Strain identifier

BacDive ID: 528

Type strain: Yes

Species: Fulvimarina pelagi

Strain history: CIP <- 2004, KCTC <- J. C. Cho and S. J. Giovannoni

NCBI tax ID(s): 217511 (species)

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General

@ref: 5971

BacDive-ID: 528

DSM-Number: 15513

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

description: Fulvimarina pelagi DSM 15513 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from sea water.

NCBI tax id

  • NCBI tax id: 217511
  • Matching level: species

strain history

@refhistory
5971<- J.-C. Cho and S. J. Giovannoni; HTCC 2506
121649CIP <- 2004, KCTC <- J. C. Cho and S. J. Giovannoni

doi: 10.13145/bacdive528.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Aurantimonadaceae
  • genus: Fulvimarina
  • species: Fulvimarina pelagi
  • full scientific name: Fulvimarina pelagi Cho and Giovannoni 2003

@ref: 5971

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Aurantimonadaceae

genus: Fulvimarina

species: Fulvimarina pelagi

full scientific name: Fulvimarina pelagi Cho and Giovannoni 2003 emend. Rathsack et al. 2011

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
23132negative0.7-1.4 µm0.4-1.0 µmrod-shapedno
69480negative99.988
121649negativerod-shapedyes

colony morphology

  • @ref: 23132
  • colony size: 0.8-1.8 mm
  • colony color: brownish-yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: marine agar 2216

pigmentation

  • @ref: 23132
  • production: yes
  • color: carotenoid pigments

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5971BACTO 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
23132Bacto marine agar 2216yes
38273Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121649CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5971positivegrowth28mesophilic
23132positivemaximum40thermophilic
23132positiveminimum4psychrophilic
23132positiveoptimum30mesophilic
38273positivegrowth30mesophilic
59721positivegrowth30mesophilic
121649positivegrowth25-37mesophilic
121649nogrowth10psychrophilic
121649nogrowth41thermophilic
121649nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
23132positiveminimum5.5
23132positivemaximum10.0alkaliphile
23132positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23132aerobe
59721aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
23132NaClpositivegrowth0-10 %(w/v)
23132NaClpositiveoptimum2.0 %(w/v)
121649NaClpositivegrowth2-10 %
121649NaClnogrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2313217234glucose-builds acid from
2313236218beta lactose-carbon source
2313216947citrate-carbon source
2313215570D-alanine-carbon source
2313217315D-glucosamine-carbon source
2313217378D-glyceraldehyde-carbon source
231326731melezitose-carbon source
2313217924D-sorbitol-carbon source
2313215428glycine-carbon source
2313217240itaconate-carbon source
2313225115malate-carbon source
2313230860methylmalonic acid-carbon source
2313217268myo-inositol-carbon source
2313227897tryptophan-energy source
231324853esculin-hydrolysis
231325291gelatin-hydrolysis
2313217108D-arabinose+carbon source
2313215824D-fructose+carbon source
2313212936D-galactose+carbon source
2313217634D-glucose+carbon source
2313216899D-mannitol+carbon source
2313216024D-mannose+carbon source
2313228053melibiose+carbon source
2313216988D-ribose+carbon source
2313215740formate+carbon source
2313217754glycerol+carbon source
2313216467L-arginine+carbon source
2313229985L-glutamate+carbon source
2313217191L-isoleucine+carbon source
2313218019L-lysine+carbon source
2313217203L-proline+carbon source
2313217115L-serine+carbon source
2313215361pyruvate+carbon source
23132167632-oxobutanoate+oxidation
23132370543-hydroxybutyrate+oxidation
2313230089acetate+oxidation
2313215963ribitol+oxidation
2313240585alpha-cyclodextrin+oxidation
2313217925alpha-D-glucose+oxidation
2313217057cellobiose+oxidation
2313215824D-fructose+oxidation
2313212936D-galactose+oxidation
2313216899D-mannitol+oxidation
2313216024D-mannose+oxidation
2313228053melibiose+oxidation
2313216634raffinose+oxidation
2313217924D-sorbitol+oxidation
2313223652dextrin+oxidation
2313215740formate+oxidation
2313228066gentiobiose+oxidation
2313232323glucuronamide+oxidation
2313217859glutaric acid+oxidation
2313217754glycerol+oxidation
2313228087glycogen+oxidation
2313221217L-alaninamide+oxidation
2313230849L-arabinose+oxidation
2313218403L-arabitol+oxidation
2313229985L-glutamate+oxidation
2313215603L-leucine+oxidation
2313217203L-proline+oxidation
2313217115L-serine+oxidation
2313224996lactate+oxidation
2313217306maltose+oxidation
23132320055methyl beta-D-glucopyranoside+oxidation
2313275146monomethyl succinate+oxidation
2313273784glycyl-l-glutamate+oxidation
2313217272propionate+oxidation
2313215361pyruvate+oxidation
2313217992sucrose+oxidation
2313217748thymidine+oxidation
2313253423tween 40+oxidation
2313216704uridine+oxidation
2313217151xylitol+oxidation
12164916947citrate-carbon source
1216494853esculin-hydrolysis
121649606565hippurate-hydrolysis
12164917632nitrate-reduction
12164916301nitrite-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
2313228971ampicillinyesyes
231323393carbenicillinyesyes
2313223456cyclodextrinyesyes
231326104kanamycinyesyes
23132100147nalidixic acidyesyes
2313217833gentamicinyesno
2313217698chloramphenicolyesyes
2313248923erythromycinyesyes
2313218208penicillin gyesyes
2313217939puromycinyesyes
2313228077rifampicinyesyes
2313217076streptomycinyesyes
2313227902tetracyclineyesyes
2313228001vancomycinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2313235581indoleno
12164935581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
2313235581indole-
12164915688acetoin-
12164917234glucose-

