Strain identifier

BacDive ID: 11210

Type strain: Yes

Species: Nocardiopsis halotolerans

Strain Designation: F100

Strain history: CIP <- 2002, DSMZ <- S. Al-Zarban, Univ. Kuwait: strain F100

NCBI tax ID(s): 1246444 (strain), 124252 (species)

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General

@ref: 11535

BacDive-ID: 11210

DSM-Number: 44410

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive

description: Nocardiopsis halotolerans F100 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from salt marsh soil.

NCBI tax id

NCBI tax idMatching level
1246444strain
124252species

strain history

@refhistory
11535<- S. Al-Zarban, Univ. of Kuwait; F100
67770DSM 44410 <-- S. Al-Zarban F100.
119828CIP <- 2002, DSMZ <- S. Al-Zarban, Univ. Kuwait: strain F100

doi: 10.13145/bacdive11210.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis halotolerans
  • full scientific name: Nocardiopsis halotolerans Al-Zarban et al. 2002

@ref: 11535

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis halotolerans

full scientific name: Nocardiopsis halotolerans Al-Zarban et al. 2002 emend. Nouioui et al. 2018

strain designation: F100

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119828positivefilament-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19664Brown beige10-14 daysISP 2
19664Beige10-14 daysISP 3
19664Beige10-14 daysISP 4
19664Beige10-14 daysISP 5
19664Brown beige10-14 daysISP 6
19664Brown beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19664yesAerial MyceliumWhiteISP 2
19664yesAerial MyceliumWhiteISP 3
19664yesAerial MyceliumISP 4
19664noISP 5
19664yesAerial MyceliumWhiteISP 6
19664yesAerial MyceliumWhiteISP 7

multimedia

  • @ref: 11535
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44410.jpg
  • caption: Medium 1240 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11535STARCH-MINERAL SALT-AGAR (STMS) + 10%NACL (DSMZ Medium 1240)yeshttps://mediadive.dsmz.de/medium/1240Name: STARCH-MINERAL SALT-AGAR + 10% NACL (DSMZ Medium 1240) Composition: NaCl 100.0 g/l Agar 15.0 g/l Starch 10.0 g/l (NH4)2SO4 2.0 g/l CaCO3 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 1.0 g/l FeSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l Distilled water
19664ISP 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
19664ISP 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:
19664ISP 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
19664ISP 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
19664ISP 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
19664ISP 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
36138MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
11535NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: NaCl 100.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
119828CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11535positivegrowth28mesophilic
19664positiveoptimum30mesophilic
36138positivegrowth30mesophilic
67770positivegrowth28mesophilic
119828positivegrowth25-37mesophilic
119828nogrowth10psychrophilic
119828nogrowth41thermophilic
119828nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119828
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes97
69480yes100

halophily

@refsaltgrowthtested relationconcentration
119828NaClpositivegrowth2-8 %
119828NaClnogrowth0 %
119828NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-10(H2), MK-10(H4), MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1966417234glucose-
1966422599arabinose-
1966417992sucrose-
1966418222xylose-
1966417268myo-inositol-
1966429864mannitol-
1966428757fructose-
1966426546rhamnose-
1966416634raffinose-
1966462968cellulose-
11982816947citrate-carbon source
1198284853esculin-hydrolysis
119828606565hippurate+hydrolysis
11982817632nitrate-reduction
11982816301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 119828
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119828
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11982815688acetoin-
11982817234glucose-

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-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
119828oxidase-
119828beta-galactosidase-3.2.1.23
119828alcohol dehydrogenase-1.1.1.1
119828gelatinase-
119828caseinase+3.4.21.50
119828catalase+1.11.1.6
119828gamma-glutamyltransferase-2.3.2.2
119828lysine decarboxylase-4.1.1.18
119828ornithine decarboxylase-4.1.1.17
119828phenylalanine ammonia-lyase-4.3.1.24
119828tryptophan deaminase-
119828urease-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
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-glucosidase+3.2.1.20
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19664-+++-+/-++--+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19664++++++-++++++++++--
119828+++-+---+-+---+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119828++--+--+-++----+--++++-+--+---------------------++----------------------+--+---++-------+--+---+-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11535salt marsh soilDesert areaKuwaitKWTAsia
67770Salt marsh soil in a desert areaAl-KhiranKuwaitKWTAsia
119828Environment, Salt marsh soilKuwaitKWTAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Salt marsh
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_5877.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_4370;99_5877&stattab=map
  • Last taxonomy: Nocardiopsis halotolerans subclade
  • 16S sequence: AJ290448
  • Sequence Identity:
  • Total samples: 90
  • soil counts: 10
  • aquatic counts: 6
  • animal counts: 71
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115351Risk group (German classification)
196641Risk group (German classification)
1198281Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11535
  • description: Nocardiopsis halototerans 16S rRNA gene, strain DSM 44410
  • accession: AJ290448
  • length: 1505
  • database: ena
  • NCBI tax ID: 1246444

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis halotolerans DSM 444101246444.3wgspatric1246444
66792Nocardiopsis halotolerans DSM 444102554235027draftimg1246444
67770Nocardiopsis halotolerans DSM 44410GCA_000341065contigncbi1246444

GC content

  • @ref: 67770
  • GC-content: 71.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
motileno91.896no
gram-positiveyes90.927no
anaerobicno98.903no
aerobicyes92.307no
halophileyes68.758no
spore-formingyes92.626no
thermophileno96.288no
glucose-utilyes86.267yes
flagellatedno97.858no
glucose-fermentno90.21yes

External links

@ref: 11535

culture collection no.: DSM 44410, JCM 11760, NRRL B-24124, BCRC 16376, CGMCC 4.2084, CIP 107430, NBRC 100347, VKM Ac-2519

straininfo link

  • @ref: 80455
  • straininfo: 87957

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931165Nocardiopsis halotolerans sp. nov., isolated from salt marsh soil in Kuwait.Al-Zarban SS, Abbas I, Al-Musallam AA, Steiner U, Stackebrandt E, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/00207713-52-2-5252002Actinomycetales/chemistry/*classification/physiology, DNA, Bacterial/chemistry, Genotype, Kuwait, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/chemistry, Sodium Chloride, *Soil MicrobiologyGenetics
Phylogeny18319481Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China.Chen YG, Cui XL, Kroppenstedt RM, Stackebrandt E, Wen ML, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.65441-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Soil/*analysis, *Soil Microbiology, Species SpecificityGenetics
Enzymology25231460New structures and composition of cell wall teichoic acids from Nocardiopsis synnemataformans, Nocardiopsis halotolerans, Nocardiopsis composta and Nocardiopsis metallicus: a chemotaxonomic value.Tul'skaya EM, Shashkov AS, Streshinskaya GM, Potekhina NV, Evtushenko LIAntonie Van Leeuwenhoek10.1007/s10482-014-0280-72014Actinobacteria/*chemistry, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Molecular Structure, Teichoic Acids/*chemistry/*isolation & purificationPhylogeny

Reference

@idauthorscataloguedoi/urltitle
11535Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44410)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44410
19664Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44410.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
36138Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4865
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/
68379Automatically annotated from API Coryne
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
80455Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87957.1StrainInfo: A central database for resolving microbial strain identifiers
119828Curators of the CIPCollection of Institut Pasteur (CIP 107430)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107430