Strain identifier

BacDive ID: 17916

Type strain: Yes

Species: Arenicella xantha

Strain Designation: Sd2-39

Strain history: N. Tanaka <-- L. A. Romanenko Sd2-39 (=KMM 3895).

NCBI tax ID(s): 644221 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17481

BacDive-ID: 17916

DSM-Number: 24032

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

description: Arenicella xantha Sd2-39 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from offshore marine sandy sample.

NCBI tax id

  • NCBI tax id: 644221
  • Matching level: species

strain history

@refhistory
17481<- N. Tanaka, NRIC <- L. A. Romanenko, KMM; Sd2-39
67770N. Tanaka <-- L. A. Romanenko Sd2-39 (=KMM 3895).

doi: 10.13145/bacdive17916.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Arenicellales
  • family: Arenicellaceae
  • genus: Arenicella
  • species: Arenicella xantha
  • full scientific name: Arenicella xantha Romanenko et al. 2010

@ref: 17481

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Arenicellales

family: Arenicellaceae

genus: Arenicella

species: Arenicella xantha

full scientific name: Arenicella xantha Romanenko et al. 2010

strain designation: Sd2-39

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29623negative3.5 µm0.55 µmrod-shapedno
69480negative99.986

pigmentation

  • @ref: 29623
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17481
  • name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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

culture temp

@refgrowthtypetemperaturerange
17481positivegrowth28mesophilic
29623positivegrowth05-35
29623positiveoptimum26.5mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
29623positivegrowth06-11alkaliphile
29623positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 29623
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
29623NaClpositivegrowth01-05 %
29623NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2962316449alanine+carbon source
2962322599arabinose+carbon source
2962317234glucose+carbon source
2962328053melibiose+carbon source
2962333942ribose+carbon source
2962318222xylose+carbon source
296234853esculin+hydrolysis

enzymes

@refvalueactivityec
29623alkaline phosphatase+3.1.3.1
29623catalase+1.11.1.6
29623gelatinase+
29623cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17481offshore marine sandy sampleSea of Japan, offshoreRussiaRUSAsia
67770Sandy sediment sample collected offshore from the Sea of JapanRussiaRUS

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_129721.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1076;96_13111;97_24205;98_86865;99_129721&stattab=map
  • Last taxonomy: Arenicella xantha subclade
  • 16S sequence: AB500096
  • Sequence Identity:
  • Total samples: 997
  • soil counts: 12
  • aquatic counts: 965
  • animal counts: 15
  • plant counts: 5

Safety information

risk assessment

  • @ref: 17481
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17481
  • description: Arenicella xantha gene for 16S ribosomal RNA, partial sequence
  • accession: AB500096
  • length: 1506
  • database: ena
  • NCBI tax ID: 644221

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenicella xantha strain DSM 24032644221.3wgspatric644221
66792Arenicella xantha DSM 240322770939506draftimg644221
67770Arenicella xantha DSM 24032GCA_003315245scaffoldncbi644221

GC content

@refGC-contentmethod
1748148.1thermal denaturation, midpoint method (Tm)
2962348.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.758yes
anaerobicno99.264yes
halophileno56.226no
spore-formingno96.815no
glucose-utilyes87.471yes
thermophileno99.537yes
flagellatedno92.652yes
aerobicyes97.025yes
motileno87.25no
glucose-fermentno91.747no

External links

@ref: 17481

culture collection no.: DSM 24032, KMM 3895, NRIC 0759, JCM 16153

straininfo link

  • @ref: 86905
  • straininfo: 403893

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19767361Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment.Romanenko LA, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.017194-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gammaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny23771619Arenicella chitinivorans sp. nov., a gammaproteobacterium isolated from the sea urchin Strongylocentrotus intermedius.Nedashkovskaya OI, Cleenwerck I, Zhukova NV, Kim SB, de Vos PInt J Syst Evol Microbiol10.1099/ijs.0.051599-02013Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, Japan, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Strongylocentrotus/*microbiology, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17481Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24032)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24032
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
29623Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2601328776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86905Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403893.1StrainInfo: A central database for resolving microbial strain identifiers