enzymes

@refvalueactivityec
23132catalase+1.11.1.6
23132cytochrome oxidase+1.9.3.1
23132tryptophan deaminase-4.1.99.1
23132urease+3.5.1.5
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
121649oxidase+
121649beta-galactosidase-3.2.1.23
121649alcohol dehydrogenase-1.1.1.1
121649gelatinase-
121649amylase+
121649caseinase-3.4.21.50
121649catalase+1.11.1.6
121649tween esterase-
121649gamma-glutamyltransferase+2.3.2.2
121649lecithinase-
121649lipase-
121649lysine decarboxylase-4.1.1.18
121649ornithine decarboxylase-4.1.1.17
121649phenylalanine ammonia-lyase-4.3.1.24
121649protease-
121649tryptophan deaminase-
121649urease+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
121649-+++-+-----+---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationsampling datecountry
5971sea waterSargasso Sea, Bermuda Atlantic Time Series
23132a depth of 10 m at the Bermuda Atlantic Time Series (BATS) stationAtlantic Ocean, western Sargasso SeaAugust 2001
59721Sea waterSargasso Sea
121649Environment, Sea waterSargasso SeaAtlantic Ocean

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5011.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2451;97_2991;98_3747;99_5011&stattab=map
  • Last taxonomy: Fulvimarina pelagi subclade
  • 16S sequence: AY178860
  • Sequence Identity:
  • Total samples: 2106
  • soil counts: 344
  • aquatic counts: 1335
  • animal counts: 274
  • plant counts: 153

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59711Risk group (German classification)
1216491Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5971
  • description: Fulvimarina pelagi strain HTCC2506 16S ribosomal RNA gene, partial sequence
  • accession: AY178860
  • length: 1442
  • database: ena
  • NCBI tax ID: 314231

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fulvimarina pelagi DSM 15513GCA_001463845contigncbi217511
66792Fulvimarina pelagi strain DSM 15513217511.4wgspatric217511
66792Fulvimarina pelagi DSM 155132657245493draftimg217511

GC content

@refGC-contentmethod
597158-60
2313247.6-59.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes69.255yes
gram-positiveno98.144no
anaerobicno98.027no
aerobicyes94.165yes
halophileyes52.858no
spore-formingno96.704no
glucose-utilyes91.785no
flagellatedno82.835yes
thermophileno96.774no
glucose-fermentno90.955no

External links

@ref: 5971

culture collection no.: DSM 15513, ATCC BAA 666, KCTC 12091, CCUG 52903, CIP 108376, HTCC 2506

straininfo link

  • @ref: 70206
  • straininfo: 107091

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny14657114Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order "Rhizobiales".Cho JC, Giovannoni SJInt J Syst Evol Microbiol10.1099/ijs.0.02644-02003Microbial Sensitivity Tests, Molecular Sequence Data, *Phylogeny, Rhizobiaceae/*classification/*genetics/isolation & purification/ultrastructure, Seawater/*microbiology, Species SpecificityGenetics
Genetics20639329Genome sequence of Fulvimarina pelagi HTCC2506T, a Mn(II)-oxidizing alphaproteobacterium possessing an aerobic anoxygenic photosynthetic gene cluster and Xanthorhodopsin.Kang I, Oh HM, Lim SI, Ferriera S, Giovannoni SJ, Cho JCJ Bacteriol10.1128/JB.00761-102010Aerobiosis, Alphaproteobacteria/*genetics/*metabolism, Bacterial Proteins/*genetics, Genome, Bacterial/*genetics, Manganese/*metabolism, Molecular Sequence Data, Multigene Family/*genetics, Oxidation-Reduction, Photosynthesis/genetics, Rhodopsins, Microbial/*geneticsMetabolism
Enzymology25884328Characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway.Pick A, Schmid J, Sieber VMicrob Biotechnol10.1111/1751-7915.122652015Aldehyde Oxidoreductases/chemistry/*genetics/*metabolism, Alphaproteobacteria/*enzymology/genetics, Buffers, DNA, Bacterial/chemistry/genetics, Enzyme Stability, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Pseudomonas syringae/enzymology/genetics, Sequence Analysis, DNA, Streptomyces/*enzymology/genetics, Substrate Specificity, TemperatureGenetics
Phylogeny31187415Fulvimarina endophytica sp. nov., a novel endophytic bacterium isolated from bark of Sonneratia caseolaris.Tuo L, Yan XRJ Microbiol10.1007/s12275-019-8627-42019Alphaproteobacteria/*classification/genetics/growth & development/isolation & purification, Bacterial Typing Techniques/methods, Base Composition, China, DNA, Bacterial/genetics, Endophytes/*classification/genetics/growth & development/isolation & purification, Lythraceae/*microbiology, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Whole Genome Sequencing/methodsEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5971Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15513)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15513
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
23132Jang-Cheon Cho, Stephen J. Giovannoni10.1099/ijs.0.02644-0Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order 'Rhizobiales'IJSEM 53: 1853-1859 200314657114
38273Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5991
59721Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52903)https://www.ccug.se/strain?id=52903
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)
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
70206Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID107091.1StrainInfo: A central database for resolving microbial strain identifiers
121649Curators of the CIPCollection of Institut Pasteur (CIP 108376)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108376