Strain identifier

BacDive ID: 23122

Type strain: Yes

Species: Salinispora pacifica

Strain Designation: CNR-114

Strain history: DSM 45820 <-- P. R. Jensen; Scripps Inst. of Oceanogr., UCSD, USA; CNR-114.

NCBI tax ID(s): 351187 (species)

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General

@ref: 18279

BacDive-ID: 23122

DSM-Number: 45820

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Salinispora pacifica CNR-114 is a mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 351187
  • Matching level: species

strain history

@refhistory
18279<- P. Jensen, SIO; CNR-114
67770DSM 45820 <-- P. R. Jensen; Scripps Inst. of Oceanogr., UCSD, USA; CNR-114.

doi: 10.13145/bacdive23122.20230509.8.1

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 pacifica
  • full scientific name: Salinispora pacifica Ahmed et al. 2014

@ref: 18279

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Salinispora

species: Salinispora pacifica

full scientific name: Salinispora pacifica Ahmed et al. 2014 emend. Nouioui et al. 2018

strain designation: CNR-114

type strain: yes

Morphology

pigmentation

@refproductionname
69404noMelanin
69404nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69404DSM_45547_image3.jpegPlates (514, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69404DSM_45547_image4.jpegPlates (514, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18279MODIFIED NUTRIENT AGAR (DSMZ Medium 1317)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1317.pdf
18279BACTO 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

culture temp

@refgrowthtypetemperaturerange
18279positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

halophily

  • @ref: 69404
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6940422599arabinose-growth
6940462968cellulose-growth
6940428757fructose-growth
6940417234glucose-growth
6940417268inositol-growth
6940437684mannose-growth
6940416634raffinose-growth
6940426546rhamnose-growth
6940417992sucrose-growth
6940418222xylose-growth
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

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
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69404+--+------+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69404++/-+/--+/-+/----+/----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18279marine sedimentwestern Pacific Ocean off the island of Guam at a depth of 82 mUSAUSANorth America
67770Marine sediment at a depth of 82 m from the Pacific Ocean off the island of Guam

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: DQ224161
  • Sequence Identity:
  • Total samples: 2007
  • soil counts: 1042
  • aquatic counts: 96
  • animal counts: 169
  • plant counts: 700

Safety information

risk assessment

  • @ref: 18279
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18279
  • description: Salinispora pacifica strain CNR-114 16S ribosomal RNA gene, partial sequence
  • accession: DQ224161
  • length: 1479
  • database: ena
  • NCBI tax ID: 351187

Genome sequences

  • @ref: 67770
  • description: Salinispora pacifica CNR114
  • accession: GCA_000514775
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1137260

GC content

@refGC-contentmethod
1827969.70sequence analysis
6777069.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.65no
flagellatedno97.944no
gram-positiveyes92.189no
anaerobicno98.275no
halophileno71.16no
spore-formingyes91.158no
thermophileno95.716yes
glucose-utilyes72.029no
aerobicyes91.642no
glucose-fermentno92.859yes

External links

@ref: 18279

culture collection no.: DSM 45820, JCM 31215, KACC 17160, CNR 114, NBRC 109968

straininfo link

  • @ref: 87358
  • straininfo: 397633

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23361994Salinispora pacifica sp. nov., an actinomycete from marine sediments.Ahmed L, Jensen PR, Freel KC, Brown R, Jones AL, Kim BY, Goodfellow MAntonie Van Leeuwenhoek10.1007/s10482-013-9886-42013Bacterial Typing Techniques, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Geologic Sediments/*microbiology, Guam, Micromonosporaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Palau, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny27707427Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).Ma Z, Zhao S, Cao T, Liu C, Huang Y, Gao Y, Yan K, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0015372016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sonchus/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
18279Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45820)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45820
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69404Wink, J.https://cdn.dsmz.de/wink/DSM%2045820.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
87358Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397633.1StrainInfo: A central database for resolving microbial strain identifiers