Strain identifier

BacDive ID: 17257

Type strain: Yes

Species: Vibrio diazotrophicus

Strain Designation: NSl, NS1

Strain history: CIP <- 1988, NCIB <- 1982, J.V. Lee, Preston Hall Hosp., Maidston, UK <- M.L. Guerinot: strain NS1

NCBI tax ID(s): 1348635 (strain), 685 (species)

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General

@ref: 1150

BacDive-ID: 17257

DSM-Number: 2604

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

description: Vibrio diazotrophicus NSl is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea urchin gastrointestinal tract.

NCBI tax id

NCBI tax idMatching level
685species
1348635strain

strain history

@refhistory
1150<- R.R. Colwell, strain NSl <- M.L. Guerinot
67770IAM 14402 <-- ATCC 33466 <-- M. L. Guerinot NS-1.
118929CIP <- 1988, NCIB <- 1982, J.V. Lee, Preston Hall Hosp., Maidston, UK <- M.L. Guerinot: strain NS1

doi: 10.13145/bacdive17257.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Vibrio
  • species: Vibrio diazotrophicus
  • full scientific name: Vibrio diazotrophicus Guerinot et al. 1982

@ref: 1150

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio diazotrophicus

full scientific name: Vibrio diazotrophicus Guerinot et al. 1982

strain designation: NSl, NS1

type strain: yes

Morphology

cell morphology

  • @ref: 118929
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1150VIBRIO MEDIUM (DSMZ Medium 308)yeshttps://mediadive.dsmz.de/medium/308Name: VIBRIO MEDIUM (DSMZ Medium 308) Composition: NaCl 10.0 g/l Tryptone 10.0 g/l MgCl2 x 6 H2O 4.0 g/l KCl 1.0 g/l Distilled water
38119Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118929CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
1150positivegrowth25mesophilic
38119positivegrowth25mesophilic
46963positivegrowth30-37mesophilic
67770positivegrowth25mesophilic
118929positivegrowth15-41
118929nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
46963aerobe
118929facultative anaerobe

halophily

  • @ref: 118929
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11892916947citrate+carbon source
1189294853esculin+hydrolysis
11892917234glucose+fermentation
11892917716lactose+fermentation
11892917632nitrate+reduction
11892916301nitrite-reduction
118929132112sodium thiosulfate-builds gas from
11892917632nitrate+respiration

antibiotic resistance

  • @ref: 118929
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118929
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11892915688acetoin-
11892917234glucose+

enzymes

@refvalueactivityec
118929oxidase+
118929beta-galactosidase+3.2.1.23
118929alcohol dehydrogenase-1.1.1.1
118929gelatinase-
118929amylase+
118929DNase-
118929caseinase-3.4.21.50
118929catalase+1.11.1.6
118929tween esterase+
118929gamma-glutamyltransferase-2.3.2.2
118929lecithinase-
118929lipase-
118929lysine decarboxylase-4.1.1.18
118929ornithine decarboxylase-4.1.1.17
118929phenylalanine ammonia-lyase-4.3.1.24
118929tryptophan deaminase-
118929urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118929-+++-+----++----+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118929++++--++---+++-+++++++++-------+-+-+-------++----++--+++---++-+--+-------+-+---++-----+--++++-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1150sea urchin gastrointestinal tractNova ScotiaCanadaCANNorth America
46963Sea urchin gastrointestinal tract
67770Sea urchin gastrointestinal tractNova ScotiaCanadaCANNorth America
118929Animal, Sea urchin gastrointestinal tractNova ScotiaCanadaCANNorth America

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Echinodermata

taxonmaps

  • @ref: 69479
  • File name: preview.99_6055.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_3549;98_4492;99_6055&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: X74701
  • Sequence Identity:
  • Total samples: 9385
  • soil counts: 394
  • aquatic counts: 4875
  • animal counts: 3964
  • plant counts: 152

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
11501Risk group (German classification)
1189292Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio diazotrophicus strain ATCC 33466 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu gene, complete sequenceAF413003461ena685
20218Vibrio diazotrophicus strain ATCC 33466 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequenceAF413004564ena685
20218Vibrio diazotrophicus 16S rRNAD11201213ena685
20218Vibrio diazotrophicus 16S rRNAD11250213ena685
20218Vibrio diazotrophicus 16S rRNAD11299193ena685
20218V.diazotrophicus 16S ribosomal RNAX565771473ena685
20218V.diazotrophicus (ATCC 33466T) gene for 16S ribosomal RNAX747011456ena685
20218Vibrio diazotrophicus gene for 16S rRNA, partial sequence, strain: NBRC 103148AB6819571468ena685

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio diazotrophicus NBRC 1031481348635.3wgspatric1348635
66792Vibrio diazotrophicus NBRC 1031482609460176draftimg1348635
67770Vibrio diazotrophicus NBRC 103148GCA_000740015contigncbi1348635

GC content

@refGC-contentmethod
115045.9
6777045.9Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes92.862no
gram-positiveno98.88no
anaerobicno98.074yes
halophileyes61.842no
spore-formingno95.217no
thermophileno99.426no
glucose-utilyes91.421no
aerobicyes82.248yes
flagellatedyes89.879no
glucose-fermentyes90.058no

External links

@ref: 1150

culture collection no.: DSM 2604, ATCC 33466, IAM 14402, CCUG 19114, JCM 21185, CIP 103191, LMG 7893, NBRC 103148, NCIMB 2169

straininfo link

  • @ref: 86256
  • straininfo: 13866

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21596509Vibrio plantisponsor sp. nov., a diazotrophic bacterium isolated from a mangrove associated wild rice (Porteresia coarctata Tateoka).Rameshkumar N, Gomez-Gil B, Sproer C, Lang E, Dinesh Kumar N, Krishnamurthi S, Nair S, Roque ASyst Appl Microbiol10.1016/j.syapm.2011.02.0052011Bacterial Typing Techniques, Base Composition, Base Sequence, DNA Gyrase/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization/methods, Oxidoreductases/genetics, Phenotype, Phylogeny, Plant Roots/microbiology, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Sequence Alignment, Vibrio/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny26296768Vibrio oceanisediminis sp. nov., a nitrogen-fixing bacterium isolated from an artificial oil-spill marine sediment.Kang SR, Srinivasan S, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0004562015Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, *Petroleum Pollution, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vibrio/*classification/genetics/isolation & purificationGenetics
Phylogeny33887169Vibrio ziniensis sp. nov., isolated from mangrove sediments.Wu J, Qu W, Lai Q, Pei S, Zhang T, Zhuang Y, Chan Z, Zeng RInt J Syst Evol Microbiol10.1099/ijsem.0.0047772021Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/*classification/isolation & purification, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1150Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2604)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2604
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38119Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14961
46963Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 19114)https://www.ccug.se/strain?id=19114
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86256Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13866.1StrainInfo: A central database for resolving microbial strain identifiers
118929Curators of the CIPCollection of Institut Pasteur (CIP 103191)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103191