Strain identifier

BacDive ID: 11109

Type strain: Yes

Species: Nocardioides aquaticus

Strain Designation: EL-17K, EL-17K T

Strain history: CIP <- 2001, P. Hirsch, Kiel Univ., Kiel, Germany: strain EL-17K T <- Pittirsch

NCBI tax ID(s): 160826 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4367

BacDive-ID: 11109

DSM-Number: 11439

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

description: Nocardioides aquaticus EL-17K is an obligate aerobe, psychrophilic, Gram-positive bacterium that was isolated from water sample.

NCBI tax id

  • NCBI tax id: 160826
  • Matching level: species

strain history

@refhistory
4367<- M. Labrenz <- P. Hirsch; EL-17K
67770DSM 11439 <-- M. Labrenz <-- P. Hirsch EL-17K.
116436CIP <- 2001, P. Hirsch, Kiel Univ., Kiel, Germany: strain EL-17K T <- Pittirsch

doi: 10.13145/bacdive11109.20230509.8.1

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 aquaticus
  • full scientific name: Nocardioides aquaticus Lawson et al. 2000

@ref: 4367

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides aquaticus

full scientific name: Nocardioides aquaticus Lawson et al. 2000

strain designation: EL-17K, EL-17K T

type strain: yes

Morphology

cell morphology

  • @ref: 116436
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18436Pastel yellow (1034)10-14 daysISP 2
18436Pastel yellow (1034)10-14 daysISP 3
18436Colorless10-14 daysISP 4
18436Pastel yellow (1034)10-14 daysISP 5
18436Pastel yellow (1034)10-14 daysISP 6
18436Pastel yellow (1034)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18436noISP 2
18436noISP 3
18436noISP 4
18436noISP 5
18436noISP 6
18436noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4367EKHO LAKE STRAINS MEDIUM (DSMZ Medium 621a)yeshttps://mediadive.dsmz.de/medium/621aName: EKHO LAKE STRAINS MEDIUM (DSMZ Medium 621a) Composition: NaCl 22.6553 g/l Agar 15.0 g/l MgCl2 x 6 H2O 4.80666 g/l Na2SO4 3.77991 g/l CaCl2 1.06343 g/l KCl 0.64076 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l NaHCO3 0.18528 g/l CaCl2 x 2 H2O 0.0703158 g/l H3BO3 0.02509 g/l SrCl2 0.02316 g/l KBr 0.00579 g/l NaF 0.002895 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water
18436ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18436ISP 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:
18436ISP 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
18436ISP 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
18436ISP 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
18436ISP 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

culture temp

@refgrowthtypetemperaturerange
18436positiveoptimum20psychrophilic
4367positivegrowth20psychrophilic
67770positivegrowth25mesophilic
116436positivegrowth10-30
116436nogrowth37mesophilic
116436nogrowth41thermophilic
116436nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116436
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 116436
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
116436esculin-hydrolysis4853
116436hippurate-hydrolysis606565
116436nitrate+reduction17632
116436nitrite-reduction16301
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea-hydrolysis16199
68379gelatin+hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose+fermentation17992
68379glycogen-fermentation28087

metabolite production

  • @ref: 116436
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11643615688acetoin-
11643617234glucose-

enzymes

@refvalueactivityec
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
116436oxidase-
116436beta-galactosidase-3.2.1.23
116436alcohol dehydrogenase-1.1.1.1
116436gelatinase-
116436amylase+
116436caseinase+3.4.21.50
116436catalase+1.11.1.6
116436tween esterase-
116436gamma-glutamyltransferase-2.3.2.2
116436lysine decarboxylase-4.1.1.18
116436ornithine decarboxylase-4.1.1.17
116436phenylalanine ammonia-lyase+4.3.1.24
116436tryptophan deaminase-
116436urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase+3.4.11.3
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
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18436--++--+---+------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18436++++++++-++--+++---
116436+++-+-+--++---+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116436+/-----+/-----+/-+/---+/---+/--------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116436++++---+----+--------+-+---------+++-+-----+----++----------+-+-+----------+---++-------+-+----++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.countryisolation date
4367water sampleEkho LakeAustralia and Oceania
67770Water sample of the hypersaline Ekho LakeVestfold HillsAntarcticaAntarcticaATA
116436Environment, WaterEkho lakeAntarcticaAntarcticaATA1990

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
43671Risk group (German classification)
184361hazard group
1164361Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4367
  • description: Nocardioides aquaticus 16S ribosomal RNA
  • accession: X94145
  • length: 1460
  • database: ena
  • NCBI tax ID: 160826

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides aquaticus KCTC 9944GCA_018459925completencbi160826
66792Nocardioides aquaticus strain KCTC 9944160826.3completepatric160826

GC content

@refGC-contentmethod
436769
6777069high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno98.66no
gram-positiveyes95.033no
anaerobicno99.059no
aerobicyes94.086no
halophileno85.371no
spore-formingno81.957no
thermophileno98.361yes
glucose-utilyes89.397no
motileno95.914no
glucose-fermentno90.084yes

External links

@ref: 4367

culture collection no.: DSM 11439, ATCC BAA 164, JCM 11266, NBRC 100371, NCFB 3076, CIP 106993, KCTC 9944, NCIMB 703076, VKM Ac-2523

straininfo link

  • @ref: 80358
  • straininfo: 45451

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10930074New LL-diaminopimelic acid-containing actinomycetes from hypersaline, heliothermal and meromictic Antarctic Ekho Lake: Nocardioides aquaticus sp. nov. and Friedmanniella [correction of Friedmannielly] lacustris sp. nov.Lawson PA, Collins MD, Schumann P, Tindall BJ, Hirsch P, Labrenz MSyst Appl Microbiol10.1016/s0723-2020(00)80008-92000Actinomycetales/*classification, Antarctic Regions, Bacterial Typing Techniques, DNA, Ribosomal/genetics, Diaminopimelic Acid/*isolation & purification, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Water MicrobiologyGenetics
Phylogeny18071922Nocardioides islandiensis sp. nov., isolated from soil in Bigeum Island Korea.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJAntonie Van Leeuwenhoek10.1007/s10482-007-9217-82007Actinomycetales/classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny18842843Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65566-02008Actinomycetales/chemistry/*classification/*genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny35246301Complete genome of Nocardioides aquaticus KCTC 9944(T) isolated from meromictic and hypersaline Ekho Lake, Antarctica.Hwang K, Choe H, Kim KMMar Genomics10.1016/j.margen.2021.1008892021Antarctic Regions, DNA, Bacterial/genetics, *Lakes, Nocardioides, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitle
4367Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11439)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11439
18436Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM11439.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
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/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
80358Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45451.1StrainInfo: A central database for resolving microbial strain identifiers
116436Curators of the CIPCollection of Institut Pasteur (CIP 106993)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106993