Strain identifier

BacDive ID: 437

Type strain: Yes

Species: Aestuariibacter halophilus

Strain Designation: JC2043

Strain history: CIP <- 2004, DSMZ <- J. Chun: strain JC2043

NCBI tax ID(s): 226011 (species)

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General

@ref: 5783

BacDive-ID: 437

DSM-Number: 15266

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, halophilic, chemoheterotroph, thermophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Aestuariibacter halophilus JC2043 is an obligate aerobe, halophilic, chemoheterotroph bacterium that forms circular colonies and was isolated from sediment sample of getbol.

NCBI tax id

  • NCBI tax id: 226011
  • Matching level: species

strain history

@refhistory
5783<- J. Chun; JC2043
67771<- J Chon, Seoul Nat. Univ.
119811CIP <- 2004, DSMZ <- J. Chun: strain JC2043

doi: 10.13145/bacdive437.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Aestuariibacter
  • species: Aestuariibacter halophilus
  • full scientific name: Aestuariibacter halophilus Yi et al. 2004

@ref: 5783

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Aestuariibacter

species: Aestuariibacter halophilus

full scientific name: Aestuariibacter halophilus Yi et al. 2004

strain designation: JC2043

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23286negative1.2-1.8 µm0.5-0.6 µmrod-shapedyesmonotrichous, polar
67771negative
69480yes97.525
69480negative99.992
119811negativerod-shapedyes

colony morphology

  • @ref: 23286
  • colony color: white, opaque
  • colony shape: circular
  • incubation period: 2 days
  • medium used: MA

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5783BACTO 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
23286CSY-3yes
23286Marine agar (MA)yes
23286SMMyes
33964Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119811CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5783positivegrowth40thermophilic
23286positivegrowth15-40
23286positiveoptimum40thermophilic
23286thermophilic
33964positivegrowth30mesophilic
67771positivegrowth40thermophilic
119811positivegrowth25-37mesophilic
119811nogrowth5psychrophilic
119811nogrowth10psychrophilic
119811nogrowth41thermophilic

culture pH

@refabilitytypepHPH range
23286positivegrowth6-11alkaliphile
23286positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23286obligate aerobe
67771aerobe

nutrition type

  • @ref: 23286
  • type: chemoheterotroph

spore formation

@refspore formationconfidence
23286no
69481no100
69480no99.979

halophily

@refhalophily levelsaltgrowthtested relationconcentration
23286halophilicNaClpositivegrowth1-8 %
23286NaClpositiveoptimum5-6 %
23286NaClpositivegrowth0 %
23286Sea Salts (S9883)positivegrowth0.5-11 %
23286Sea Salts (S9883)positiveoptimum2-3 %
119811NaClnogrowth0 %
119811NaClnogrowth2 %
119811NaClnogrowth4 %
119811NaClnogrowth6 %
119811NaClnogrowth8 %
119811NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2328627856acetamide-carbon source
2328616708adenine-carbon source
2328616150benzoate-carbon source
2328616947citrate-carbon source
2328617057cellobiose-carbon source
2328615824D-fructose-carbon source
2328612936D-galactose-carbon source
2328616024D-mannose-carbon source
2328616634raffinose-carbon source
2328665327D-xylose-carbon source
2328616236ethanol-carbon source
2328615428glycine-carbon source
2328617268myo-inositol-carbon source
2328615443inulin-carbon source
2328617561L-cysteine-carbon source
2328618019L-lysine-carbon source
2328615729L-ornithine-carbon source
2328662345L-rhamnose-carbon source
2328617716lactose-carbon source
23286178242-propanol-carbon source
2328617814salicin-carbon source
2328630762salicylate-carbon source
2328630911sorbitol-carbon source
2328630031succinate-carbon source
2328626948thiamine-carbon source
232862509agar-degradation
2328658187alginate-degradation
2328662968cellulose-degradation
2328617029chitin-degradation
2328630089acetate+carbon source
2328617634D-glucose+carbon source
2328616988D-ribose+carbon source
2328616467L-arginine+carbon source
23286506227N-acetylglucosamine+carbon source
2328617992sucrose+carbon source
23286casein+degradation
2328616991dna+degradation
23286egg yolk+degradation
232864853esculin+degradation
232865291gelatin+degradation
2328628017starch+degradation
2328653426tween 80+degradation
2328617632nitrate+reduction
1198114853esculin+hydrolysis
11981117632nitrate+reduction
11981116301nitrite-reduction
119811132112sodium thiosulfate-builds gas from

metabolite production

@refChebi-IDmetaboliteproduction
2328653388polyhydroxybutyrateno
2328635581indoleno
2328616136hydrogen sulfideno
2328631624fluoresceinno
11981135581indoleno

