Strain identifier

BacDive ID: 11086

Type strain: Yes

Species: Nocardioides aequoreus

Strain Designation: SST-45

Strain history: CIP <- 2007, JCM <- S.D. Lee, Cheju Unvi., Jeju, Korea: strain SST-45

NCBI tax ID(s): 397278 (species)

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General

@ref: 15786

BacDive-ID: 11086

DSM-Number: 21547

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

description: Nocardioides aequoreus SST-45 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sandy sediment.

NCBI tax id

  • NCBI tax id: 397278
  • Matching level: species

strain history

@refhistory
15786<- JCM <- S. D. Lee; SST-45
67770S. D. Lee SST-45.
116056CIP <- 2007, JCM <- S.D. Lee, Cheju Unvi., Jeju, Korea: strain SST-45

doi: 10.13145/bacdive11086.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides aequoreus
  • full scientific name: Nocardioides aequoreus (Lee 2007) Wang et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Marmoricola aequoreus

@ref: 15786

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Marmoricola

species: Marmoricola aequoreus

full scientific name: Marmoricola aequoreus Lee 2007

strain designation: SST-45

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotility
31947positive0.6 µmcoccus-shapedno
116056positivecoccus-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15786R2A 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
15786TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf
37803MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
116056CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
15786positivegrowth28mesophilic
31947positivegrowth10-37
31947positiveoptimum23.5psychrophilic
37803positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31947positivegrowth5.1-12.1alkaliphile
31947positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

  • @ref: 31947
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31947
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31947NaClpositivegrowth0.0-7.0 %
31947NaClpositiveoptimum5 %

observation

@refobservation
31947aggregates in clumps
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3194730089acetate+carbon source
3194717057cellobiose+carbon source
3194716947citrate+carbon source
3194728757fructose+carbon source
3194728260galactose+carbon source
3194717234glucose+carbon source
3194717754glycerol+carbon source
3194717716lactose+carbon source
3194725115malate+carbon source
3194717306maltose+carbon source
3194729864mannitol+carbon source
3194737684mannose+carbon source
3194737657methyl D-glucoside+carbon source
3194733942ribose+carbon source
3194717814salicin+carbon source
3194730911sorbitol+carbon source
3194730031succinate+carbon source
3194717992sucrose+carbon source
3194727082trehalose+carbon source
3194718222xylose+carbon source
319474853esculin+hydrolysis
3194717632nitrate+reduction
11605617632nitrate+reduction
11605616301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3194716136hydrogen sulfideyes
11605635581indoleno

enzymes

@refvalueactivityec
31947alkaline phosphatase+3.1.3.1
31947gelatinase+
116056oxidase-
116056catalase+1.11.1.6
116056urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116056-+++-+-------+-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15786sandy sedimentJeju Island, Samyang beachRepublic of KoreaKORAsia
67770Sandy sediment of Samyang BeachJeju IslandRepublic of KoreaKORAsia
116056Environment, Sandy sedimentSamyang beach, Jeju IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1247.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_723;97_846;98_986;99_1247&stattab=map
  • Last taxonomy: Marmoricola aequoreus
  • 16S sequence: AM295338
  • Sequence Identity:
  • Total samples: 703
  • soil counts: 193
  • aquatic counts: 53
  • animal counts: 393
  • plant counts: 64

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
157861Risk group (German classification)
1160561Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15786
  • description: Marmoricola aequoreus partial 16S rRNA gene, type strain SST-45T
  • accession: AM295338
  • length: 1398
  • database: ena
  • NCBI tax ID: 397278

Genome sequences

  • @ref: 67770
  • description: Marmoricola aequoreus NRRL B-24464
  • accession: GCA_000720335
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 397278

GC content

@refGC-contentmethod
1578672.4
6777072.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno62.851yes
flagellatedno91.834yes
gram-positiveyes89.228yes
anaerobicno98.925no
halophileno93.572no
spore-formingno89.984no
glucose-utilyes89.13yes
aerobicyes93.17no
thermophileno97.834yes
glucose-fermentno88.614no

External links

@ref: 15786

culture collection no.: DSM 21547, CIP 109645, JCM 13812, NRRL B-24464

straininfo link

  • @ref: 80335
  • straininfo: 309460

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625163Marmoricola aequoreus sp. nov., a novel actinobacterium isolated from marine sediment.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64696-02007Actinomycetales/chemistry/*classification/*isolation & purification/physiology, Aerobiosis, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Vitamin K 2/analysisGenetics
Phylogeny18450688Marmoricola bigeumensis sp. nov., a member of the family Nocardioidaceae.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65576-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny20693360Marmoricola korecus sp. nov.Lee SD, Lee DW, Ko YHInt J Syst Evol Microbiol10.1099/ijs.0.025460-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lipids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, *Volcanic EruptionsGenetics
Phylogeny25754550Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola.Kim SJ, Lim JM, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.0001842015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26231541Marmoricola aquaticus sp. nov., an actinomycete isolated from a marine sponge.de Menezes CBA, Tonin MF, Silva LJ, de Souza WR, Parma M, de Melo IS, Zucchi TD, Destefano SAL, Fantinatti-Garboggini FInt J Syst Evol Microbiol10.1099/ijs.0.0002542015Actinomycetales/*classification/genetics/isolation & purification, Animals, Base Composition, Brazil, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15786Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21547)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21547
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
31947Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2820328776041
37803Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7411
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
80335Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309460.1StrainInfo: A central database for resolving microbial strain identifiers
116056Curators of the CIPCollection of Institut Pasteur (CIP 109645)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109645