Strain identifier

BacDive ID: 3766

Type strain: Yes

Species: Arcicella aurantiaca

Strain Designation: TNR-18

Strain history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; TNR-18

NCBI tax ID(s): 591202 (species)

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

@ref: 16206

BacDive-ID: 3766

DSM-Number: 22214

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

description: Arcicella aurantiaca TNR-18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from stream water.

NCBI tax id

  • NCBI tax id: 591202
  • Matching level: species

strain history

  • @ref: 16206
  • history: <- J.-H. Chou, Natl. Kaohsiung Marine Univ. Taiwan <- W.-M. Chen; TNR-18

doi: 10.13145/bacdive3766.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Arcicella
  • species: Arcicella aurantiaca
  • full scientific name: Arcicella aurantiaca Sheu et al. 2010

@ref: 16206

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Arcicella

species: Arcicella aurantiaca

full scientific name: Arcicella aurantiaca Sheu et al. 2010 emend. Chen et al. 2013

strain designation: TNR-18

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29806negative01-03 µm0.5-0.6 µmrod-shapedno
69480no91.192
69480negative99.999

pigmentation

  • @ref: 29806
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16206
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16206positivegrowth28mesophilic
29806positivegrowth10-30
29806positiveoptimum25mesophilic

culture pH

@refabilitytypepHPH range
29806positivegrowth06-10alkaliphile
29806positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29806
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29806no
69481no100
69480no99.994

halophily

  • @ref: 29806
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.2 %

observation

  • @ref: 29806
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2980616449alanine+carbon source
2980635391aspartate+carbon source
2980617057cellobiose+carbon source
2980623652dextrin+carbon source
2980628757fructose+carbon source
2980633984fucose+carbon source
2980628260galactose+carbon source
2980617234glucose+carbon source
2980629987glutamate+carbon source
2980628087glycogen+carbon source
2980617716lactose+carbon source
2980617306maltose+carbon source
2980637684mannose+carbon source
2980628053melibiose+carbon source
2980651850methyl pyruvate+carbon source
2980616634raffinose+carbon source
2980626546rhamnose+carbon source
2980617822serine+carbon source
2980630911sorbitol+carbon source
2980617992sucrose+carbon source
2980627082trehalose+carbon source
298064853esculin+hydrolysis
2980617632nitrate+reduction

enzymes

@refvalueactivityec
29806catalase+1.11.1.6
29806cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 16206
  • sample type: stream water
  • geographic location: Kaohsiung Prefecture
  • country: Taiwan
  • origin.country: TWN
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_174211.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_200;96_14607;97_22353;98_114058;99_174211&stattab=map
  • Last taxonomy: Arcicella aurantiaca subclade
  • 16S sequence: FJ593908
  • Sequence Identity:
  • Total samples: 45
  • aquatic counts: 41
  • plant counts: 4

Safety information

risk assessment

  • @ref: 16206
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16206
  • description: Arcicella aurantiaca 16S ribosomal RNA gene, partial sequence
  • accession: FJ593908
  • length: 1411
  • database: ena
  • NCBI tax ID: 591202

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arcicella aurantiaca DSM 22214GCA_003148625scaffoldncbi591202
66792Arcicella aurantiaca strain DSM 22214591202.3wgspatric591202
66792Arcicella aurantiaca DSM 222142595698202draftimg591202

GC content

@refGC-contentmethod
1620639.9high performance liquid chromatography (HPLC)
2980639.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.938yes
gram-positiveno98.006yes
anaerobicno99.343yes
halophileno96.432yes
spore-formingno95.154yes
glucose-utilyes86.404yes
aerobicyes90.22yes
thermophileno98.249no
motileno93.414yes
glucose-fermentno89.21no

External links

@ref: 16206

culture collection no.: DSM 22214, BCRC 17969, LMG 25207

straininfo link

  • @ref: 73278
  • straininfo: 360697

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20118286Arcicella aurantiaca sp. nov., isolated from stream water.Sheu SY, Yang CS, Chen MH, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.021527-02010Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyGenetics
Phylogeny22368167Arcicella rigui sp. nov., isolated from water of a wetland, and emended descriptions of the genus Arcicella, Arcicella aquatica, Arcicella rosea and Arcicella aurantiaca.Chen WM, Yang SH, Young CC, Sheu SYInt J Syst Evol Microbiol10.1099/ijs.0.037242-02012Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, *Water Microbiology, WetlandsGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16206Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22214)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22214
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
29806Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2618328776041
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
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
73278Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360697.1StrainInfo: A central database for resolving microbial strain identifiers