Strain identifier

BacDive ID: 13757

Type strain: Yes

Species: Roseivivax halodurans

Strain history: CIP <- 1999, Y. Nishimura, Tokyo Univ., Tokyo, Japan: strain Och 239 <- Shiba

NCBI tax ID(s): 1449350 (strain), 93683 (species)

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General

@ref: 5893

BacDive-ID: 13757

DSM-Number: 15395

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

description: Roseivivax halodurans DSM 15395 is a mesophilic, Gram-negative bacterium that was isolated from charophytes on the stromatolites of a saline lake.

NCBI tax id

NCBI tax idMatching level
93683species
1449350strain

strain history

@refhistory
5893<- JCM <- Y. Nishimura <- T. Shiba; OCh 239
67770Y. Nishimura <-- T. Shiba OCh 239.
119805CIP <- 1999, Y. Nishimura, Tokyo Univ., Tokyo, Japan: strain Och 239 <- Shiba

doi: 10.13145/bacdive13757.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Roseivivax
  • species: Roseivivax halodurans
  • full scientific name: Roseivivax halodurans Suzuki et al. 1999

@ref: 5893

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Roseivivax

species: Roseivivax halodurans

full scientific name: Roseivivax halodurans Suzuki et al. 1999

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.998
119805negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5893PPES-II AGAR MEDIUM (DSMZ Medium 1075)yeshttps://mediadive.dsmz.de/medium/1075Name: PPES-II AGAR MEDIUM (DSMZ Medium 1075) Composition: NaCl 30.0 g/l Agar 15.0 g/l MgCl2 x 6 H2O 10.8 g/l MgSO4 x 7 H2O 5.4 g/l Peptone 2.0 g/l Proteose peptone no. 3 1.0 g/l Soytone 1.0 g/l Yeast extract 1.0 g/l CaCl2 x 2 H2O 1.0 g/l KCl 0.7 g/l Fe(III)-EDTA 0.1 g/l Distilled water
40256Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119805CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5893positivegrowth28mesophilic
40256positivegrowth30mesophilic
67770positivegrowth27mesophilic
119805positivegrowth15-41
119805nogrowth5psychrophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.989

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1198054853esculin+hydrolysis
119805606565hippurate-hydrolysis
11980517234glucose+/-degradation

metabolite production

  • @ref: 119805
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11980515688acetoin-
11980517234glucose-

enzymes

@refvalueactivityec
119805oxidase+
119805beta-galactosidase+3.2.1.23
119805alcohol dehydrogenase-1.1.1.1
119805gelatinase-
119805amylase-
119805caseinase-3.4.21.50
119805catalase+1.11.1.6
119805tween esterase-
119805gamma-glutamyltransferase+2.3.2.2
119805lecithinase-
119805lipase-
119805lysine decarboxylase-4.1.1.18
119805ornithine decarboxylase-4.1.1.17
119805phenylalanine ammonia-lyase-4.3.1.24
119805protease-
119805urease-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
119805-+++-+----++----+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5893charophytes on the stromatolites of a saline lakeLake CliftonAustraliaAUSAustralia and Oceania
67770Charophytes on the stromatolites
119805EpiphyteClifton lakeAustraliaAUSAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Host#Algae#Green algae
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_7659.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3293;97_4039;98_5603;99_7659&stattab=map
  • Last taxonomy: Roseivivax halodurans subclade
  • 16S sequence: LC506141
  • Sequence Identity:
  • Total samples: 1709
  • soil counts: 125
  • aquatic counts: 1285
  • animal counts: 259
  • plant counts: 40

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58931Risk group (German classification)
1198051Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Roseivivax halodurans strain NBRC16685 16S ribosomal RNA gene, partial sequenceDQ9156211306ena93683
5893Roseivivax halodurans gene for 16S rRNA, strain: OCh 239D858291410ena93683
67770Roseivivax halodurans JCM 10272 gene for 16S ribosomal RNA, partial sequenceLC5061411385ena93683

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseivivax halodurans JCM 102721449350.3wgspatric1449350
66792Roseivivax halodurans JCM 102722563367175draftimg1449350
67770Roseivivax halodurans JCM 10272GCA_000521785contigncbi1449350

GC content

@refGC-contentmethod
589364.4
6777064.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes53.411no
gram-positiveno98.245no
anaerobicno96.112no
halophileyes73.808no
spore-formingno95.831no
glucose-utilyes88.831no
thermophileno97.576yes
aerobicyes89.734no
flagellatedno80.302no
glucose-fermentno89.246no

External links

@ref: 5893

culture collection no.: DSM 15395, ATCC 700843, CIP 105983, IFO 16685, JCM 10272, NBRC 16685, OCh 239, BCRC 80020

straininfo link

  • @ref: 82938
  • straininfo: 44171

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319485Roseivivax halodurans gen. nov., sp. nov. and Roseivivax halotolerans sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from a saline lake.Suzuki T, Muroga Y, Takahama M, Nishimura YInt J Syst Bacteriol10.1099/00207713-49-2-6291999Bacteria, Aerobic/*classification/cytology/isolation & purification/physiology, Bacteriochlorophylls/*analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Water MicrobiologyGenetics
Phylogeny24567080Roseivivax atlanticus sp. nov., isolated from surface seawater of the Atlantic Ocean.Li G, Lai Q, Liu X, Sun F, Shao ZAntonie Van Leeuwenhoek10.1007/s10482-014-0140-52014Atlantic Ocean, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny24812358Roseivivax marinus sp. nov., isolated from deep water.Dai X, Shi X, Gao X, Liu J, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.062760-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics
Phylogeny29043957Rhodosalinus sediminis gen. nov., sp. nov., isolated from marine saltern.Guo LY, Ling SK, Li CM, Chen GJ, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0024242017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, *Salinity, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5893Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15395)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15395
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
40256Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18062
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
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
82938Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44171.1StrainInfo: A central database for resolving microbial strain identifiers
119805Curators of the CIPCollection of Institut Pasteur (CIP 105983)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105983