Strain identifier

BacDive ID: 13788

Type strain: Yes

Species: Ruegeria marina

Strain Designation: ZH17

Strain history: Y.-Y. Huo ZH17.

NCBI tax ID(s): 639004 (species)

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General

@ref: 17783

BacDive-ID: 13788

DSM-Number: 24837

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Ruegeria marina ZH17 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 639004
  • Matching level: species

strain history

@refhistory
17783<- JCM <- M. Wu, Zhejiang Univ., Hangzhou, China; ZH17
67770Y.-Y. Huo ZH17.

doi: 10.13145/bacdive13788.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Ruegeria
  • species: Ruegeria marina
  • full scientific name: Ruegeria marina Huo et al. 2011

@ref: 17783

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Ruegeria

species: Ruegeria marina

full scientific name: Ruegeria marina Huo et al. 2011

strain designation: ZH17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29847negative3.25 µm0.75 µmrod-shapedno
69480negative99.999

colony morphology

  • @ref: 17783
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

  • @ref: 17783
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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
17783positivegrowth30mesophilic
29847positivegrowth10-42
29847positiveoptimum36mesophilic
67770positivegrowth35mesophilic

culture pH

@refabilitytypepHPH range
29847positivegrowth6.5-9.0alkaliphile
29847positiveoptimum7.5

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
29847NaClpositivegrowth0-7.5 %
29847NaClpositiveoptimum1.75 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2984730089acetate+carbon source
2984716449alanine+carbon source
2984729016arginine+carbon source
2984716947citrate+carbon source
2984716236ethanol+carbon source
298475291gelatin+carbon source
2984717234glucose+carbon source
2984729987glutamate+carbon source
2984717754glycerol+carbon source
2984727570histidine+carbon source
2984724996lactate+carbon source
2984725115malate+carbon source
2984715792malonate+carbon source
2984718257ornithine+carbon source
2984717272propionate+carbon source
2984715361pyruvate+carbon source
2984717822serine+carbon source
2984730031succinate+carbon source
2984753424tween 20+carbon source
2984718222xylose+carbon source
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
17783catalase+1.11.1.6
17783cytochrome-c oxidase+1.9.3.1
29847catalase+1.11.1.6
29847gelatinase+
29847cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
17783--------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17783marine sedimentEast China Sea near Zhenhai, Zhejiang ProvinceChinaCHNAsia
67770Marine sediment of the East China Sea

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_166714.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_42219;97_53973;98_71347;99_166714&stattab=map
  • Last taxonomy: Ruegeria marina subclade
  • 16S sequence: FJ872535
  • Sequence Identity:
  • Total samples: 221
  • soil counts: 7
  • aquatic counts: 207
  • animal counts: 7

Safety information

risk assessment

  • @ref: 17783
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17783
  • description: Ruegeria marina strain ZH17 16S ribosomal RNA gene, partial sequence
  • accession: FJ872535
  • length: 1386
  • database: ena
  • NCBI tax ID: 639004

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruegeria marina strain CGMCC 1.9108639004.3wgspatric639004
66792Ruegeria marina CGMCC 1.91082617270884draftimg639004
67770Ruegeria marina CGMCC 1.9108GCA_900101475scaffoldncbi639004

GC content

@refGC-contentmethod
1778363.5high performance liquid chromatography (HPLC)
2984763.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.149yes
anaerobicno98.775no
halophileyes74.564no
spore-formingno96.535no
glucose-utilno50no
thermophileno96.457no
flagellatedno94.885yes
aerobicyes94.716no
motileno88.935yes
glucose-fermentno90.929yes

External links

@ref: 17783

culture collection no.: DSM 24837, CGMCC 1.9108, JCM 16262

straininfo link

  • @ref: 82966
  • straininfo: 399049

literature

  • topic: Phylogeny
  • Pubmed-ID: 20228209
  • title: Ruegeria marina sp. nov., isolated from marine sediment.
  • authors: Huo YY, Xu XW, Li X, Liu C, Cui HL, Wang CS, Wu M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022400-0
  • year: 2010
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analysis, *Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17783Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24837)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24837
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
29847Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2622128776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
82966Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399049.1StrainInfo: A central database for resolving microbial strain identifiers