Strain identifier

BacDive ID: 13747

Type strain: Yes

Species: Rhodovulum marinum

Strain Designation: 3Vi, JA 128

Strain history: Ch. Sasikala and Ch. V. Romana JA128.

NCBI tax ID(s): 320662 (species)

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General

@ref: 7356

BacDive-ID: 13747

DSM-Number: 18063

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, ovoid-shaped

description: Rhodovulum marinum 3Vi is an anaerobe, Gram-negative, ovoid-shaped bacterium that was isolated from Sea shore water.

NCBI tax id

  • NCBI tax id: 320662
  • Matching level: species

strain history

@refhistory
7356<- C. Sasikala, Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA 128 <- P. Anil Kumar
67770Ch. Sasikala and Ch. V. Romana JA128.

doi: 10.13145/bacdive13747.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Rhodovulum
  • species: Rhodovulum marinum
  • full scientific name: Rhodovulum marinum Srinivas et al. 2006

@ref: 7356

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rhodovulum

species: Rhodovulum marinum

full scientific name: Rhodovulum marinum Srinivas et al. 2006

strain designation: 3Vi, JA 128

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31665negative01-02 µm0.6-0.8 µmovoid-shapedno
69480negative100

colony morphology

  • @ref: 59456
  • incubation period: 2 days

pigmentation

  • @ref: 31665
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31665positivegrowth25-35
31665positiveoptimum30
59456positivegrowth30
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
31665positivegrowth5.5-7.5
31665positiveoptimum6-6.8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7356anaerobe
31665anaerobe

spore formation

@refspore formationconfidence
31665no
69481no90
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31665NaClpositivegrowth0.5-3 %
31665NaClpositiveoptimum0.5-3 %

observation

  • @ref: 31665
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3166530089acetate+carbon source
3166516236ethanol+carbon source
3166517754glycerol+carbon source
3166524996lactate+carbon source
3166529864mannitol+carbon source
3166515361pyruvate+carbon source
3166530911sorbitol+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7356Sea shore waterVisakhapatnamIndiaINDAsia
59456Water,tidalVisakhapatnam,R.K.beachIndiaINDAsia
67770Marine tidesVisakhapatnamIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_25026.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_12514;97_15191;98_18814;99_25026&stattab=map
  • Last taxonomy: Rhodovulum marinum subclade
  • 16S sequence: AJ891122
  • Sequence Identity:
  • Total samples: 28
  • soil counts: 3
  • aquatic counts: 20
  • animal counts: 5

Safety information

risk assessment

  • @ref: 7356
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7356
  • description: Rhodovulum marinum partial 16S rRNA gene, type strain JA128
  • accession: AJ891122
  • length: 1376
  • database: ena
  • NCBI tax ID: 320662

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodovulum marinum strain DSM 18063320662.3wgspatric320662
66792Rhodovulum marinum DSM 180632795385476draftimg320662
67770Rhodovulum marinum DSM 18063GCA_004343075scaffoldncbi320662

GC content

@refGC-contentmethod
3166562
6777062thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
gram-positiveno98.272yes
anaerobicno63.787yes
halophileyes71.894no
spore-formingno94.524yes
glucose-utilyes70.644no
flagellatedno79.021yes
thermophileno95.681yes
aerobicno81.401yes
motileyes60.368yes
glucose-fermentno90.49no

External links

@ref: 7356

culture collection no.: DSM 18063, CCUG 52183, JCM 13300, ATCC BAA 1215, BCRC 80541

straininfo link

  • @ref: 82929
  • straininfo: 297331

literature

  • topic: Phylogeny
  • Pubmed-ID: 16825644
  • title: Rhodovulum marinum sp. nov., a novel phototrophic purple non-sulfur alphaproteobacterium from marine tides of Visakhapatnam, India.
  • authors: Srinivas TNR, Kumar PA, Sasikala C, Ramana CV, Suling J, Imhoff JF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64005-0
  • year: 2006
  • mesh: Carotenoids/analysis, Cell Membrane/ultrastructure, Chlorophyll/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hydrogen-Ion Concentration, India, Microscopy, Electron, Transmission, Microscopy, Phase-Contrast, Molecular Sequence Data, Organic Chemicals/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodovulum/*classification/cytology/*isolation & purification/physiology, Saline Solution, Hypertonic, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Thiamine/pharmacology, Vitamin B Complex/pharmacology, Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7356Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18063)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18063
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
31665Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2794528776041
59456Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52183)https://www.ccug.se/strain?id=52183
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)
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.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
82929Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297331.1StrainInfo: A central database for resolving microbial strain identifiers