Strain identifier

BacDive ID: 1829

Type strain: Yes

Species: Salinarimonas rosea

Strain history: <- X.-L. Cui, YIM; YIM YD3 <- J.-H. Liu

NCBI tax ID(s): 1123229 (strain), 552063 (species)

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General

@ref: 15575

BacDive-ID: 1829

DSM-Number: 21201

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

description: Salinarimonas rosea DSM 21201 is a facultative anaerobe, halotolerant, mesophilic bacterium that forms circular colonies and was isolated from sediment from a salt mine.

NCBI tax id

NCBI tax idMatching level
552063species
1123229strain

strain history

  • @ref: 15575
  • history: <- X.-L. Cui, YIM; YIM YD3 <- J.-H. Liu

doi: 10.13145/bacdive1829.20230509.8.1

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 rosea
  • full scientific name: Salinarimonas rosea Liu et al. 2010

@ref: 15575

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Salinarimonadaceae

genus: Salinarimonas

species: Salinarimonas rosea

full scientific name: Salinarimonas rosea Liu et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23332negative1.20-1.45 µm0.4-1.0 µmrod-shapedyesmonotrichous, polar
69480yes90.109
69480negative99.994

colony morphology

  • @ref: 23332
  • colony size: 2.5 mm
  • colony color: pink
  • colony shape: circular
  • incubation period: 5 days

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21201_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21201_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21201_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21201_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21201_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15575BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 30.0 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
23332MY mediumyes
23332Nutrient agar (NA)yes
23332Trypticase Soy Agar (TSA)yes

culture temp

@refgrowthtypetemperaturerange
15575positivegrowth28mesophilic
23332positivegrowth15-37
23332positiveoptimum28-30mesophilic

culture pH

@refabilitytypepHPH range
23332positivegrowth6.0-9.0alkaliphile
23332positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 23332
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.818

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23332halotolerant
23332NaClpositivegrowth0-5 %
23332NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2333227856acetamide-carbon source
2333216150benzoate-carbon source
2333217057cellobiose-carbon source
2333212936D-galactose-carbon source
2333216236ethanol-carbon source
2333262345L-rhamnose-carbon source
2333265328L-xylose-carbon source
2333218300maleic acid-carbon source
2333216634raffinose-carbon source
2333217814salicin-carbon source
23332132950tartrate-carbon source
2333227082trehalose-carbon source
233325291gelatin-hydrolysis
2333228017starch-hydrolysis
23332168082-dehydro-D-gluconate+builds acid from
2333215824D-fructose+builds acid from
2333228847D-fucose+builds acid from
2333212936D-galactose+builds acid from
2333217634D-glucose+builds acid from
2333216024D-mannose+builds acid from
2333216988D-ribose+builds acid from
2333217754glycerol+builds acid from
2333230849L-arabinose+builds acid from
2333217306maltose+builds acid from
2333216634raffinose+builds acid from
2333217992sucrose+builds acid from
2333227082trehalose+builds acid from
2333232528turanose+builds acid from
2333218222xylose+builds acid from
2333230089acetate+carbon source
23332casamino acids+carbon source
2333216947citrate+carbon source
2333215824D-fructose+carbon source
2333217634D-glucose+carbon source
2333216024D-mannose+carbon source
2333265327D-xylose+carbon source
2333217754glycerol+carbon source
2333228087glycogen+carbon source
2333217268myo-inositol+carbon source
2333215443inulin+carbon source
2333216467L-arginine+carbon source
2333217196L-asparagine+carbon source
2333218019L-lysine+carbon source
2333215729L-ornithine+carbon source
2333217203L-proline+carbon source
23332peptone+carbon source
2333215361pyruvate+carbon source
2333233942ribose+carbon source
2333230911sorbitol+carbon source
2333230031succinate+carbon source
2333217992sucrose+carbon source
23332tryptone+carbon source
233324853esculin+degradation
2333217368hypoxanthine+degradation
2333215318xanthine+degradation
2333217632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
2333217833gentamicinyesyes10 µg (disc)
2333228971ampicillinyesyes10 µg (disc)
23332100246norfloxacinyesyes10 µg (disc)
2333218208penicillin gyesyes10 µg (disc)
233323393carbenicillinyesyes100 µg (disc)
2333248923erythromycinyesyes15 µg (disc)
233322637amikacinyesyes30 µg (disc)
233323542cephalothinyesyes30 µg (disc)
2333217698chloramphenicolyesyes30 µg (disc)
23332100241ciprofloxacinyesyes5 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
2333235581indoleno
2333216136hydrogen sulfideno
233328295beta-hydroxybutyrateno
2333230033bacteriochlorophyll alphano

