Strain identifier

BacDive ID: 5484

Type strain: Yes

Species: Arenibacter certesii

Strain history: CIP <- 2004, CCUG <- 2003, KMM

NCBI tax ID(s): 1121011 (strain), 228955 (species)

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General

@ref: 8341

BacDive-ID: 5484

DSM-Number: 19833

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

description: Arenibacter certesii DSM 19833 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from green alga Ulva fenestrata.

NCBI tax id

NCBI tax idMatching level
228955species
1121011strain

strain history

@refhistory
8341<- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 3941
67770KMM 3941 <-- O. I. Nedashkovskaya.
67771<- SB Kim <- OI Nedashkovskaya, KMM, Russia
118218CIP <- 2004, CCUG <- 2003, KMM

doi: 10.13145/bacdive5484.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Arenibacter
  • species: Arenibacter certesii
  • full scientific name: Arenibacter certesii Nedashkovskaya et al. 2004

@ref: 8341

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Arenibacter

species: Arenibacter certesii

full scientific name: Arenibacter certesii Nedashkovskaya et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30041negative4 µm0.55 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.95
118218negativerod-shapedno

colony morphology

@refincubation period
579472 days
118218

pigmentation

@refproductionname
30041yes
118218noFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8341BACTO 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
33969Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118218CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8341positivegrowth28mesophilic
30041positivegrowth4.0-38
30041positiveoptimum16psychrophilic
33969positivegrowth30mesophilic
57947positivegrowth30mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic
118218positivegrowth5-37
118218nogrowth41thermophilic
118218nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30041aerobe
57947aerobe
67771aerobe
118218obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
30041NaClpositivegrowth1.0-10 %
30041NaClpositiveoptimum5.5 %
118218NaClpositivegrowth2-10 %
118218NaClnogrowth0 %

observation

@refobservation
67770quinones: MK-6
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3004122599arabinose+carbon source
3004117057cellobiose+carbon source
3004133984fucose+carbon source
3004128260galactose+carbon source
3004117234glucose+carbon source
3004117716lactose+carbon source
3004117306maltose+carbon source
3004137684mannose+carbon source
3004128053melibiose+carbon source
30041506227N-acetylglucosamine+carbon source
3004116634raffinose+carbon source
3004117992sucrose+carbon source
3004117632nitrate+reduction
1182184853esculin+hydrolysis
118218606565hippurate-hydrolysis
11821817632nitrate+reduction
11821816301nitrite-reduction
11821815792malonate-assimilation
11821817632nitrate-respiration

metabolite production

  • @ref: 118218
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11821815688acetoin-
11821817234glucose-

enzymes

@refvalueactivityec
30041alkaline phosphatase+3.1.3.1
30041catalase+1.11.1.6
30041cytochrome oxidase+1.9.3.1
30041urease+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
118218oxidase+
118218beta-galactosidase+3.2.1.23
118218alcohol dehydrogenase-1.1.1.1
118218gelatinase+/-
118218amylase+
118218DNase-
118218caseinase-3.4.21.50
118218catalase+1.11.1.6
118218tween esterase-
118218gamma-glutamyltransferase+2.3.2.2
118218lecithinase-
118218lipase-
118218lysine decarboxylase-4.1.1.18
118218ornithine decarboxylase-4.1.1.17
118218phenylalanine ammonia-lyase-4.3.1.24
118218tryptophan deaminase-
118218urease+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
118218-+++-++++-+++--++++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118218++-++-+++++++++++++---+--------+--++-----+-----------------+---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcontinentsampling datecountryorigin.countryisolation date
8341green alga Ulva fenestrataUlva fenestrataSea of Japan, Gulf of Peter the Great, Troitsa BayAsia
57947Green alga,Ulva fenestrataTroitsa Bay,Gulf of P GreatAsia2000-06-01Sea of Japan
67770Green alga, Ulva fenestrataUlva fenestrataTroitsa Bay, Gulf of Peter the Great
67771From green alga, `Ulva fenestrata`Sea of JapanInternational waters
118218Green alga, Ulva fenestrataAsiaJapanJPN2000

isolation source categories

  • Cat1: #Host
  • Cat2: #Algae
  • Cat3: #Green algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_161296.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_102;96_8695;97_10454;98_12812;99_161296&stattab=map
  • Last taxonomy: Arenibacter certesii
  • 16S sequence: AY271622
  • Sequence Identity:
  • Total samples: 162
  • soil counts: 2
  • aquatic counts: 152
  • animal counts: 8

