Strain identifier

BacDive ID: 13761

Type strain: Yes

Species: Roseivivax sediminis

Strain history: <- X Cui, Yunnan Inst., China

NCBI tax ID(s): 936889 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16074

BacDive-ID: 13761

DSM-Number: 21977

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

description: Roseivivax sediminis DSM 21977 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from salt mine sediment from a crystallizer pond.

NCBI tax id

  • NCBI tax id: 936889
  • Matching level: species

strain history

@refhistory
16074<- X.-L. Cui, YIM <- J.-H. Liu and Y.-X. Wang
67771<- X Cui, Yunnan Inst., China

doi: 10.13145/bacdive13761.20230509.8.1

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 sediminis
  • full scientific name: Roseivivax sediminis Xiao et al. 2012

@ref: 16074

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Roseivivax

species: Roseivivax sediminis

full scientific name: Roseivivax sediminis Xiao et al. 2012

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30483negativerod-shapedno
67771negative
69480negative99.981

pigmentation

  • @ref: 30483
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16074
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: NaCl 100.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16074positivegrowth28mesophilic
30483positivegrowth15-42
30483positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30483positivegrowth6.5-8.5alkaliphile
30483positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30483facultative anaerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.957

halophily

@refsaltgrowthtested relationconcentration
30483NaClpositivegrowth1-15 %
30483NaClpositiveoptimum7.50 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3048322599arabinose+carbon source
3048316236ethanol+carbon source
3048317234glucose+carbon source
3048317754glycerol+carbon source
3048317306maltose+carbon source
3048337684mannose+carbon source
3048315361pyruvate+carbon source
3048326546rhamnose+carbon source
3048330911sorbitol+carbon source
304834853esculin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30483acid phosphatase+3.1.3.2
30483alkaline phosphatase+3.1.3.1
30483alpha-galactosidase+3.2.1.22
30483catalase+1.11.1.6
30483cytochrome oxidase+1.9.3.1
30483urease+3.5.1.5
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
16074-----+-+/-++-+-++/---++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
16074salt mine sediment from a crystallizer pondYunnan Province, Fenggang salt mine (23° 28' N 100° 43' E)ChinaCHNAsia23.4667100.717
67771From salt mine sediment, soda lakeYunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Aquatic#Pond (small)
#Environmental#Terrestrial#Sediment
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_18645.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_3750;97_4610;98_5918;99_18645&stattab=map
  • Last taxonomy: Roseivivax sediminis
  • 16S sequence: HQ615878
  • Sequence Identity:
  • Total samples: 639
  • soil counts: 34
  • aquatic counts: 467
  • animal counts: 122
  • plant counts: 16

Safety information

risk assessment

  • @ref: 16074
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16074
  • description: Roseivivax sediminis strain YIM D21 16S ribosomal RNA gene, partial sequence
  • accession: HQ615878
  • length: 1449
  • database: ena
  • NCBI tax ID: 936889

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseivivax sediminis YIM D21,KCTC 23444,ACCC 10710GCA_900112685scaffoldncbi936889
66792Roseivivax sediminis strain YIM D21,KCTC 23444,ACCC 10710936889.3wgspatric936889

GC content

@refGC-contentmethod
1607467.7high performance liquid chromatography (HPLC)
3048367.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno72.187yes
flagellatedno91.23yes
gram-positiveno98.413no
anaerobicno96.552yes
aerobicyes87.426no
halophileyes82.494yes
spore-formingno95.423no
glucose-fermentno90.798yes
thermophileno97.27yes
glucose-utilyes93.928yes

External links

@ref: 16074

culture collection no.: DSM 21977, ACCC 10710, KCTC 23444, YIM D21, YIM D21(T)

straininfo link

  • @ref: 82941
  • straininfo: 402709

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21984676Roseivivax sediminis sp. nov., a moderately halophilic bacterium isolated from salt mine sediment.Xiao W, Wang YX, Liu JH, Wang ZG, Zhang XX, Ji KY, Lai YH, Wen ML, Cui XLInt J Syst Evol Microbiol10.1099/ijs.0.037119-02011Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Mining, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Sodium Chloride, *Soil MicrobiologyGenetics
Phylogeny25155864Roseivivax jejudonensis sp. nov., isolated from the junction between the ocean and a freshwater spring at Jeju Island, South Korea.Jung YT, Lee JS, Yoon JHAntonie Van Leeuwenhoek10.1007/s10482-014-0265-62014Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, *Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16074Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21977)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21977
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
30483Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2681728776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
82941Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402709.1StrainInfo: A central database for resolving microbial strain identifiers