Strain identifier

BacDive ID: 8027

Type strain: Yes

Species: Salinispora arenicola

Strain history: CIP <- 2005, DSMZ <- P. Jensen, California Univ., San Diego, California, USA: strain CNH643

NCBI tax ID(s): 391967 (strain), 168697 (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: 12115

BacDive-ID: 8027

DSM-Number: 44819

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

description: Salinispora arenicola DSM 44819 is an aerobe, spore-forming, mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

NCBI tax idMatching level
391967strain
168697species

strain history

@refhistory
12115<- P. Jensen; CNH643 (Salinospora arenicola)
67770DSM 44819 <-- P. R. Jensen CNH-643.
116485CIP <- 2005, DSMZ <- P. Jensen, California Univ., San Diego, California, USA: strain CNH643

doi: 10.13145/bacdive8027.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Salinispora
  • species: Salinispora arenicola
  • full scientific name: Salinispora arenicola Maldonado et al. 2005

@ref: 12115

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Salinispora

species: Salinispora arenicola

full scientific name: Salinispora arenicola Maldonado et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31465positivecoccus-shapedno
116485positiveno

colony morphology

@refcolony colorincubation periodmedium used
19877Deep orange10-14 daysISP 2
19877Deep orange10-14 daysISP 3
1987710-14 daysISP 4
1987710-14 daysISP 5
1987710-14 daysISP 6
1987710-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19877noISP 2
19877noISP 3
19877noISP 4
19877noISP 5
19877noISP 7

pigmentation

  • @ref: 31465
  • production: yes

multimedia

  • @ref: 12115
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44819.jpg
  • caption: Medium 514 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12115TCG MEDIUM (DSMZ Medium 1009)yeshttps://mediadive.dsmz.de/medium/1009Name: TCG MEDIUM (DSMZ Medium 1009) Composition: Casitone 5.0 g/l Glucose 4.0 g/l Tryptone 3.0 g/l Sea water
12115BACTO 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
19877ISP 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
19877ISP 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
19877ISP 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:
19877ISP 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
19877ISP 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
19877ISP 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
32693MEDIUM 661 - for Salinispora arenicolayesDistilled water make up to (1000.000 ml);Glucose (4.000 g);Casitone (5.000 g);Tryptone (3.000 g);Sea salts (32.000 g)
116485CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
19877positiveoptimum28mesophilic
12115positivegrowth28mesophilic
31465positivegrowth10-30
31465positiveoptimum24psychrophilic
32693positivegrowth25mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31465
  • oxygen tolerance: aerobe

spore formation

@refspore formation
31465yes
116485no

observation

@refobservation
31465aggregates in clumps
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3146526271proline+carbon source
3146517814salicin+carbon source
3146526986threonine+carbon source
11648517632nitrate+reduction
11648516301nitrite-reduction

metabolite production

  • @ref: 116485
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116485oxidase-
116485alcohol dehydrogenase-1.1.1.1
116485catalase+1.11.1.6
116485lysine decarboxylase-4.1.1.18
116485ornithine decarboxylase-4.1.1.17
116485urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382beta-glucosidase+3.2.1.21
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19877+---+--+--+----+-+-
116485+++-+---------+++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12115marine sedimentBahamasBHSMiddle and South America
67770Coarse sand off the Bahamas
116485Environment, Marine sedimentBahamasBHSNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_651.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_457;98_526;99_651&stattab=map
  • Last taxonomy: Salinispora
  • 16S sequence: AY040619
  • Sequence Identity:
  • Total samples: 1078
  • soil counts: 653
  • aquatic counts: 102
  • animal counts: 78
  • plant counts: 245

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121151Risk group (German classification)
198771Risk group (German classification)
1164851Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Salinispora arenicola ATCC BAA-917 strain 16S ribosomal RNA gene, partial sequenceAY0406191479ena391967
31465Salinispora arenicola strain CNH-643 16S-23S ribosomal RNA intergenic spacer, complete sequenceAY371897420nuccore391967

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinispora arenicola NBRC 105043GCA_018332675contigncbi168697
66792Salinispora arenicola strain DSM 44819168697.8wgspatric168697
66792Salinispora arenicola strain NBRC 105043168697.12wgspatric168697
66792Salinispora arenicola DSM 448192814122978draftimg168697
67770Salinispora arenicola ATCC BAA-917 CNH-643GCA_000259615contigncbi391967
67770Salinispora arenicola DSM 44819GCA_006716065contigncbi168697

GC content

  • @ref: 31465
  • GC-content: 71.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.268yes
gram-positiveyes91.917yes
anaerobicno98.009yes
aerobicyes91.395no
halophileno74.458no
spore-formingyes90.615yes
glucose-utilyes71.937no
flagellatedno98.007no
thermophileno94.054yes
glucose-fermentno93.634no

External links

@ref: 12115

culture collection no.: DSM 44819, ATCC BAA 917, CIP 108942, JCM 13856, CNH 643, BCRC 16821, NBRC 105043

straininfo link

  • @ref: 77457
  • straininfo: 215506

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166663Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae.Maldonado LA, Fenical W, Jensen PR, Kauffman CA, Mincer TJ, Ward AC, Bull AT, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.63625-02005DNA, Bacterial/analysis, DNA, Ribosomal Spacer/analysis, Genes, rRNA, Micromonosporaceae/*classification/*genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Seawater/*microbiologyGenetics
Phylogeny24179039Salinispora arenicola from temperate marine sediments: new intra-species variations and atypical distribution of secondary metabolic genes.Goo KS, Tsuda M, Ulanova DAntonie Van Leeuwenhoek10.1007/s10482-013-0067-22013Bacterial Proteins/*genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Genetic Variation, Geologic Sediments/chemistry/*microbiology, Micromonosporaceae/classification/*genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/chemistry/*microbiology, Secondary Metabolism, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12115Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44819)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44819
19877Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44819.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31465Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127766
32693Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6628
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/
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
77457Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215506.1StrainInfo: A central database for resolving microbial strain identifiers
116485Curators of the CIPCollection of Institut Pasteur (CIP 108942)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108942