Strain identifier

BacDive ID: 6283

Type strain: Yes

Species: Serinicoccus marinus

Strain Designation: JC1078

Strain history: CIP <- 2004, KCTC <- J Chun, Seoul Nat. Univ.

NCBI tax ID(s): 1123251 (strain), 247333 (species)

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General

@ref: 5789

BacDive-ID: 6283

DSM-Number: 15273

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive, coccus-shaped

description: Serinicoccus marinus JC1078 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from sea water.

NCBI tax id

NCBI tax idMatching level
1123251strain
247333species

strain history

@refhistory
5789<- J. Chun; JC1078
360522004, KCTC
67770KCTC 9980 <-- J. Chun JC1078.
67771<- J Chun, Seoul Nat. Univ.
120820CIP <- 2004, KCTC <- J Chun, Seoul Nat. Univ.

doi: 10.13145/bacdive6283.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Ornithinimicrobiaceae
  • genus: Serinicoccus
  • species: Serinicoccus marinus
  • full scientific name: Serinicoccus marinus Yi et al. 2004

@ref: 5789

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Ornithinimicrobiaceae

genus: Serinicoccus

species: Serinicoccus marinus

full scientific name: Serinicoccus marinus Yi et al. 2004

strain designation: JC1078

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
30182positive0.7 µmcoccus-shapedno
67771positive
69480no93.092
69480positive100
120820positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18522Corn yellow (1006)10-14 daysISP 2
18522Corn yellow (1006)10-14 daysISP 3
18522Corn yellow (1006)10-14 daysISP 4
18522Corn yellow (1006)10-14 daysISP 5
18522Corn yellow (1006)10-14 daysISP 6
18522Corn yellow (1006)10-14 daysISP 7
593822 days
120820

multicellular morphology

@refforms multicellular complexmedium name
18522noISP 2
18522noISP 3
18522noISP 4
18522noISP 5
18522noISP 6
18522noISP 7

pigmentation

  • @ref: 30182
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15273_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15273_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15273_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15273_4.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5789BACTO 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
18522ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18522ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18522ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18522ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18522ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18522ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
36052Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120820CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
18522positiveoptimum22psychrophilic
5789positivegrowth30mesophilic
30182positivegrowth10-35
30182positiveoptimum35mesophilic
36052positivegrowth30mesophilic
59382positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
120820positivegrowth25-30mesophilic
120820nogrowth10psychrophilic
120820nogrowth15psychrophilic
120820nogrowth37mesophilic
120820nogrowth41thermophilic
120820nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
30182positivegrowth06-11alkaliphile
30182positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30182aerobe
59382aerobe
67771aerobe
120820obligate aerobe

spore formation

@refspore formationconfidence
30182no
69481no100
69480no99.987

halophily

@refsaltgrowthtested relationconcentration
30182NaClpositivegrowth0-14 %
30182NaClpositiveoptimum2.5 %
120820NaClpositivegrowth2-10 %
120820NaClnogrowth0 %

observation

@refobservation
67770quinones: MK-8(H4)
67771quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1852262968cellulose+
1852216634raffinose+
1852226546rhamnose-
1852228757fructose+
1852229864mannitol+
1852217268myo-inositol-
1852218222xylose-
1852217992sucrose+
1852222599arabinose-
1852217234glucose+
3018230089acetate+carbon source
3018217057cellobiose+carbon source
3018228757fructose+carbon source
3018228260galactose+carbon source
301825291gelatin+carbon source
3018217234glucose+carbon source
3018217754glycerol+carbon source
3018229864mannitol+carbon source
3018237684mannose+carbon source
3018230911sorbitol+carbon source
3018217992sucrose+carbon source
3018227082trehalose+carbon source
3018253426tween 80+carbon source
301824853esculin+hydrolysis
3018217632nitrate+reduction
12082016947citrate-carbon source
1208204853esculin-hydrolysis
120820606565hippurate+hydrolysis
12082017632nitrate-reduction
12082016301nitrite-reduction
12082017632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose-fermentation

metabolite production

  • @ref: 120820
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12082015688acetoin-
12082017234glucose-