enzymes

@refvalueactivityec
23332Acid phosphatase+3.1.3.2
23332Alkaline phosphatase+3.1.3.1
23332alpha-chymotrypsin+3.4.21.1
23332alpha-fucosidase-3.2.1.51
23332alpha-galactosidase-3.2.1.22
23332alpha-glucosidase-3.2.1.20
23332alpha-mannosidase-3.2.1.24
23332arginine dihydrolase+3.5.3.6
23332beta-galactosidase-3.2.1.23
23332beta-glucosidase-3.2.1.21
23332beta-glucuronidase-3.2.1.31
23332catalase+1.11.1.6
23332cystine arylamidase+3.4.11.3
23332cytochrome oxidase+1.9.3.1
23332esterase (C 4)+
23332esterase lipase (C 8)+
23332leucine arylamidase+3.4.11.1
23332lipase (C 14)+
23332lysine decarboxylase+4.1.1.18
23332N-acetyl-beta-glucosaminidase-3.2.1.52
23332naphthol-AS-BI-phosphohydrolase+
23332ornithine decarboxylase+4.1.1.17
23332trypsin+3.4.21.4
23332urease+3.5.1.5
23332valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
15575sediment from a salt mineYunnanChinaCHNAsia
23332Moxie, Yunnan ProvinceMarine agar 221614 days28dilution-plating

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Condition#Saline
#Environmental#Terrestrial#Sediment
#Environmental#Terrestrial#Geologic

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: EU878006
  • Sequence Identity:
  • Total samples: 2629
  • soil counts: 576
  • aquatic counts: 1113
  • animal counts: 815
  • plant counts: 125

Safety information

risk assessment

  • @ref: 15575
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15575
  • description: Salinarimonas rosea strain YIM YD3 16S ribosomal RNA gene, partial sequence
  • accession: EU878006
  • length: 1412
  • database: ena
  • NCBI tax ID: 552063

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinarimonas rosea DSM 21201GCA_000429045scaffoldncbi1123229
66792Salinarimonas rosea DSM 212011123229.3wgspatric1123229
66792Salinarimonas rosea DSM 212012522572188draftimg1123229

GC content

  • @ref: 15575
  • GC-content: 71.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.544yes
flagellatedyes51.817yes
gram-positiveno97.888yes
anaerobicno94.792no
aerobicyes72.459yes
halophileno78.907no
spore-formingno90.667no
glucose-utilyes89.734yes
thermophileno96.714yes
glucose-fermentno91.801no

External links

@ref: 15575

culture collection no.: DSM 21201, CCTCC AA 208038, KCTC 22346, YIM YD3

straininfo link

  • @ref: 71474
  • straininfo: 405840

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19648350Salinarimonas rosea gen. nov., sp. nov., a new member of the alpha-2 subgroup of the Proteobacteria.Liu JH, Wang YX, Zhang XX, Wang ZG, Chen YG, Wen ML, Xu LH, Peng Q, Cui XLInt J Syst Evol Microbiol10.1099/ijs.0.006981-02009Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Mining, Molecular Sequence Data, Phylogeny, Proteobacteria/*classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
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
Pathogenicity28749956Functional characterization of sodium-pumping rhodopsins with different pumping properties.Tsunoda SP, Prigge M, Abe-Yoshizumi R, Inoue K, Kozaki Y, Ishizuka T, Yawo H, Yizhar O, Kandori HPLoS One10.1371/journal.pone.01792322017Animals, Cells, Cultured, Gene Silencing, Humans, Mice, Optogenetics, Rats, Sprague-Dawley, Rhodopsin/*metabolism, Sodium-Potassium-Exchanging ATPase/*metabolism, Spectrum 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
15575Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21201)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21201
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
23332Ji-Hui Liu, Yong-Xia Wang, Xiao-Xia Zhang, Zhi-Gang Wang, Yi-Guang Chen, Meng-Liang Wen, Li-Hua Xu, Qian Peng, Xiao-Long Cui10.1099/ijs.0.006981-0Salinarimonas rosea gen. nov., sp. nov., a new member of the a-2 subgroup of the ProteobacteriaIJSEM 60: 55-60 201019648350
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
71474Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405840.1StrainInfo: A central database for resolving microbial strain identifiers