Strain identifier

BacDive ID: 13874

Type strain: Yes

Species: Afifella marina

Strain Designation: BN 126

Strain history: CIP <- 1995, NCIMB <- DSM <- J.F. Imhoff: strain BN 126

NCBI tax ID(s): 1120955 (strain), 1080 (species)

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General

@ref: 1205

BacDive-ID: 13874

DSM-Number: 2698

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile

description: Afifella marina BN 126 is an anaerobe, mesophilic, motile bacterium that was isolated from marine sponge.

NCBI tax id

NCBI tax idMatching level
1080species
1120955strain

strain history

@refhistory
1205<- J.F. Imhoff, strain BN 126
120813CIP <- 1995, NCIMB <- DSM <- J.F. Imhoff: strain BN 126

doi: 10.13145/bacdive13874.20230509.8.1

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 marina
  • full scientific name: Afifella marina (Imhoff 1984) Urdiain et al. 2009

  • synonyms

    @refsynonym
    20215Rhodopseudomonas marina
    20215Rhodobium marinum

@ref: 1205

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Afifellaceae

genus: Afifella

species: Afifella marina

full scientific name: Afifella marina (Imhoff 1984) Urdiain et al. 2009

strain designation: BN 126

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.819
6948099.991negative
120813yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1205RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)yeshttps://mediadive.dsmz.de/medium/27Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27; with strain-specific modifications) Composition: NaCl 30.0 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
38498Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120813CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
1205positivegrowth25mesophilic
38498positivegrowth30mesophilic
120813positivegrowth10-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
1205anaerobe
120813obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

compound production

  • @ref: 1205
  • compound: hydrogen

halophily

  • @ref: 120813
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12081316947citrate-carbon source
1208134853esculin-hydrolysis
12081317632nitrate-reduction
12081316301nitrite+reduction
12081315792malonate+assimilation

antibiotic resistance

  • @ref: 120813
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120813
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
120813oxidase+
120813beta-galactosidase-3.2.1.23
120813alcohol dehydrogenase-1.1.1.1
120813gelatinase+/-
120813amylase-
120813caseinase-3.4.21.50
120813catalase+1.11.1.6
120813lecithinase-
120813lysine decarboxylase-4.1.1.18
120813ornithine decarboxylase-4.1.1.17
120813urease+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
120813-+++-+--+-+---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120813-+----------------------------+--------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountry
1205marine spongeAdriatic shore
120813Animal, Marine spongeShoreAdriatic Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Porifera (Sponges)

taxonmaps

  • @ref: 69479
  • File name: preview.99_27021.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_187;96_2477;97_3025;98_3794;99_27021&stattab=map
  • Last taxonomy: Hyphomicrobiales
  • 16S sequence: HE978266
  • Sequence Identity:
  • Total samples: 2154
  • soil counts: 981
  • aquatic counts: 820
  • animal counts: 275
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
12051Risk group (German classification)
1208131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Rhodobium marinum 16S rRNA gene, complete sequenceD307901390ena1080
20218Rhodobium marinum strain DSM 2698 16S-23S ribosomal RNA intergenic spacer, partial sequenceEU786782766ena1080
1205Afifella marina partial 16S rRNA gene, type strain DSM 2698THE9782661461ena1120955

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Afifella marina DSM 2698GCA_900102695contigncbi1120955
66792Afifella marina DSM 2698GCA_016584015contigncbi1120955
66792Afifella marina DSM 2698GCA_003258905scaffoldncbi1120955
66792Afifella marina DSM 26981120955.6wgspatric1120955
66792Afifella marina DSM 26981120955.3wgspatric1120955
66792Afifella marina DSM 26982595699009draftimg1120955

GC content

  • @ref: 1205
  • GC-content: 63.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.577no
flagellatedno58.852no
gram-positiveno98.542no
anaerobicyes54.316yes
aerobicno56.416yes
halophileno75.641no
spore-formingno96.435no
glucose-utilyes87.69no
thermophileno96.649yes
glucose-fermentno87.579no

External links

@ref: 1205

culture collection no.: DSM 2698, ATCC 35675, CIP 104405, NBRC 100434, NCIMB 2201

straininfo link

  • @ref: 83049
  • straininfo: 265439

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18774253Reclassification of Rhodobium marinum and Rhodobium pfennigii as Afifella marina gen. nov. comb. nov. and Afifella pfennigii comb. nov., a new genus of photoheterotrophic Alphaproteobacteria and emended descriptions of Rhodobium, Rhodobium orientis and Rhodobium gokarnense.Urdiain M, Lopez-Lopez A, Gonzalo C, Busse HJ, Langer S, Kampfer P, Rossello-Mora RSyst Appl Microbiol10.1016/j.syapm.2008.07.0022008Alphaproteobacteria/*classification/genetics/growth & development/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis/isolation & purification, Geologic Sediments/microbiology, Heterotrophic Processes, Molecular Sequence Data, Nucleic Acid Hybridization, Phototrophic Processes, RNA, Ribosomal, 16S/genetics, Rhizobiaceae/*classification/genetics/isolation & purification, Rhodopseudomonas/classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Species SpecificityEnzymology
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/urltitlejournalpubmed
1205Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2698)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2698
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
38498Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16309
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
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
83049Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265439.1StrainInfo: A central database for resolving microbial strain identifiers
120813Curators of the CIPCollection of Institut Pasteur (CIP 104405)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104405