Strain identifier

BacDive ID: 1830

Type strain: Yes

Species: Salinarimonas ramus

Strain Designation: SL014B-41A4

Strain history: <- Y.-Q. Tang, Peking Univ., Beijing, China; SL014B-41A4 <- H. Cai et al.

NCBI tax ID(s): 690164 (species)

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General

@ref: 16560

BacDive-ID: 1830

DSM-Number: 22962

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

description: Salinarimonas ramus SL014B-41A4 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from crude oil-polluted saline soil.

NCBI tax id

  • NCBI tax id: 690164
  • Matching level: species

strain history

  • @ref: 16560
  • history: <- Y.-Q. Tang, Peking Univ., Beijing, China; SL014B-41A4 <- H. Cai et al.

doi: 10.13145/bacdive1830.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Salinarimonadaceae
  • genus: Salinarimonas
  • species: Salinarimonas ramus
  • full scientific name: Salinarimonas ramus Cai et al. 2011

@ref: 16560

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Salinarimonadaceae

genus: Salinarimonas

species: Salinarimonas ramus

full scientific name: Salinarimonas ramus Cai et al. 2011

strain designation: SL014B-41A4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23333negative1.25-25 µm0.6-4.0 µmrod-shapedyesmonotrichous, polar
69480yes93.999
69480negative99.989

colony morphology

  • @ref: 23333
  • colony color: deep red
  • colony shape: circular
  • incubation period: 7 days
  • medium used: ASW

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16560BACTO 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
23333ASWyes

culture temp

@refgrowthtypetemperaturerange
16560positivegrowth28mesophilic
23333positivegrowth4-50
23333positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
23333positiveoptimum7.0
23333positivegrowth6.0-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 23333
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.876

halophily

@refsaltgrowthtested relationconcentration
23333NaClpositiveoptimum4 %
23333NaClpositivegrowth0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2333316947citrate-assimilation
2333325115malate-assimilation
2333318401phenylacetate-assimilation
2333317108D-arabinose-builds acid from
2333315824D-fructose-builds acid from
2333312936D-galactose-builds acid from
2333317634D-glucose-builds acid from
2333316024D-mannose-builds acid from
2333317754glycerol-builds acid from
2333365328L-xylose-builds acid from
2333317306maltose-builds acid from
2333317992sucrose-builds acid from
2333327082trehalose-builds acid from
2333336219alpha-lactose-carbon source
2333316150benzoate-carbon source
2333316947citrate-carbon source
2333316899D-mannitol-carbon source
2333316988D-ribose-carbon source
2333315740formate-carbon source
2333317268myo-inositol-carbon source
2333330849L-arabinose-carbon source
2333316634raffinose-carbon source
2333330911sorbitol-carbon source
2333316449alanine-nitrogen source
2333329016arginine-nitrogen source
2333315428glycine-nitrogen source
2333329991L-aspartate-nitrogen source
2333318257ornithine-nitrogen source
2333328044phenylalanine-nitrogen source
2333317822serine-nitrogen source
2333327897tryptophan-nitrogen source
23333174265-dehydro-D-gluconate+builds acid from
2333316947citrate+builds acid from
233334853esculin+builds acid from
2333330849L-arabinose+builds acid from
2333317151xylitol+builds acid from
2333315824D-fructose+carbon source
2333312936D-galactose+carbon source
2333316813galactitol+carbon source
2333326546rhamnose+carbon source
2333330031succinate+carbon source
2333327082trehalose+carbon source
2333318222xylose+carbon source
2333317203L-proline+nitrogen source
2333328017starch+/-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
233338309polymyxin byesyes300 Unit
233333745clindamycinyesyes2 µg
2333328001vancomycinyesyes30 µg
2333318208penicillin gyesyes10 Unit
233332676amoxicillinyesyes10 µg
2333348923erythromycinyesyes15 µg
233333508ceftazidimeyesyes30 µg
23333204928cefotaximeyesyes30 µg
233336104kanamycinyesyes30 µg
233337507neomycinyesyes30 µg
2333327902tetracyclineyesyes30 µg
2333317076streptomycinyesyes300 µg
233339332sulfamethoxazoleyesyes300 µg
2333328368novobiocinyesyes5 µg
233337731ofloxacinyesyes5 µg

metabolite production

@refChebi-IDmetaboliteproduction
2333315688acetoinno
233338295beta-hydroxybutyrateyes

metabolite tests

  • @ref: 23333
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
23333acid phosphatase-3.1.3.2
23333alpha-chymotrypsin-3.4.21.1
23333arginine dihydrolase-3.5.3.6
23333beta-galactosidase+3.2.1.23
23333cytochrome oxidase-1.9.3.1
23333esterase (C 4)-
23333lipase (C 14)-
23333urease-3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 16560
  • sample type: crude oil-polluted saline soil
  • geographic location: Shengli Oilfield
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Engineered#Industrial#Oil reservoir
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_8138.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_3753;97_4615;98_5924;99_8138&stattab=map
  • Last taxonomy: Salinarimonas
  • 16S sequence: GU125653
  • Sequence Identity:
  • Total samples: 2629
  • soil counts: 576
  • aquatic counts: 1113
  • animal counts: 815
  • plant counts: 125

Safety information

risk assessment

  • @ref: 16560
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16560
  • description: Salinarimonas ramus strain SL014B-41A4 16S ribosomal RNA gene, partial sequence
  • accession: GU125653
  • length: 1421
  • database: ena
  • NCBI tax ID: 690164

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinarimonas ramus CGMCC 1.9161GCA_014645695contigncbi690164
66792Salinarimonas ramus strain CGMCC 1.9161690164.3wgspatric690164

GC content

  • @ref: 16560
  • GC-content: 67.68
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.144yes
anaerobicno95.042yes
halophileno80.351no
spore-formingno90.522no
glucose-utilyes89.494no
flagellatedno52.737no
thermophileno95.191yes
motileyes85.531yes
aerobicyes75.669no
glucose-fermentno90.144no

External links

@ref: 16560

culture collection no.: DSM 22962, CGMCC 1.9161

straininfo link

  • @ref: 71475
  • straininfo: 396939

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20802058Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil.Cai M, Wang L, Cai H, Li Y, Wang YN, Tang YQ, Wu XLInt J Syst Evol Microbiol10.1099/ijs.0.025932-02010DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Petroleum/*analysis/microbiology, Phylogeny, Propionibacteriaceae/*classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, Sodium Chloride/*analysis, Soil/analysis, *Soil Microbiology, Soil Pollutants/*analysisMetabolism
Phylogeny35225758Salinarimonas soli sp. nov., isolated from soil.Jin CZ, Jin L, Liu MJ, Kang MK, Park SH, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijsem.0.0050952022Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16560Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22962)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22962
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
23333Man Cai, Lu Wang, Hua Cai, Yan Li, Ya-Nan Wang, Yue-Qin Tang, Xiao-Lei Wu10.1099/ijs.0.025932-0Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soilIJSEM 61: 1767-1775 201120802058
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)
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
71475Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396939.1StrainInfo: A central database for resolving microbial strain identifiers