Workshop and Q&A October 6th

Strain identifier

BacDive ID: 24008

Type strain: Yes

Species: Ferrimonas sediminum

Strain Designation: JYr13

Strain history: X.-H. Zhang <-- R. Zhao JYr13.

NCBI tax ID(s): 718193 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 20561

BacDive-ID: 24008

DSM-Number: 23317

keywords: Gram-negative, psychrophilic, facultative anaerobe, Bacteria, 16S sequence, genome sequence, motile, rod-shaped

description: Ferrimonas sediminum JYr13 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from coastal sediment of an amphioxus breeding zone.

NCBI tax id

  • NCBI tax id: 718193
  • Matching level: species

strain history

doi: 10.13145/bacdive24008.20220920.7

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Ferrimonadaceae
  • genus: Ferrimonas
  • species: Ferrimonas sediminum
  • full scientific name: Ferrimonas sediminum Ji et al. 2013

@ref: 20561

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Ferrimonadaceae

genus: Ferrimonas

species: Ferrimonas sediminum

full scientific name: Ferrimonas sediminum Ji et al. 2013

strain designation: JYr13

type strain: yes

Morphology

cell morphology

  • @ref: 30700
  • gram stain: negative
  • cell length: 1.35 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 30700
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20561
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://bacmedia.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
20561positivegrowth16psychrophilic
30700positivegrowth16-42
30700positiveoptimum26.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
30700positivegrowth07-10
30700positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30700
  • oxygen tolerance: facultative anaerobe

halophily

  • @ref: 30700
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 3 %

observation

  • @ref: 67770
  • observation: quinones: MK-7, Q-7, Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3070016449alanine+carbon source
3070029987glutamate+carbon source
3070017596inosine+carbon source
3070024996lactate+carbon source
3070017748thymidine+carbon source
3070053423tween 40+carbon source
3070053426tween 80+carbon source
3070016704uridine+carbon source
307004853esculin+hydrolysis
3070017632nitrate+reduction

metabolite production

  • @ref: 30700
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
30700catalase+1.11.1.6
30700gelatinase+
30700cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20561coastal sediment of an amphioxus breeding zoneQingdao, China (36° 5' N 120° 32' E)ChinaCHNAsia36.0833120.533
67770Coastal sediment of an amphioxus breeding zone in QingdaoChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 20561
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20561
  • description: Ferrimonas sediminum strain JYr13 16S ribosomal RNA gene, partial sequence
  • accession: GU391222
  • length: 1416
  • database: ena
  • NCBI tax ID: 718193

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ferrimonas sediminum DSM 23317GCA_900100175scaffoldncbi718193
66792Ferrimonas sediminum strain DSM 23317718193.3wgspatric718193
66792Ferrimonas sediminum DSM 233172634166324draftimg718193

GC content

@refGC-contentmethod
2056159high performance liquid chromatography (HPLC)
3070059

External links

@ref: 20561

culture collection no.: DSM 23317, LMG 25564, JCM 17552

straininfo link

@refpassport
20218http://www.straininfo.net/strains/885124
20218http://www.straininfo.net/strains/854003

literature

  • topic: Phylogeny
  • Pubmed-ID: 22685103
  • title: Ferrimonas sediminum sp. nov., isolated from coastal sediment of an amphioxus breeding zone.
  • authors: Ji S, Zhao R, Li Z, Li B, Shi X, Zhang XH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.042408-0
  • year: 2012
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, China, Chordata, DNA, Bacterial/genetics, Fatty Acids/analysis, Ferric Compounds/metabolism, Gammaproteobacteria/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urljournalpubmedcatalogueID_cross_reference
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.StrainInfo introduces electronic passports for microorganisms.10.1016/j.syapm.2013.11.002Syst Appl Microbiol. 37: 42-50 201424321274
20561Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-23317Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23317)
2703110.1099/ijs.0.042408-022685103
30700Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172877604127031
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/