Strain identifier

BacDive ID: 2458

Type strain: Yes

Species: Arsukibacterium perlucidum

Strain Designation: BA 131, BA131

Strain history: CIP <- 2006, I. Brettar, Braunschweig, Germany: strain BA131

NCBI tax ID(s): 368811 (species)

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General

@ref: 7481

BacDive-ID: 2458

DSM-Number: 18276

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

description: Arsukibacterium perlucidum BA 131 is a Gram-negative bacterium that was isolated from water sample 5m depth.

NCBI tax id

  • NCBI tax id: 368811
  • Matching level: species

strain history

@refhistory
7481<- I. Brettar, GBF; BA 131
406342006, I. Brettar, Braunschweig, Germany: strain BA131
121682CIP <- 2006, I. Brettar, Braunschweig, Germany: strain BA131

doi: 10.13145/bacdive2458.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Gammaproteobacteria, not assigned to order
  • family: Gammaproteobacteria, not assigned to family
  • genus: Arsukibacterium
  • species: Arsukibacterium perlucidum
  • full scientific name: Arsukibacterium perlucidum (Brettar et al. 2006) Wang et al. 2022

  • synonyms

    • @ref: 20215
    • synonym: Rheinheimera perlucida

@ref: 7481

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Chromatiales

family: Chromatiaceae

genus: Rheinheimera

species: Rheinheimera perlucida

full scientific name: Rheinheimera perlucida Brettar et al. 2006

strain designation: BA 131, BA131

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121682negativerod-shapedyes
69480negative99

colony morphology

  • @ref: 121682

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7481HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)yeshttps://mediadive.dsmz.de/medium/514aName: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a) Composition: Agar 15.0 g/l NaCl 9.725 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled water
40634Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121682CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
7481positivegrowth20
40634positivegrowth25

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121682nitrate+reduction17632
121682nitrite-reduction16301

metabolite production

  • @ref: 121682
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
121682oxidase+
121682alcohol dehydrogenase-1.1.1.1
121682catalase+1.11.1.6
121682lysine decarboxylase-4.1.1.18
121682ornithine decarboxylase-4.1.1.17
121682urease-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
121682-+++-+--++++-----+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121682---------------------+/---+/---+/-+/--+/-----+/-+/-------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryisolation date
7481water sample 5m depthcentral Baltic Sea
121682Environment, Sea waterBaltic Sea1998

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_4074.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_43;96_86;97_2437;98_3014;99_4074&stattab=map
  • Last taxonomy: Chromatiaceae
  • 16S sequence: AM183347
  • Sequence Identity:
  • Total samples: 897
  • soil counts: 25
  • aquatic counts: 431
  • animal counts: 427
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74811Risk group (German classification)
1216821Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7481
  • description: Rheinheimera perlucida 16S rRNA gene, type strain BA131T
  • accession: AM183347
  • length: 1476
  • database: nuccore
  • NCBI tax ID: 368811

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arsukibacterium perlucidum DSM 18276GCA_000382165scaffoldncbi1123054
66792Rheinheimera perlucida DSM 182761123054.4wgspatric1123054
66792Rheinheimera perlucida DSM 182762521172649draftimg1123054

GC content

  • @ref: 7481
  • GC-content: 48.9

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.022no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes70.246no
69480spore-formingspore-formingAbility to form endo- or exosporesno87.987no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.302no
69480flagellatedmotile2+Ability to perform flagellated movementyes85.802no

External links

@ref: 7481

culture collection no.: DSM 18276, CIP 109200, LMG 23581

straininfo link

  • @ref: 72002
  • straininfo: 290810

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957117Rheinheimera perlucida sp. nov., a marine bacterium of the Gammaproteobacteria isolated from surface water of the central Baltic Sea.Brettar I, Christen R, Hofle MGInt J Syst Evol Microbiol10.1099/ijs.0.64172-02006Baltic States, Base Composition/genetics, Fatty Acids/*analysis, Gammaproteobacteria/classification/genetics/*isolation & purification, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis/genetics, Seawater/*microbiologyGenetics
Phylogeny35852492Arsukibacterium indicum sp. nov., isolated from deep-sea sediment, and transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. and Arsukibacterium perlucidum comb. nov.Wang Z, Cheng JH, Zhang XY, Xu F, Fu HH, Li CY, Zhang YZ, Chen XL, Song XY, Zhang XYInt J Syst Evol Microbiol10.1099/ijsem.0.0054552022Bacterial Typing Techniques, Base Composition, Chromatiaceae, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
7481Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18276)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18276
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
40634Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6915
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)
68371Automatically annotated from API 50CH acid
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
72002Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290810.1StrainInfo: A central database for resolving microbial strain identifiers
121682Curators of the CIPCollection of Institut Pasteur (CIP 109200)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109200