial sequenceDQ9156081306ena245187
20218Loktanella fryxellensis gene for 16S rRNA, partial sequence, strain: NBRC 102485AB6818241388ena245187
67770Loktanella fryxellensis 16S rRNA gene, type strain LMG 22007TAJ5822251415ena245187

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Loktanella fryxellensis strain DSM 16213245187.6wgspatric245187
66792Loktanella fryxellensis DSM 162132622736532draftimg245187
67770Loktanella fryxellensis DSM 16213GCA_900110065scaffoldncbi245187

GC content

@refGC-contentmethod
3015566.05
6777065.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno62.374yes
gram-positiveno98.316yes
anaerobicno97.833yes
aerobicyes89.88yes
halophileno61.923no
spore-formingno95.859yes
glucose-utilyes92.383no
thermophileno98.499yes
flagellatedno89.243yes
glucose-fermentno88.306no

External links

@ref: 6329

culture collection no.: DSM 16213, LMG 22007, JCM 21635, CIP 108323, IAM 15180, NBRC 102485

straininfo link

  • @ref: 82857
  • straininfo: 21643

literature

  • topic: Phylogeny
  • Pubmed-ID: 15280301
  • title: Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes.
  • authors: Van Trappen S, Mergaert J, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.03006-0
  • year: 2004
  • mesh: Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA Fingerprinting, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Gentian Violet, Geologic Sediments/microbiology, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Repetitive Sequences, Nucleic Acid, Rhodobacteraceae/*classification/cytology/*isolation & purification/physiology, Sequence Analysis, DNA, Sequence Homology, Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6329Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16213)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16213
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
30155Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126506
37381Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5933
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
82857Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID21643.1StrainInfo: A central database for resolving microbial strain identifiers
119473Curators of the CIPCollection of Institut Pasteur (CIP 108323)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108323