Strain identifier

BacDive ID: 13865

Type strain: Yes

Species: Planktotalea frisia

Strain Designation: SH6-1, SH6_1

Strain history: <- S. Hahnke, ICMB, Univ. Oldenburg, Germany; SH6_1

NCBI tax ID(s): 696762 (species)

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General

@ref: 204

BacDive-ID: 13865

DSM-Number: 23709

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

description: Planktotalea frisia SH6-1 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 696762
  • Matching level: species

strain history

  • @ref: 204
  • history: <- S. Hahnke, ICMB, Univ. Oldenburg, Germany; SH6_1

doi: 10.13145/bacdive13865.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Planktotalea
  • species: Planktotalea frisia
  • full scientific name: Planktotalea frisia Hahnke et al. 2012

@ref: 204

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Planktotalea

species: Planktotalea frisia

full scientific name: Planktotalea frisia Hahnke et al. 2012

strain designation: SH6-1, SH6_1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30328negative2.25 µm0.7 µmrod-shaped
69480no92.189
69480negative99.974

colony morphology

  • @ref: 204
  • incubation period: >14 days

pigmentation

  • @ref: 30328
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
204SH SEAWATER MEDIUM (DSMZ Medium 1282)yeshttps://mediadive.dsmz.de/medium/1282Name: SH SEAWATER MEDIUM (DSMZ Medium 1282) Composition: NaCl 24.32 g/l Agar 15.0 g/l MgCl2 x 6 H2O 10.0 g/l Na2SO4 4.0 g/l HEPES 2.38 g/l CaCl2 x 2 H2O 1.5 g/l KCl 0.66 g/l Peptone 0.2 g/l NaHCO3 0.2 g/l Yeast extract 0.1 g/l KBr 0.09996 g/l H3BO3 0.024736 g/l SrCl2 0.023778 g/l NH4Cl 0.021396 g/l Na2MoO4 x 2 H2O 0.01 g/l KH2PO4 0.0054434 g/l NH4NO3 0.0032 g/l NaF 0.00293917 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 0.0001 g/l ZnCl2 3.6e-05 g/l Lipoic acid 2.5e-05 g/l Cyanocobalamine 2.5e-05 g/l Pyridoxine hydrochloride 2.5e-05 g/l Thiamine hydrochloride 2.5e-05 g/l Riboflavin 2.5e-05 g/l Calcium pantothenate 2.5e-05 g/l Para-aminobenzoic acid 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Folic acid 1e-05 g/l Biotin 1e-05 g/l CuCl2 x 2 H2O 2e-07 g/l Double distilled water Distilled water
204ANAEROCELLA MEDIUM (DSMZ Medium 1538)yeshttps://mediadive.dsmz.de/medium/1538Name: ANAEROBACTERIUM MEDIUM (DSMZ Medium 1538) Composition: Cellobiose 10.0 g/l NaHCO3 2.52 g/l Yeast extract 1.0 g/l NaCl 1.0 g/l KCl 0.5 g/l MgCl2 x 6 H2O 0.4 g/l Na2S x 9 H2O 0.36 g/l NH4Cl 0.25 g/l KH2PO4 0.2 g/l CaCl2 x 2 H2O 0.15 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l NaOH 0.0005 g/l Thiamine-HCl x 2 H2O 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l ZnCl2 7e-05 g/l Vitamin B12 5e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Biotin 2e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
204positivegrowth20psychrophilic
30328positivegrowth04-32
30328positiveoptimum22.5psychrophilic

culture pH

@refabilitytypepHPH range
30328positivegrowth6-9.5alkaliphile
30328positiveoptimum8.25

Physiology and metabolism

oxygen tolerance

  • @ref: 30328
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
30328NaClpositivegrowth1.25-8 %
30328NaClpositiveoptimum3.75 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3032816449alanine+carbon source
3032829016arginine+carbon source
3032835391aspartate+carbon source
3032817057cellobiose+carbon source
3032816947citrate+carbon source
3032828757fructose+carbon source
3032828260galactose+carbon source
3032817234glucose+carbon source
3032817754glycerol+carbon source
3032817716lactose+carbon source
3032817306maltose+carbon source
3032829864mannitol+carbon source
3032837684mannose+carbon source
3032826271proline+carbon source
3032833942ribose+carbon source
3032817822serine+carbon source
3032817992sucrose+carbon source
3032827082trehalose+carbon source
3032816296D-tryptophan+carbon source
3032853426tween 80+carbon source
3032818222xylose+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30328cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382esterase (C 4)-
68382lipase (C 14)-
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
204-+/--+/--+/---------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
204-----+-+------------