enzymes

@refvalueactivityec
30182catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
120820oxidase-
120820beta-galactosidase+3.2.1.23
120820alcohol dehydrogenase-1.1.1.1
120820gelatinase+/-
120820amylase-
120820DNase-
120820caseinase-3.4.21.50
120820catalase+1.11.1.6
120820tween esterase-
120820gamma-glutamyltransferase+2.3.2.2
120820lecithinase-
120820lipase-
120820lysine decarboxylase-4.1.1.18
120820ornithine decarboxylase-4.1.1.17
120820phenylalanine ammonia-lyase-4.3.1.24
120820protease+
120820tryptophan deaminase-
120820urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18522-+---+-+-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18522-+--++-+---+--+----
120820-++-++---+----+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5789sea waterEast SeaRepublic of KoreaKORAsia
59382SeawaterRepublic of KoreaKORAsia
67770SeawaterRepublic of KoreaKORAsia
67771From a sea-water-sample from the East SeaRepublic of KoreaKORAsia
120820Environment, Sea water sampleEast seaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_4740.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2346;97_2856;98_3553;99_4740&stattab=map
  • Last taxonomy: Serinicoccus
  • 16S sequence: AY382898
  • Sequence Identity:
  • Total samples: 2890
  • soil counts: 156
  • aquatic counts: 431
  • animal counts: 2265
  • plant counts: 38

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185221Risk group (German classification)
57891Risk group (German classification)
1208201Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5789
  • description: Serinicoccus marinus strain JC1078 16S ribosomal RNA gene, partial sequence
  • accession: AY382898
  • length: 1408
  • database: ena
  • NCBI tax ID: 247333

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Serinicoccus marinus DSM 15273GCA_008386315completencbi1123251
66792Serinicoccus marinus DSM 152731123251.10completepatric1123251
66792Serinicoccus marinus DSM 152731123251.3wgspatric1123251
66792Serinicoccus marinus DSM 152732524614805draftimg1123251
67770Serinicoccus marinus DSM 15273GCA_000421245contigncbi1123251

GC content

@refGC-contentmethod
3018272
6777072high performance liquid chromatography (HPLC)
6777171.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.95no
flagellatedno98.529yes
gram-positiveyes90.233no
anaerobicno99no
aerobicyes93.987no
halophileno74.456no
spore-formingno90.621yes
glucose-utilyes90.904no
thermophileno96.101yes
glucose-fermentno87.2no

External links

@ref: 5789

culture collection no.: DSM 15273, IMSNU 14026, KCTC 9980, CCUG 51944, JCM 13024, CIP 108477

straininfo link

  • @ref: 75759
  • straininfo: 134308

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388714Serinicoccus marinus gen. nov., sp. nov., a novel actinomycete with L-ornithine and L-serine in the peptidoglycan.Yi H, Schumann P, Sohn K, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.03036-02004Actinomycetales/*classification/cytology/*isolation & purification/physiology, Aerobiosis, Anti-Bacterial Agents/pharmacology, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Glycerophospholipids/analysis, Korea, Molecular Sequence Data, Movement, Ornithine/*analysis, Peptidoglycan/*chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic/pharmacology, Seawater/*microbiology, Sequence Analysis, DNA, Serine/*analysis, Spores, Bacterial, Vitamin K 2/analysis, Water MicrobiologyEnzymology
Phylogeny20118285Serinicoccus profundi sp. nov., an actinomycete isolated from deep-sea sediment, and emended description of the genus Serinicoccus.Xiao J, Luo Y, Xie S, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.019976-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny20639223Serinicoccus chungangensis sp. nov., isolated from tidal flat sediment, and emended description of the genus Serinicoccus.Traiwan J, Park MH, Kim WInt J Syst Evol Microbiol10.1099/ijs.0.025635-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics
Phylogeny31050624Serinicoccus sediminis sp. nov., isolated from tidal flat sediment.Lee DW, Yoo Y, Lee H, Kwon BO, Khim JS, Yim UH, Kim BS, Kim GH, Kim JJInt J Syst Evol Microbiol10.1099/ijsem.0.0034152019Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32375934Serinicoccus hydrothermalis sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island.Zhang Q, Ye J, Yu L, Lin D, Tang KInt J Syst Evol Microbiol10.1099/ijsem.0.0041452020Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Hydrothermal Vents/*microbiology, Islands, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
5789Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15273)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15273
18522Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15273.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
30182Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2653028776041
36052Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6220
59382Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51944)https://www.ccug.se/strain?id=51944
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 life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
75759Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134308.1StrainInfo: A central database for resolving microbial strain identifiers
120820Curators of the CIPCollection of Institut Pasteur (CIP 108477)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108477