Strain identifier

BacDive ID: 130156

Type strain: Yes

Species: Marinobacter similis

Strain Designation: A3d10

Strain history: CIP <- 2013, E. Ivanova, Swinburne Univ., Hawthorn, Victoria, Australia: strain A3d10 <- H. Webb

NCBI tax ID(s): 1420916 (species)

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: 22045

BacDive-ID: 130156

DSM-Number: 27079

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

description: Marinobacter similis A3d10 is a mesophilic, motile bacterium that was isolated from sea water collected one metre below the water surface.

NCBI tax id

  • NCBI tax id: 1420916
  • Matching level: species

strain history

@refhistory
22045<- E. P. Ivanova, Swinburne Univ. Technol., IRIS, Hawthorn, Australia; A3d10
67770E. P. Ivanova A3d10.
122617CIP <- 2013, E. Ivanova, Swinburne Univ., Hawthorn, Victoria, Australia: strain A3d10 <- H. Webb

doi: 10.13145/bacdive130156.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Alteromonadaceae
  • genus: Marinobacter
  • species: Marinobacter similis
  • full scientific name: Marinobacter similis Ng et al. 2015

@ref: 22045

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Alteromonadaceae

genus: Marinobacter

species: Marinobacter similis

full scientific name: Marinobacter similis Ng et al. 2015

strain designation: A3d10

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.356
6948099.957negative
122617yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22045BACTO 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
122617CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
22045positivegrowth25mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no100

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
22045sea water collected one metre below the water surfacePacific Ocean, Tasman Sea, Port Philip Bay, St Kilda Beach (37°51'50''S 144°58'55''E)AustraliaAUSAustralia and Oceania-37.8639144.982
67770Seawater from the 1st meter below the water surface from St. Kilda BeachPort Philip Bay, VictoriaAustraliaAUSAustralia and Oceania
122617Environment, Sea waterPort Phillip bay, MelbourneAustraliaAUSAustralia and Oceania2009-01-02

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_34863.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_89;96_1317;97_1564;98_4746;99_34863&stattab=map
  • Last taxonomy: Marinobacter
  • 16S sequence: KJ547704
  • Sequence Identity:
  • Total samples: 227
  • soil counts: 5
  • aquatic counts: 218
  • animal counts: 2
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
220451Risk group (German classification)
1226171Risk group (French classification)

Sequence information

16S sequences

  • @ref: 22045
  • description: Marinobacter similis strain A3d10 16S ribosomal RNA gene, partial sequence
  • accession: KJ547704
  • length: 1532
  • database: ena
  • NCBI tax ID: 1420916

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marinobacter similis A3d10GCA_000830985completencbi1420916
66792Marinobacter similis A3d101420916.4completepatric1420916
66792Marinobacter similis A3d102667527567completeimg1420916

GC content

  • @ref: 22045
  • GC-content: 57.6
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.429no
flagellatedyes88.84no
gram-positiveno98.679no
anaerobicno98.044no
aerobicyes92.031no
halophileyes93.866no
spore-formingno97.126no
glucose-utilyes53.654no
thermophileno98.323yes
glucose-fermentno87.637no

External links

@ref: 22045

culture collection no.: DSM 27079, CIP 110589, JCM 19398, KMM 7501

straininfo link

  • @ref: 88709
  • straininfo: 402002

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics24855296Draft Genome Sequences of Marinobacter similis A3d10T and Marinobacter salarius R9SW1T.Ivanova EP, Ng HJ, Webb HK, Feng G, Oshima K, Hattori M, Ohkuma M, Sergeev AF, Mikhailov VV, Crawford RJ, Sawabe TGenome Announc10.1128/genomeA.00442-142014
Phylogeny25198502Marinobacter salarius sp. nov. and Marinobacter similis sp. nov., isolated from sea water.Ng HJ, Lopez-Perez M, Webb HK, Gomez D, Sawabe T, Ryan J, Vyssotski M, Bizet C, Malherbe F, Mikhailov VV, Crawford RJ, Ivanova EPPLoS One10.1371/journal.pone.01065142014DNA, Bacterial/genetics, *Marine Biology, Marinobacter/*classification/isolation & purification, Nucleic Acid Hybridization, Phylogeny, Seawater/*microbiology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationEnzymology
Phylogeny27902222Marinobacter salinus sp. nov., a moderately halophilic bacterium isolated from a tidal flat environment.Rani S, Koh HW, Kim H, Rhee SK, Park SJInt J Syst Evol Microbiol10.1099/ijsem.0.0015872017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Marinobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
22045Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27079Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27079)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88709Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402002.1
122617Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110589Collection of Institut Pasteur (CIP 110589)