Strain identifier

BacDive ID: 5477

Type strain: Yes

Species: Aequorivita sublithincola

Strain Designation: 9-3

Strain history: CIP <- 2017, DSMZ <- J. Bowman, Tasmania Univ., Tasmania, Australia: strain 9-3 <- M. Smith

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General

@ref: 5266

BacDive-ID: 5477

DSM-Number: 14238

keywords: genome sequence, Bacteria, obligate aerobe, chemoheterotroph, psychrophilic, Gram-negative, filament-shaped

description: Aequorivita sublithincola 9-3 is an obligate aerobe, chemoheterotroph, psychrophilic bacterium that was isolated from quartz stone sublith.

NCBI tax id

NCBI tax idMatching level
746697strain
101385species

strain history

@refhistory
5266<- J. P. Bowman; 9-3 <- M. Smith
123346CIP <- 2017, DSMZ <- J. Bowman, Tasmania Univ., Tasmania, Australia: strain 9-3 <- M. Smith

doi: 10.13145/bacdive5477.20230509.8.1

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 sublithincola
  • full scientific name: Aequorivita sublithincola Bowman and Nichols 2002

@ref: 5266

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Aequorivita

species: Aequorivita sublithincola

full scientific name: Aequorivita sublithincola Bowman and Nichols 2002

strain designation: 9-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43341negative0.5-20 µm0.4-0.5 µmfilament-shapedno
69480negative99.991
123346negativerod-shapedno

colony morphology

@refcolony color
43341orange
123346

pigmentation

@refproductionname
43341noFlexirubin-Type
123346yesFlexirubin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_14238_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5266BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) 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
42118MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123346CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5266positivegrowth2-10psychrophilic
42118positivegrowth25mesophilic
43341positivegrowth-2-25
123346positivegrowth15-25psychrophilic
123346nogrowth5psychrophilic
123346nogrowth30mesophilic
123346nogrowth37mesophilic
123346nogrowth41thermophilic
123346nogrowth45thermophilic

culture pH

  • @ref: 43341
  • ability: positive
  • type: optimum
  • pH: 7-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43341obligate aerobe
123346microaerophile

nutrition type

  • @ref: 43341
  • type: chemoheterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
43341NaClpositivegrowth6 %
43341NaClinconsistentgrowth10 %
43341NaClnogrowth12-99 %
123346NaClnogrowth0 %
123346NaClnogrowth2 %
123346NaClnogrowth4 %
123346NaClnogrowth6 %
123346NaClnogrowth8 %
123346NaClnogrowth10 %

observation

@refobservation
43341fermentation of sugars and alcohols
43341hydrolysis of polysaccharides

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43341casein-hydrolysis
43341cellulose-degradation62968
43341elastin-hydrolysis4767
43341esculin-hydrolysis4853
43341gelatin+hydrolysis5291
43341L-tyrosine+hydrolysis17895
43341starch-hydrolysis28017
43341tributyrin-hydrolysis35020
43341uric acid-degradation27226
43341xanthine-degradation15318
43341xylan-degradation37166
123346esculin-hydrolysis4853
123346hippurate-hydrolysis606565
123346nitrate-reduction17632
123346nitrite-reduction16301
123346malonate-assimilation15792
123346nitrate-respiration17632

metabolite production

@refChebi-IDmetaboliteproduction
4334115688acetoinno
4334135581indoleno
12334635581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
4334115688acetoin-
12334615688acetoin-
12334617234glucose-

enzymes

@refvalueactivityec
43341alkaline phosphatase+3.1.3.1
43341esterase-
43341esterase+
43341lysine decarboxylase-4.1.1.18
43341arginine dihydrolase-3.5.3.6
43341ornithine decarboxylase-4.1.1.17
43341alpha-arabinosidase-3.2.1.55
43341alpha-fucosidase-3.2.1.51
43341beta-glucosidase-3.2.1.21
43341beta-galactosidase-3.2.1.23
433416-phospho-beta-galactosidase-3.2.1.85
43341beta-glucuronidase-3.2.1.31
43341N-acetyl-beta-glucosaminidase+3.2.1.52
43341lipase-
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
123346oxidase-
123346beta-galactosidase+3.2.1.23
123346alcohol dehydrogenase-1.1.1.1
123346gelatinase+/-
123346amylase-
123346DNase-
123346caseinase-3.4.21.50
123346catalase+1.11.1.6
123346tween esterase+
123346gamma-glutamyltransferase+2.3.2.2
123346lecithinase-
123346lipase-
123346lysine decarboxylase-4.1.1.18
123346ornithine decarboxylase-4.1.1.17
123346phenylalanine ammonia-lyase-4.3.1.24
123346tryptophan deaminase-
123346urease-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
123346-+++-++-++++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentenrichment cultureisolation procedurecountryorigin.countryisolation date
5266quartz stone sublithVestfold HillsAustralia and Oceania
43341quartz stone aublithic materialmarine agar (Difco, Oxoid)sublithic biomass is scraped , vortexed and then diluted in trypicase soy broth
123346Quartz stone sublimVestfold hillsAntarcticaAntarcticaATA1998

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Geologic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
52661Risk group (German classification)
1233461Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aequorivita sublithincola DSM 14238GCA_000265385completencbi746697
66792Aequorivita sublithincola DSM 14238746697.3completepatric746697
66792Aequorivita sublithincola QSSC9-3, DSM 142382509276063completeimg746697

GC content

  • @ref: 5266
  • GC-content: 36-37

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.927yes
flagellatedno95.907yes
gram-positiveno98.355no
anaerobicno99.32yes
aerobicyes92.635no
halophileyes79.618yes
spore-formingno94.585no
thermophileno99.73yes
glucose-utilyes79.335no
glucose-fermentno91.452no

External links

@ref: 5266

culture collection no.: DSM 14238, ACAM 643, CIP 107454, LMG 21432

straininfo link

  • @ref: 74965
  • straininfo: 86436

literature

  • topic: Phylogeny
  • Pubmed-ID: 12361255
  • title: Aequorivita gen. nov., a member of the family Flavobacteriaceae isolated from terrestrial and marine Antarctic habitats.
  • authors: Bowman JP, Nichols DS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-5-1533
  • year: 2002
  • mesh: Antarctic Regions, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gram-Negative Aerobic Rods and Cocci/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Seawater/microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5266Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14238)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14238
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
42118Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4891
4334110.1007/978-0-387-68572-4
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
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
74965Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID86436.1StrainInfo: A central database for resolving microbial strain identifiers
123346Curators of the CIPCollection of Institut Pasteur (CIP 107454)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107454