enzymes

@refvalueactivityec
23286acid phosphatase+3.1.3.2
23286alkaline phosphatase+3.1.3.1
23286alpha-chymotrypsin-3.4.21.1
23286alpha-fucosidase-3.2.1.51
23286alpha-galactosidase-3.2.1.22
23286alpha-glucosidase-3.2.1.20
23286alpha-mannosidase-3.2.1.24
23286arginine dihydrolase-3.5.3.6
23286beta-galactosidase-3.2.1.23
23286beta-glucosidase+3.2.1.21
23286beta-glucuronidase-3.2.1.31
23286catalase+1.11.1.6
23286cystine arylamidase-3.4.11.3
23286cytochrome oxidase+1.9.3.1
23286esterase (C 4)+
23286esterase lipase (C 8)+
23286leucine arylamidase+3.4.11.1
23286lipase (C 14)-
23286N-acetyl-beta-glucosaminidase-3.2.1.52
23286naphthol-AS-BI-phosphohydrolase+
23286trypsin+3.4.21.4
23286urease-3.5.1.5
23286valine arylamidase-
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
119811oxidase+
119811beta-galactosidase-3.2.1.23
119811alcohol dehydrogenase-1.1.1.1
119811gelatinase+
119811amylase+
119811DNase+
119811caseinase+3.4.21.50
119811catalase+1.11.1.6
119811tween esterase-
119811lecithinase-
119811lipase-
119811lysine decarboxylase-4.1.1.18
119811ornithine decarboxylase-4.1.1.17
119811protease-
119811tryptophan deaminase-
119811urease-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
119811-+++-++++-++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitudeisolation procedureisolation date
5783sediment sample of getbolKorea, Ganghwa islandRepublic of KoreaKORAsia
23286sediment sample of getbol, the Korean tidal flatGanghwa islandRepublic of KoreaKORAsiaAugust 200237.5922126.457diluted with sterilized artificial sea water
67771From a sediment sample of getbol, the Korean tidal flatRepublic of KoreaKORAsia
119811Environment, Sediment sample of getbol (korean tidal flat)Ganghwa IslandRepublic of KoreaKORAsia2002

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57831Risk group (German classification)
1198111Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5783
  • description: Aestuariibacter halophilus strain JC2043 16S ribosomal RNA gene, partial sequence
  • accession: AY207503
  • length: 1455
  • database: ena
  • NCBI tax ID: 226011

Genome sequences

  • @ref: 66792
  • description: Aestuariibacter halophilus JC2043
  • accession: GCA_020687825
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 226011

GC content

  • @ref: 23286
  • GC-content: 54.00
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes90.277yes
gram-positiveno99.107yes
anaerobicno96.94yes
aerobicyes83.827no
halophileyes59.849no
spore-formingno97.157no
motileyes90.545no
thermophileno99.517no
glucose-utilyes88.631no
glucose-fermentno77.69no

External links

@ref: 5783

culture collection no.: DSM 15266, KCTC 12043, IMSNU 14007, CIP 108412

straininfo link

  • @ref: 70116
  • straininfo: 131410

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15023977Aestuariibacter salexigens gen. nov., sp. nov. and Aestuariibacter halophilus sp. nov., isolated from tidal flat sediment, and emended description of Alteromonas macleodii.Yi H, Bae KS, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.02798-02004Acetylglucosamine/metabolism, Alteromonadaceae/*classification/genetics/isolation & purification/physiology, Alteromonas/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/chemistry/genetics, Geologic Sediments/*microbiology, Glucose/metabolism, Korea, Molecular Sequence Data, PhylogenyMetabolism
Phylogeny19651716Aestuariibacter litoralis sp. nov., isolated from a sandy sediment of the Sea of Japan.Tanaka N, Romanenko LA, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.012435-02009Alteromonadaceae/*classification/genetics/physiology, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, RNA, *Water MicrobiologyGenetics
Genetics34913711Draft Genome Sequence of Aestuariibacter halophilus Type Strain JC2043.Emsley SA, Pfannmuller KM, Ushijima B, Saw JH, Gaylor MO, Videau PMicrobiol Resour Announc10.1128/MRA.01093-212021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5783Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15266)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15266
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
23286Hana Yi, Kyung Sook Bae, Jongsik Chun10.1099/ijs.0.02798-0Aestuariibacter salexigens gen. nov., sp. nov. and Aestuariibacter halophilus sp. nov., isolated from tidal flat sediment, and emended description of Alteromonas macleodiiIJSEM 54: 571-576 200415023977
33964Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6032
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
68382Automatically annotated from API zym
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
70116Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131410.1StrainInfo: A central database for resolving microbial strain identifiers
119811Curators of the CIPCollection of Institut Pasteur (CIP 108412)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108412