Strain identifier

BacDive ID: 1370

Type strain: Yes

Species: Marinococcus halotolerans

Strain history: <- WJ Li, Yunnan Univ., China

NCBI tax ID(s): 1122203 (strain), 301092 (species)

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General

@ref: 6412

BacDive-ID: 1370

DSM-Number: 16375

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, coccus-shaped, colony-forming, pigmented

description: Marinococcus halotolerans DSM 16375 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and has a orange pigmentation.

NCBI tax id

NCBI tax idMatching level
1122203strain
301092species

strain history

@refhistory
6412<- Wen-Jun Li, YIM 70157
67771<- WJ Li, Yunnan Univ., China

doi: 10.13145/bacdive1370.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Marinococcus
  • species: Marinococcus halotolerans
  • full scientific name: Marinococcus halotolerans Li et al. 2005

@ref: 6412

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Marinococcus

species: Marinococcus halotolerans

full scientific name: Marinococcus halotolerans Li et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityflagellum arrangementconfidence
23006positive1.0-1.2 µmcoccus-shapedyesmonotrichous, polar
67771coccus-shapedyesmonotrichous, polar
67771sphere-shaped
67771positive
69480positive100

colony morphology

  • @ref: 23006
  • colony size: 1.5-1.8 mm
  • colony color: orange
  • colony shape: circular
  • incubation period: 2 days

pigmentation

  • @ref: 23006
  • production: yes
  • color: orange

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6412CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53; with strain-specific modifications) Composition: MgCl2 100.0 g/l Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
6412ISP 5 MEDIUM (DSMZ Medium 993)yeshttps://mediadive.dsmz.de/medium/993Name: ISP 5 MEDIUM (DSMZ Medium 993) Composition: Agar 20.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l L-Asparagine 1.0 g/l FeSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6412positivegrowth28mesophilic
23006positiveoptimum28.0mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
23006positiveoptimum7.0-7.5
23006positivegrowth6.5-9.0alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23006aerobe
67771aerobe

spore formation

@refspore formationconfidence
23006no
67771no
69481no96
69480no96.804

halophily

@refsaltgrowthtested relationconcentration
23006NaClpositivegrowth0.0-25.0 %
23006KClpositivegrowth0.0-25.0 %
23006NaCloptimum10.0 %(w/v)
23006KCloptimum10.0 %(w/v)

observation

  • @ref: 67771
  • observation: quinones: MK-7 and MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2300615963ribitol-carbon source
2300622599arabinose-carbon source
2300622605arabinitol-carbon source
2300617268myo-inositol-carbon source
2300626546rhamnose-carbon source
2300630911sorbitol-carbon source
2300628017starch-degradation
2300653424tween 20-degradation
2300653426tween 80-degradation
2300617234glucose-fermentation
2300662968cellulose-growth
23006casein-hydrolysis
230065291gelatin-hydrolysis
2300628017starch-hydrolysis
230064853esculin+builds acid from
2300617234glucose+builds acid from
2300629864mannitol+builds acid from
2300627856acetamide+carbon source
2300617057cellobiose+carbon source
2300623652dextrin+carbon source
2300628757fructose+carbon source
2300628260galactose+carbon source
2300617234glucose+carbon source
2300617306maltose+carbon source
2300629864mannitol+carbon source
2300637684mannose+carbon source
2300617814salicin+carbon source
2300618222xylose+carbon source
2300617632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
2300689634melaninno
2300616136hydrogen sulfideno
2300628938ammoniumno
2300615688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2300615688acetoin-
2300617234glucose-

enzymes

@refvalueactivityec
23006alpha-galactosidase-3.2.1.22
23006arginine dihydrolase-3.5.3.6
23006beta-galactosidase+3.2.1.23
23006beta-glucosidase+3.2.1.21
23006catalase+1.11.1.6
23006cytochrome oxidase-1.9.3.1
23006L-aspartate arylamidase-3.4.11.21
23006lipase+
23006lysine decarboxylase-4.1.1.18
23006ornithine decarboxylase-4.1.1.17

