Strain identifier

BacDive ID: 8026

Type strain: Yes

Species: Salinispora tropica

Strain history: CIP <- 2005, DSMZ <- P. Jensen, California Univ., San Diego, California, USA: strain CNB440

NCBI tax ID(s): 168695 (species)

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General

@ref: 12114

BacDive-ID: 8026

DSM-Number: 44818

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

description: Salinispora tropica DSM 44818 is an aerobe, spore-forming, mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 168695
  • Matching level: species

strain history

@refhistory
12114<- P. Jensen; CNB440 (Salinospora tropicalis) <- P. Jensen
67770DSM 44818 <-- P. R. Jensen CNB-440.
123591CIP <- 2005, DSMZ <- P. Jensen, California Univ., San Diego, California, USA: strain CNB440

doi: 10.13145/bacdive8026.20230509.8.1

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 tropica
  • full scientific name: Salinispora tropica Maldonado et al. 2005

@ref: 12114

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Salinispora

species: Salinispora tropica

full scientific name: Salinispora tropica Maldonado et al. 2005 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31465positiverod-shaped
123591positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19876Deep orange10-14 daysISP 2
19876Deep orange10-14 daysISP 3
19876Pastel orange10-14 daysISP 4
19876Deep orange10-14 daysISP 5
19876Deep orange10-14 daysISP 6
19876Deep orange10-14 daysISP 7
123591

multicellular morphology

@refforms multicellular complexmedium name
19876noISP 2
19876noISP 3
19876noISP 4
19876noISP 5
19876noISP 6
19876noISP 7

pigmentation

  • @ref: 31465
  • production: yes

multimedia

  • @ref: 12114
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44818.jpg
  • caption: Medium 514 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12114TCG 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
12114BACTO 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
19876ISP 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
19876ISP 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:
19876ISP 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
19876ISP 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
19876ISP 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
19876ISP 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
123591CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
19876positiveoptimum28mesophilic
12114positivegrowth28mesophilic
31465positivegrowth10-30
31465positiveoptimum21.5psychrophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31465aerobe
123591facultative anaerobe

spore formation

@refspore formation
31465yes
123591no

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3146517057cellobiose+carbon source
3146528260galactose+carbon source
3146517716lactose+carbon source
12359117632nitrate+reduction
12359116301nitrite-reduction

metabolite production

  • @ref: 123591
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
123591oxidase-
123591alcohol dehydrogenase-1.1.1.1
123591catalase+1.11.1.6
123591lysine decarboxylase-4.1.1.18
123591ornithine decarboxylase-4.1.1.17
123591urease-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
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
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-mannosidase-3.2.1.24
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
19876+++-++----+---+++--
123591+++-+----------+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12114marine sedimentBahamasBHSMiddle and South America
67770Coarse sand off the Bahamas
123591Environment, Marine sedimentBahamasBHSNorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_652.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_457;98_526;99_652&stattab=map
  • Last taxonomy: Salinispora
  • 16S sequence: AY040617
  • Sequence Identity:
  • Total samples: 2007
  • soil counts: 1042
  • aquatic counts: 96
  • animal counts: 169
  • plant counts: 700

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121141Risk group (German classification)
198761Risk group (German classification)
1235911Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Salinispora tropica strain CNB440 16S ribosomal RNA gene, partial sequenceAY0406171480ena369723
31465Salinispora tropica strain CNB-440 16S-23S ribosomal RNA intergenic spacer, complete sequenceAY371895417nuccore369723

Genome sequences

  • @ref: 67770
  • description: Salinispora tropica CNB-440
  • accession: GCA_000016425
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 369723

GC content

@refGC-contentmethod
3146571.5
6777069.5genome sequence analysis

External links

@ref: 12114

culture collection no.: DSM 44818, ATCC BAA 916, CIP 108943, JCM 13857, CNB 440, BCRC 16822, NBRC 105044

straininfo link

  • @ref: 77456
  • straininfo: 215505

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
Metabolism18677472Growth of Salinispora tropica strains CNB440, CNB476, and NPS21184 in nonsaline, low-sodium media.Tsueng G, Lam KSAppl Microbiol Biotechnol10.1007/s00253-008-1614-z2008Culture Media/*chemistry/*metabolism, Lactones, Micromonosporaceae/*growth & development/isolation & purification/*metabolism, Pyrroles, Seawater/*microbiology, Sodium Chloride/*metabolismCultivation
Genetics30665399Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora.Contador CA, Rodriguez V, Andrews BA, Asenjo JABMC Syst Biol10.1186/s12918-019-0683-12019Actinomycetales/*genetics/*metabolism, Biomass, Genes, Bacterial/genetics, *Genomics, Metabolic Networks and Pathways, *Models, Biological, PhylogenyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12114Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44818)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44818
19876Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44818.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
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
77456Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215505.1StrainInfo: A central database for resolving microbial strain identifiers
123591Curators of the CIPCollection of Institut Pasteur (CIP 108943)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108943