Strain identifier

BacDive ID: 24014

Type strain: Yes

Species: Aequorivita viscosa

Strain Designation: 8-1b

Strain history: X.-Q. Zhang 8-1b.

NCBI tax ID(s): 797419 (species)

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General

@ref: 20254

BacDive-ID: 24014

DSM-Number: 26349

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

description: Aequorivita viscosa 8-1b is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seaweed from intertidal zone.

NCBI tax id

  • NCBI tax id: 797419
  • Matching level: species

strain history

@refhistory
20254<- J. Liu, Zhejiang Univ., Hangzhou, China; 8-1b <- C. Bai
67770X.-Q. Zhang 8-1b.

doi: 10.13145/bacdive24014.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Aequorivita
  • species: Aequorivita viscosa
  • full scientific name: Aequorivita viscosa Liu et al. 2013

@ref: 20254

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Aequorivita

species: Aequorivita viscosa

full scientific name: Aequorivita viscosa Liu et al. 2013

strain designation: 8-1b

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31008negative4.25 µm2 µmrod-shapedno
69480negative99.975

pigmentation

  • @ref: 31008
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20254
  • name: MODIFIED BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 1517)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1517
  • composition: Name: MODIFIED BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 1517) Composition: NaCl 19.45 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 NaHCO3 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
20254positivegrowth28mesophilic
31008positivegrowth04-39
31008positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31008positivegrowth6.0-9.5alkaliphile
31008positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 31008
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31008no
69481no100
69480no99.98

halophily

@refsaltgrowthtested relationconcentration
31008NaClpositivegrowth0.5-8 %
31008NaClpositiveoptimum2 %

observation

@refobservation
31008aggregates in clumps
67770quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3100822653asparagine+carbon source
3100835391aspartate+carbon source
3100828087glycogen+carbon source
3100824996lactate+carbon source
3100837684mannose+carbon source

metabolite production

  • @ref: 31008
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31008acid phosphatase+3.1.3.2
31008alkaline phosphatase+3.1.3.1
31008catalase+1.11.1.6
31008gelatinase+
31008urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20254seaweed from intertidal zoneEast China Sea, Zhoushan sea areaChinaCHNAsia
67770Seaweed from the intertidal zone of Zhoushan sea areaEast China Sea

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Host#Plants#Aquatic plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_181242.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_74;96_182;97_9943;98_118187;99_181242&stattab=map
  • Last taxonomy: Aequorivita viscosa subclade
  • 16S sequence: HM485318
  • Sequence Identity:
  • Total samples: 410
  • soil counts: 56
  • aquatic counts: 140
  • animal counts: 208
  • plant counts: 6

Safety information

risk assessment

  • @ref: 20254
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20254
  • description: Aequorivita viscosa strain 8-1b 16S ribosomal RNA gene, partial sequence
  • accession: HM485318
  • length: 1488
  • database: ena
  • NCBI tax ID: 797419

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aequorivita viscosa strain CGMCC 1.11023797419.3wgspatric797419
66792Aequorivita viscosa strain DSM 26349797419.4wgspatric797419
66792Aequorivita viscosa CGMCC 1.110232667527447draftimg797419
66792Aequorivita viscosa DSM 263492622736533draftimg797419
67770Aequorivita viscosa CGMCC 1.11023GCA_900106795scaffoldncbi797419
67770Aequorivita viscosa DSM 26349GCA_900141955scaffoldncbi797419

GC content

@refGC-contentmethod
2025436.6high performance liquid chromatography (HPLC)
3100836.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.91yes
flagellatedno95.834yes
gram-positiveno97.892no
anaerobicno97.873yes
halophileyes64.613no
spore-formingno95.718yes
thermophileno99.415yes
glucose-utilyes76.365no
aerobicyes85.593no
glucose-fermentno88.871no

External links

@ref: 20254

culture collection no.: DSM 26349, CGMCC 1.11023, JCM 18497

straininfo link

  • @ref: 87988
  • straininfo: 400547

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23435250Aequorivita viscosa sp. nov., isolated from an intertidal zone, and emended descriptions of Aequorivita antarctica and Aequorivita capsosiphonis.Liu JJ, Zhang XQ, Pan J, Sun C, Zhang Y, Li CQ, Zhu XF, Wu MInt J Syst Evol Microbiol10.1099/ijs.0.049635-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Glycolipids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny32375986Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov.Wang Q, Cai SD, Liu J, Zhang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0041742020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Geologic Sediments/*microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20254Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26349Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26349)
31008Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172733828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic 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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
87988Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID400547.1