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
83411Risk group (German classification)
1182181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8341
  • description: Arenibacter sp. KMM 3941 16S ribosomal RNA gene, partial sequence
  • accession: AY271622
  • length: 1438
  • database: ena
  • NCBI tax ID: 228955

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenibacter certesii KCTC 12113GCA_014651295scaffoldncbi228955
66792Arenibacter certesii DSM 198331121011.3wgspatric1121011
66792Arenibacter certesii strain KCTC 12113228955.3wgspatric228955
66792Arenibacter certesii DSM 198332523231023draftimg1121011
67770Arenibacter certesii DSM 19833GCA_000429545scaffoldncbi1121011

GC content

@refGC-contentmethod
834137.7
6777037.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.422yes
flagellatedno95.819yes
gram-positiveno97.371no
anaerobicno99.541yes
aerobicyes91.405yes
halophileno54.095yes
spore-formingno95.428no
thermophileno98.832yes
glucose-utilyes92.16no
glucose-fermentno89.302no

External links

@ref: 8341

culture collection no.: DSM 19833, CCUG 48006, JCM 13507, KCTC 12113, KMM 3941, CIP 108496, NCIMB 14240

straininfo link

  • @ref: 74971
  • straininfo: 99602

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280287Arenibacter certesii sp. nov., a novel marine bacterium isolated from the green alga Ulva fenestrata.Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Mikhailov VV, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.02872-02004Aerobiosis, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Flavobacteriaceae/*classification/cytology/*isolation & purification/physiology, Genes, rRNA, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Pacific Ocean, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Ulva/*microbiology, Water MicrobiologyEnzymology
Genetics16168974Structural characterization of the carbohydrate backbone of the lipooligosaccharide of the marine bacterium Arenibacter certesii strain KMM 3941(T).Silipo A, Molinaro A, Nazarenko EL, Sturiale L, Garozzo D, Gorshkova RP, Nedashkovskaya OI, Lanzetta R, Parrilli MCarbohydr Res10.1016/j.carres.2005.08.0212005Carbohydrate Conformation, Carbohydrate Sequence, Flavobacteriaceae/*chemistry/growth & development, Lipopolysaccharides/*chemistry, Magnetic Resonance Spectroscopy, Marine Biology, Molecular Sequence Data, Molecular Structure, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Phylogeny28945544Arenibacter antarcticus sp. nov., isolated from marine sediment.Li AZ, Lin LZ, Zhang MX, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0023402017Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Phospholipids/analysis, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32955652Arenibacter lacus sp. nov., Isolated from Chilika Lagoon, India.Kumar D, Smita N, Kumar G, Suresh G, Jagadeeshwari U, Sasikala C, Ramana CVCurr Microbiol10.1007/s00284-020-02205-x2020Bacterial Typing Techniques, DNA, Bacterial/genetics, *Ecosystem, Fatty Acids/analysis, Flavobacteriaceae, India, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Vitamin K 2Transcriptome
Phylogeny33502300Arenibacter amylolyticus sp. nov., an amylase-producing bacterium of the family Flavobacteriaceae isolated from marine water in India.Sidhu C, Saini MK, Srinivas Tanuku NR, Pinnaka AKInt J Syst Evol Microbiol10.1099/ijsem.0.0046642021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8341Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19833)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19833
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
30041Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2640228776041
33969Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6124
57947Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48006)https://www.ccug.se/strain?id=48006
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
74971Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99602.1StrainInfo: A central database for resolving microbial strain identifiers
118218Curators of the CIPCollection of Institut Pasteur (CIP 108496)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108496