Strain identifier

BacDive ID: 6002

Type strain: Yes

Species: Cobetia marina

Strain history: CIP <- 1996, NCIMB <- G.E. Jones, Arthrobacter marinus

NCBI tax ID(s): 28258 (species)

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

@ref: 1747

BacDive-ID: 6002

DSM-Number: 4741

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Cobetia marina DSM 4741 is an obligate aerobe, mesophilic, motile bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 28258
  • Matching level: species

strain history

@refhistory
1747<- ATCC <- A.B. Cobet <- G. Jones <- C. Wirsen
67770IAM 14107 <-- ATCC 25374 <-- A. B. Cobet ("Arthrobacter marinus") <-- G. Jones <-- C. Wirsen.
120797CIP <- 1996, NCIMB <- G.E. Jones, Arthrobacter marinus

doi: 10.13145/bacdive6002.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Cobetia
  • species: Cobetia marina
  • full scientific name: Cobetia marina (Cobet et al. 1970) Arahal et al. 2002
  • synonyms

    @refsynonym
    20215Pseudomonas marina
    20215Halomonas marina
    20215Arthrobacter marinus
    20215Halomonas halodurans
    20215Deleya marina

@ref: 1747

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Cobetia

species: Cobetia marina

full scientific name: Cobetia marina (Cobet et al. 1970) Arahal et al. 2002 emend. Romanenko et al. 2013

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes96.519
6948099.988negative
120797yesnegative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1747BACTO 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
39090Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120797CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
1747positivegrowth26mesophilic
39090positivegrowth25mesophilic
67770positivegrowth25mesophilic
120797positivegrowth5-41
120797nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120797
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
120797NaClpositivegrowth2-10 %
120797NaClnogrowth0 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120797esculin-hydrolysis4853
120797hippurate-hydrolysis606565
120797nitrate-reduction17632
120797nitrite-reduction16301
120797phenol-degradation15882
120797malonate+assimilation15792
120797nitrate-respiration17632

antibiotic resistance

  • @ref: 120797
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120797
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
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
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
120797oxidase-
120797beta-galactosidase-3.2.1.23
120797alcohol dehydrogenase-1.1.1.1
120797gelatinase-
120797DNase-
120797caseinase-3.4.21.50
120797catalase+1.11.1.6
120797gamma-glutamyltransferase+2.3.2.2
120797lecithinase-
120797lipase-
120797lysine decarboxylase-4.1.1.18
120797ornithine decarboxylase-4.1.1.17
120797protease-
120797tryptophan deaminase-
120797urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120797-+++-+----++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120797---------++++-+-----------+++----------+/---+/-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120797++++---+-++--------+------+----+++-+-------------+++-+------+----------+-+-++--++-------+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1747seawater
67770Littoral water sample at Woods HoleMAUSAUSANorth America
120797Environment, Littoral seawater sampleWoods Hole, MassachusettsUnited States of AmericaUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_895.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_532;97_613;98_707;99_895&stattab=map
  • Last taxonomy: Cobetia
  • 16S sequence: NR_042065
  • Sequence Identity:
  • Total samples: 19571
  • soil counts: 974
  • aquatic counts: 12909
  • animal counts: 5462
  • plant counts: 226

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17471Risk group (German classification)
1207971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Deleya marina (ATCC 25374) 16S ribosomal RNA (16S rRNA) geneM933541483ena28258
1747Halomonas marina partial 16S rRNA gene, strain DSM 4741AJ3068901536ena28258
1747Cobetia marina strain DSM 4741 16S ribosomal RNA, partial sequenceNR_0420651536nuccore28258
67770Cobetia marina gene for 16S rRNA, partial sequence, strain: NBRC 102605AB6818801466ena28258

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cobetia marina JCM 21022GCA_001720485completencbi28258
66792Cobetia marina strain JCM 2102228258.9completepatric28258
66792Cobetia sp. MM1IDA2H-1 strain MM1IDA2H-1AD1268241.8wgspatric1268241
66792Cobetia marina JCM 210222751185720completeimg28258

GC content

  • @ref: 67770
  • GC-content: 63.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes76.505no
gram-positiveno98.755no
anaerobicno98.908no
aerobicyes93.874no
halophileyes91.838no
spore-formingno97.022no
glucose-utilyes92.69no
thermophileno99.048yes
motileyes92.18no
glucose-fermentno76.069no

