Strain identifier

BacDive ID: 7439

Type strain: Yes

Species: Microbacterium aquimaris

Strain Designation: JS54-2

Strain history: CIP <- 2013, DSMZ <- J.S. Lee, Korea: strain JS54-2

NCBI tax ID(s): 459816 (species)

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General

@ref: 8042

BacDive-ID: 7439

DSM-Number: 19713

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

description: Microbacterium aquimaris JS54-2 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 459816
  • Matching level: species

strain history

@refhistory
8042<- Jung-Sook Lee; JS54-2
67770KCTC 19124 <-- J.-S. Lee JS54-2.
67771<- JS Lee, KRIBB
116460CIP <- 2013, DSMZ <- J.S. Lee, Korea: strain JS54-2

doi: 10.13145/bacdive7439.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium aquimaris
  • full scientific name: Microbacterium aquimaris Kim et al. 2008

@ref: 8042

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium aquimaris

full scientific name: Microbacterium aquimaris Kim et al. 2008

strain designation: JS54-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32605positive1.25 µm0.7 µmrod-shapedno
67771positive
116460positiverod-shapedno
69480no95

colony morphology

@refcolony colorincubation periodmedium used
19786Rapeseed yellow (1021)10-14 daysISP 3
1978610-14 daysISP 4
1978610-14 daysISP 5
1978610-14 daysISP 6
1978610-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19786noISP 3
19786noISP 4
19786noISP 5
19786noISP 6
19786noISP 7

pigmentation

  • @ref: 32605
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8042R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
19786ISP 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:
19786ISP 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
19786ISP 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
19786ISP 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
19786ISP 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
33591MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
116460CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperature
8042positivegrowth28
19786positiveoptimum28
32605positivegrowth15-37
32605positiveoptimum27.5
33591positivegrowth30
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepHPH range
32605positivegrowth06-10alkaliphile
32605positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32605no
69481no94

halophily

  • @ref: 32605
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 10 %

murein

  • @ref: 8042
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32605581435-dehydro-D-gluconate+carbon source
326054853esculin+hydrolysis
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
32605catalase+1.11.1.6
32605cytochrome oxidase+1.9.3.1
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19786+++--++++--++/--+----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19786-++-++----++--+++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8042seawaterJejuRepublic of KoreaKORAsia
67770SeawaterJejuRepublic of KoreaKORAsia
67771From seawaterJejuRepublic of KoreaKORAsia
116460Environment, SeawaterJeju IslandRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
80421Risk group (German classification)
197861Risk group (German classification)
1164601Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8042
  • description: Microbacterium aquimaris partial 16S rRNA gene, type strain JS54-2T
  • accession: AM778449
  • length: 1431
  • database: nuccore
  • NCBI tax ID: 459816

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium aquimaris JCM 15625GCA_015278225scaffoldncbi459816
66792Microbacterium aquimaris strain JCM 15625459816.3wgspatric459816

GC content

@refGC-contentmethod
804269.3
6777069.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno94no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes88.132yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.607yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.336yes
69480spore-formingspore-formingAbility to form endo- or exosporesno68.862yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.429yes
69480flagellatedmotile2+Ability to perform flagellated movementno95no

External links

@ref: 8042

culture collection no.: DSM 19713, CIP 110688, KCTC 19124, JCM 15625

straininfo link

  • @ref: 76887
  • straininfo: 399256

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599704Microbacterium aquimaris sp. nov., isolated from seawater.Kim KK, Lee KC, Oh HM, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.65763-02008Actinomycetales/chemistry/*classification/genetics/metabolism, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Species SpecificityGenetics
Phylogeny34491524Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria.Xie F, Niu S, Lin X, Pei S, Jiang L, Tian Y, Zhang GJ Microbiol10.1007/s12275-021-1186-52021Base Composition, Carotenoids/chemistry/*metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Microbacterium/classification/genetics/*isolation & purification/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8042Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19713)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19713
19786Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19713.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
32605Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2881828776041
33591Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30493
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
68379Automatically annotated from API Coryne
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
76887Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399256.1StrainInfo: A central database for resolving microbial strain identifiers
116460Curators of the CIPCollection of Institut Pasteur (CIP 110688)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110688