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
23006hypersaline soil sampleQinghaiChinaCHNAsiaModified medium SGcontaining (g l-1): Casamino acids (7.5), yeast extract (10.0),trisodium citrate (3.0), NaCl (2.0), KCl (2.0), MgCl2.6H2O (250), MgSO4.7H2O (1.0), FeSO4.7H2O (0.05), MnSO4.7H2O (0.0002)14 days28.0
6412soilQinghai ProvinceChinaCHNAsia
67771From saline soilQinghaiChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_6855.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_605;96_3225;97_3957;98_5046;99_6855&stattab=map
  • Last taxonomy: Marinococcus
  • 16S sequence: AB769482
  • Sequence Identity:
  • Total samples: 2817
  • soil counts: 176
  • aquatic counts: 1141
  • animal counts: 1431
  • plant counts: 69

Safety information

risk assessment

  • @ref: 6412
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Marinococcus halotolerans gene for 16S ribosomal RNA, partial sequence, strain: KCTC 19045AB7694821491ena301092
6412Marinococcus halotolerans strain YIM 70157 16S ribosomal RNA gene, partial sequenceAY8174931454ena301092

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinococcus halotolerans DSM 16375GCA_000420725contigncbi1122203
66792Marinococcus halotolerans DSM 163751122203.4wgspatric1122203
66792Marinococcus halotolerans DSM 163752524614596draftimg1122203

GC content

@refGC-contentmethod
641248.5
2300648.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileyes86.061no
flagellatedyes69.287yes
gram-positiveyes91.345yes
anaerobicno99.481yes
aerobicyes95.766yes
halophileyes96.204no
spore-formingno83.76yes
thermophileno97.363yes
glucose-utilyes91.081no
glucose-fermentno80.976no

External links

@ref: 6412

culture collection no.: DSM 16375, CIP 108945, KCTC 19045, YIM 70157, NBRC 106070

straininfo link

  • @ref: 71021
  • straininfo: 133633

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166669Marinococcus halotolerans sp. nov., isolated from Qinghai, north-west China.Li WJ, Schumann P, Zhang YQ, Chen GZ, Tian XP, Xu LH, Stackebrandt E, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63596-02005Bacterial Typing Techniques, China, DNA, Bacterial/analysis, Genes, rRNA, Gram-Positive Bacteria/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, *Sodium Chloride, *Soil MicrobiologyGenetics
Phylogeny19628611Marinococcus luteus sp. nov., a halotolerant bacterium isolated from a salt lake, and emended description of the genus Marinococcus.Wang Y, Cao LL, Tang SK, Lou K, Mao PH, Jin X, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.009670-02009Bacillaceae/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Salt Tolerance, Sodium Chloride/metabolism, *Water MicrobiologyGenetics
Phylogeny23504966Marinococcus tarijensis sp. nov., a moderately halophilic bacterium isolated from a salt mine.Balderrama-Subieta A, Guzman D, Minegishi H, Echigo A, Shimane Y, Hatada Y, Quillaguaman JInt J Syst Evol Microbiol10.1099/ijs.0.045401-02013Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Bolivia, DNA, Bacterial/genetics, Fatty Acids/analysis, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27349661Marinococcus salis sp., nov., a moderately halophilic bacterium isolated from a salt marsh.Vishnuvardhan Reddy S, Thirumala M, Farooq M, Sasikala C, Venkata Ramana CArch Microbiol10.1007/s00203-016-1263-z2016Bacillaceae/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, India, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/analysis, WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6412Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16375)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16375
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
23006Wen-Jun Li,Peter Schumann,Yu-Qin Zhang,Guo-Zhong Chen,Xin-Peng Tian,Li-Hua Xu,Erko Stackebrandt,Cheng-Lin Jiang10.1099/ijs.0.63596-0Marinococcus halotolerans sp. nov., isolated from Qinghai, north-west ChinaIJSEM 55: 1801-1804 200516166669
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
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
71021Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID133633.1StrainInfo: A central database for resolving microbial strain identifiers