Isolation, sampling and environmental information

isolation

  • @ref: 204
  • sample type: seawater
  • geographic location: North Sea (54°42' N 06° 48' E) at 2 m depth
  • country: Germany
  • origin.country: DEU
  • continent: Europe
  • latitude: 54.7
  • longitude: 6.8

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_6665.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_945;97_1099;98_1310;99_6665&stattab=map
  • Last taxonomy: Planktotalea
  • 16S sequence: FJ882052
  • Sequence Identity:
  • Total samples: 541
  • soil counts: 21
  • aquatic counts: 515
  • animal counts: 5

Safety information

risk assessment

  • @ref: 204
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 204
  • description: Planktotalea frisia strain SH6-1 16S ribosomal RNA gene, partial sequence
  • accession: FJ882052
  • length: 1336
  • database: ena
  • NCBI tax ID: 696762

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Planktotalea frisia SH6-1GCA_001890925contigncbi696762
66792Planktotalea frisia DSM 23709GCA_003254185scaffoldncbi696762
66792Planktotalea frisia strain DSM 23709696762.6wgspatric696762
66792Planktotalea frisia SH6-12703719202draftimg696762
66792Planktotalea frisia DSM 237092593339277draftimg696762

GC content

@refGC-contentmethod
20453.8high performance liquid chromatography (HPLC)
3032853.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno90.948no
gram-positiveno97.351no
anaerobicno98.473no
halophileyes78.621no
spore-formingno95.601no
aerobicyes92.671yes
glucose-utilyes62.652no
thermophileno97.833no
motileno73.916no
glucose-fermentno92.089yes

External links

@ref: 204

culture collection no.: DSM 23709, LMG 25294

straininfo link

  • @ref: 83041
  • straininfo: 380592

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21890723Planktotalea frisia gen. nov., sp. nov., isolated from the southern North Sea.Hahnke S, Tindall BJ, Schumann P, Sperling M, Brinkhoff T, Simon MInt J Syst Evol Microbiol10.1099/ijs.0.033563-02011Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Heterotrophic Processes, Hydrogen-Ion Concentration, Molecular Sequence Data, North Sea, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, TemperatureGenetics
Metabolism23711338Distinct seasonal growth patterns of the bacterium Planktotalea frisia in the North Sea and specific interaction with phytoplankton algae.Hahnke S, Sperling M, Langer T, Wichels A, Gerdts G, Beardsley C, Brinkhoff T, Simon MFEMS Microbiol Ecol10.1111/1574-6941.121512013Bacteria/metabolism, Diatoms/metabolism, Haptophyta/metabolism, North Sea, Phytoplankton/*metabolism, Polysaccharides/metabolism, Roseobacter/*growth & development/isolation & purification/*metabolism, *Seasons, Seawater/*microbiologyEnzymology
Phylogeny28840817Planktotalea arctica sp. nov., isolated from Arctic seawater.Baek K, Choi A, Lee YM, Lee HK, Cho JCInt J Syst Evol Microbiol10.1099/ijsem.0.0021522017Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny28984545Planktotalealamellibrachiae sp. nov., isolated from a marine organism in Kagoshima Bay, Japan.Nogi Y, Nishi S, Koyama SInt J Syst Evol Microbiol10.1099/ijsem.0.0023752017Aquatic Organisms/*microbiology, Bacterial Typing Techniques, Base Composition, Bays, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Genetics29682168Genome sequence of Planktotalea frisia type strain (SH6-1(T)), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom.Bakenhus I, Voget S, Poehlein A, Brinkhoff T, Daniel R, Simon MStand Genomic Sci10.1186/s40793-018-0311-52018

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
204Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23709)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23709
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
30328Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2666928776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
68369Automatically annotated from API 20NE
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
83041Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID380592.1StrainInfo: A central database for resolving microbial strain identifiers