External links

@ref: 1747

culture collection no.: DSM 4741, ATCC 25374, JCM 21022, CCUG 49558, CECT 4278, CIP 104765, IAM 14107, LMG 2217, NBRC 102605, NCIMB 1877

straininfo link

  • @ref: 75491
  • straininfo: 2165

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phenotype1781675Comparison of the adhesion properties of Deleya marina and the exopolysaccharide-defective mutant strain DMR.Shea C, Nunley JW, Williamson JC, Smith-Somerville HEAppl Environ Microbiol10.1128/aem.57.11.3107-3113.19911991Bacteria/genetics/ultrastructure, *Bacterial Adhesion, *Bacterial Physiological Phenomena, Colony Count, Microbial, Microscopy, Electron, Scanning, *Mutation, Phenotype, Polysaccharides, Bacterial/genetics/*physiology/ultrastructure
Metabolism9271247N-acyl amino acid biosynthesis in marine bacterium, Deleya marina.Yagi H, Corzo G, Nakahara TBiochim Biophys Acta10.1016/s0304-4165(97)00009-31997Bacteria/*metabolism, Marine Biology, Ornithine/analogs & derivatives/*biosynthesis/chemistry, Protein Conformation, Seawater
Enzymology9714788Novel diglycosyldiacylglycerol from the gram-negative bacterium Deleya marina.Yagi H, Maruyama ABiochim Biophys Acta10.1016/s0005-2760(98)00070-81998Glycolipids/chemistry/*isolation & purification, Gram-Negative Bacteria/*metabolism, Magnetic Resonance Spectroscopy/methods, *Water MicrobiologyPhylogeny
Phylogeny12353874Proposal of Cobetia marina gen. nov., comb. nov., within the family Halomonadaceae, to include the species Halomonas marina.Arahal DR, Castillo AM, Ludwig W, Schleifer KH, Ventosa ASyst Appl Microbiol10.1078/0723-2020-001132002Base Sequence, Gammaproteobacteria/*classification, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Pathogenicity17453727Combinatorial materials research applied to the development of new surface coatings III. Utilisation of a high-throughput multiwell plate screening method to rapidly assess bacterial biofilm retention on antifouling surfaces.Stafslien S, Daniels J, Chisholm B, Christianson DBiofouling10.1080/089270106011273112007Bacteria/drug effects/*isolation & purification, Bacterial Adhesion, Biofilms/drug effects/*growth & development, Coated Materials, Biocompatible, Disinfectants/pharmacology, Marine Biology, Materials Testing/methods, Polymethyl Methacrylate, Ships, Water MicrobiologyEnzymology
Phylogeny19654339Cobetia crustatorum sp. nov., a novel slightly halophilic bacterium isolated from traditional fermented seafood in Korea.Kim MS, Roh SW, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.008847-02009Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, *Fermentation, Halomonadaceae/*classification/genetics/*isolation & purification/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sodium Chloride/*metabolismMetabolism
Phylogeny22427450Description of Cobetia amphilecti sp. nov., Cobetia litoralis sp. nov. and Cobetia pacifica sp. nov., classification of Halomonas halodurans as a later heterotypic synonym of Cobetia marina and emended descriptions of the genus Cobetia and Cobetia marina.Romanenko LA, Tanaka N, Svetashev VI, Falsen EInt J Syst Evol Microbiol10.1099/ijs.0.036863-02012Alaska, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Halomonadaceae/*classification/genetics/isolation & purification, Halomonas/classification/genetics/isolation & purification, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, *Water MicrobiologyEnzymology
24192832Inhibition of larval barnacle attachment to bacterial films: An investigation of physical properties.Maki JS, Rittschof D, Mitchell RMicrob Ecol10.1007/BF001659101992
Metabolism34930259High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741(T) and in silico analyses of the genus specific PhaC2 polymerase variant.Christensen M, Jablonski P, Altermark B, Irgum K, Hansen HMicrob Cell Fact10.1186/s12934-021-01713-02021Acetates/metabolism, Bacterial Proteins/metabolism, Halomonadaceae/*genetics/*metabolism, Metabolic Engineering/*methods, Phylogeny, Polyhydroxyalkanoates/analysis/*biosynthesisPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1747Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4741)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4741
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
39090Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16709
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
75491Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2165.1StrainInfo: A central database for resolving microbial strain identifiers
120797Curators of the CIPCollection of Institut Pasteur (CIP 104765)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104765