Strain identifier

BacDive ID: 462

Type strain: Yes

Species: Marinobacterium rhizophilum

Strain Designation: CL-YJ9

Strain history: <- B. C. Cho, Seoul Nat. Univ., Republic of Korea; CL-YJ9

NCBI tax ID(s): 1122202 (strain), 420402 (species)

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General

@ref: 7714

BacDive-ID: 462

DSM-Number: 18822

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

description: Marinobacterium rhizophilum CL-YJ9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment associated with the roots of the coastal plant Suaeda japonica inhabiting a tidal flat.

NCBI tax id

NCBI tax idMatching level
420402species
1122202strain

strain history

  • @ref: 7714
  • history: <- B. C. Cho, Seoul Nat. Univ., Republic of Korea; CL-YJ9

doi: 10.13145/bacdive462.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Marinobacterium
  • species: Marinobacterium rhizophilum
  • full scientific name: Marinobacterium rhizophilum Kim et al. 2008

@ref: 7714

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacterium

species: Marinobacterium rhizophilum

full scientific name: Marinobacterium rhizophilum Kim et al. 2008

strain designation: CL-YJ9

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32238negative0.7 µm0.35 µmrod-shapedyes
69480yes97.493
69480negative99.998

Culture and growth conditions

culture medium

  • @ref: 7714
  • 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
7714positivegrowth28mesophilic
32238positivegrowth05-30
32238positiveoptimum25mesophilic

culture pH

@refabilitytypepHPH range
32238positivegrowth06-09alkaliphile
32238positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32238
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.974

halophily

@refsaltgrowthtested relationconcentration
32238NaClpositivegrowth01-05 %
32238NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3223822599arabinose+carbon source
3223829016arginine+carbon source
3223822653asparagine+carbon source
3223828757fructose+carbon source
3223828260galactose+carbon source
3223817234glucose+carbon source
3223829987glutamate+carbon source
3223817754glycerol+carbon source
3223815428glycine+carbon source
3223825017leucine+carbon source
3223829864mannitol+carbon source
3223837684mannose+carbon source
32238506227N-acetylglucosamine+carbon source
3223817992sucrose+carbon source
3223827082trehalose+carbon source

enzymes

@refvalueactivityec
32238acid phosphatase+3.1.3.2
32238alkaline phosphatase+3.1.3.1
32238catalase+1.11.1.6
32238cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 7714
  • sample type: sediment associated with the roots of the coastal plant Suaeda japonica inhabiting a tidal flat
  • host species: Suaeda japonica
  • geographic location: Youngjong Island, Eulwangri
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Tidal flat
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6838.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_914;97_1064;98_5037;99_6838&stattab=map
  • Last taxonomy: Marinobacterium rhizophilum subclade
  • 16S sequence: EF192391
  • Sequence Identity:
  • Total samples: 569
  • soil counts: 110
  • aquatic counts: 403
  • animal counts: 40
  • plant counts: 16

Safety information

risk assessment

  • @ref: 7714
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7714
  • description: Marinobacterium rhizophilum strain CL-YJ9 16S ribosomal RNA gene, partial sequence
  • accession: EF192391
  • length: 1371
  • database: ena
  • NCBI tax ID: 420402

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacterium rhizophilum DSM 18822GCA_000378045scaffoldncbi1122202
66792Marinobacterium rhizophilum DSM 188221122202.3wgspatric1122202
66792Marinobacterium rhizophilum DSM 188222518645605draftimg1122202

GC content

@refGC-content
771461.0
3223861

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.244yes
flagellatedyes79.721no
gram-positiveno99.127yes
anaerobicno97.753yes
aerobicyes84.192yes
halophileyes70.784no
spore-formingno95.109no
glucose-utilyes92.69yes
thermophileno99.544yes
glucose-fermentno83.631no

External links

@ref: 7714

culture collection no.: DSM 18822, KCCM 42386

straininfo link

  • @ref: 70141
  • straininfo: 403386

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175703Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.Kim YG, Jin YA, Hwang CY, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.65176-02008Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny26813672Marinobacterium profundum sp. nov., a marine bacterium from deep-sea sediment.Yeon Hwang C, Jung Yoon S, Lee I, Baek K, Mi Lee Y, Yoo KC, Il Yoon H, Kum Lee HInt J Syst Evol Microbiol10.1099/ijsem.0.0009182016
Genetics29093768Draft genome sequence of Marinobacterium rhizophilum CL-YJ9(T) (DSM 18822(T)), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.Choi DH, Jang GI, Lapidus A, Copeland A, Reddy TBK, Mukherjee S, Huntemann M, Varghese N, Ivanova N, Pillay M, Tindall BJ, Goker M, Woyke T, Klenk HP, Kyrpides NC, Cho BCStand Genomic Sci10.1186/s40793-017-0275-x2017
Phylogeny29303694Marinobacterium aestuarii sp. nov., a benzene-degrading marine bacterium isolated from estuary sediment.Bae SS, Jung J, Chung D, Baek KInt J Syst Evol Microbiol10.1099/ijsem.0.0025612018Bacterial Typing Techniques, Base Composition, Benzene, DNA, Bacterial/genetics, *Estuaries, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Oceanospirillaceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7714Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18822)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18822
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
32238Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2847928776041
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)
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
70141Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403386.1StrainInfo: A central database for resolving microbial strain identifiers