Strain identifier

BacDive ID: 13876

Type strain: Yes

Species: Afifella pfennigii

Strain Designation: AR2102

Strain history: <- ATCC <- R. Guyoneaud, Lab. d’Ecologie Moléculaire-Microbiol., EA3525, Univ. Pau et Pays de l’Adour, France; AR2102

NCBI tax ID(s): 1120956 (strain), 209897 (species)

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General

@ref: 6788

BacDive-ID: 13876

DSM-Number: 17143

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

description: Afifella pfennigii AR2102 is a mesophilic, Gram-negative, motile bacterium that was isolated from benthic microbial mat in a brackish pond located on the rim of the Rangiroa atoll.

NCBI tax id

NCBI tax idMatching level
1120956strain
209897species

strain history

  • @ref: 6788
  • history: <- ATCC <- R. Guyoneaud, Lab. d’Ecologie Moléculaire-Microbiol., EA3525, Univ. Pau et Pays de l’Adour, France; AR2102

doi: 10.13145/bacdive13876.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Afifellaceae
  • genus: Afifella
  • species: Afifella pfennigii
  • full scientific name: Afifella pfennigii (Caumette et al. 2007) Urdiain et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Rhodobium pfennigii

@ref: 6788

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Afifellaceae

genus: Afifella

species: Afifella pfennigii

full scientific name: Afifella pfennigii (Caumette et al. 2007) Urdiain et al. 2009

strain designation: AR2102

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31992negative01-02 µm0.6 µmrod-shapedyes
69480yes90.631
69480negative99.986

pigmentation

  • @ref: 31992
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6788
  • name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/27
  • composition: Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27; with strain-specific modifications) Composition: NaCl 10.0 g/l Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l MgSO4 x 7 H2O 0.4 g/l NH4Cl 0.4 g/l L-Cysteine HCl 0.3 g/l Yeast extract 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Resazurin 0.005 g/l Fe(III) citrate 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water

culture temp

@refgrowthtypetemperaturerange
6788positivegrowth28mesophilic
31992positivegrowth30-35mesophilic
31992positiveoptimum32.5mesophilic

culture pH

@refabilitytypepHPH range
31992positivegrowth6.3-8.5alkaliphile
31992positiveoptimum7.2-7.5

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
31992NaClpositivegrowth0-5 %
31992NaClpositiveoptimum01-02 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3199230089acetate+carbon source
3199235391aspartate+carbon source
3199224996lactate+carbon source
3199225115malate+carbon source
3199217272propionate+carbon source
3199215361pyruvate+carbon source
3199230031succinate+carbon source
3199231011valerate+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 6788
  • sample type: benthic microbial mat in a brackish pond (R2) located on the rim of the Rangiroa atoll
  • geographic location: Tuamotu Islands
  • country: French Polynesia
  • origin.country: PYF
  • continent: Australia and Oceania

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Pond (small)
#Environmental#Terrestrial#Tidal flat
#Host#Microbial

taxonmaps

  • @ref: 69479
  • File name: preview.99_5082.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_187;96_2477;97_3025;98_3794;99_5082&stattab=map
  • Last taxonomy: Afifella pfennigii
  • 16S sequence: FR733717
  • Sequence Identity:
  • Total samples: 1866
  • soil counts: 1125
  • aquatic counts: 604
  • animal counts: 85
  • plant counts: 52

Safety information

risk assessment

  • @ref: 6788
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Afifella pfennigii partial 16S rRNA gene, type strain DSM17143TFR7337171455ena209897
6788Rhodobium pfennigii partial 16S rRNA gene, type strain AR2102TAJ510235858ena1120956

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Afifella pfennigii DSM 17143GCA_000688515scaffoldncbi1120956
66792Afifella pfennigii DSM 171431120956.3wgspatric1120956
66792Afifella pfennigii DSM 171432556921008draftimg1120956

GC content

@refGC-contentmethod
678867.5high performance liquid chromatography (HPLC)
3199267.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes85.488no
flagellatedno68.549no
gram-positiveno98.299no
anaerobicno72.32no
halophileno78.713no
spore-formingno96.596no
glucose-utilyes82.391no
aerobicno50no
thermophileno93.565yes
glucose-fermentno91.286no

External links

@ref: 6788

culture collection no.: DSM 17143, ATCC BAA 1145

straininfo link

  • @ref: 83051
  • straininfo: 404089

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17551038Rhodobium pfennigii sp. nov., a phototrophic purple non-sulfur bacterium with unusual bacteriochlorophyll a antennae, isolated from a brackish microbial mat on Rangiroa atoll, French Polynesia.Caumette P, Guyoneaud R, Duran R, Cravo-Laureau C, Matheron RInt J Syst Evol Microbiol10.1099/ijs.0.64775-02007Alphaproteobacteria/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Bacteriochlorophyll A/*analysis/chemistry, Carotenoids/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flagella/physiology, Genes, rRNA, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Organelles/physiology, Photosynthesis, Phylogeny, Polynesia, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Spectrum Analysis, Thiosulfates/metabolismGenetics
Phylogeny31592760Afifella aestuarii sp. nov., a phototrophic bacterium.Buddhi S, G S, Gupta D, Ch S, Ch V RInt J Syst Evol Microbiol10.1099/ijsem.0.0037562020Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Bacteriochlorophyll A/chemistry, Base Composition, DNA, Bacterial/genetics, *Estuaries, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Photosynthesis, Phototrophic Processes, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, Vitamin K 2/chemistry, Xanthophylls/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6788Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17143)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17143
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
31992Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128246
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)
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
83051Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404089.1StrainInfo: A central database for resolving microbial strain identifiers