Strain identifier

BacDive ID: 159708

Type strain: Yes

Species: Marinicella sediminis

Strain Designation: F2

Strain history: <- Zongjun Du, Shandong Univ., China

NCBI tax ID(s): 1792834 (species)

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General

@ref: 66592

BacDive-ID: 159708

keywords: genome sequence, 16S sequence, Bacteria, aerobe, heterotroph, Gram-negative, rod-shaped, colony-forming

description: Marinicella sediminis F2 is an aerobe, heterotroph, Gram-negative bacterium that forms circular colonies and was isolated from marine sediment sample.

NCBI tax id

  • NCBI tax id: 1792834
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zongjun Du, Shandong Univ., China

doi: 10.13145/bacdive159708.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Marinicellaceae
  • genus: Marinicella
  • species: Marinicella sediminis
  • full scientific name: Marinicella sediminis Wang et al. 2018

@ref: 66592

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Gammaproteobacteria, not assigned to order

family: Gammaproteobacteria, not assigned to family

genus: Marinicella

species: Marinicella sediminis

strain designation: F2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66592negative3-4 µm0.4-0.6 µmrod-shapedno
69480negative97.5

colony morphology

  • @ref: 66592
  • colony size: 1 mm
  • colony color: pale yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Marine agar (MA) 2216

Culture and growth conditions

culture medium

  • @ref: 66592
  • name: Marine agar (MA) 2216
  • growth: yes

culture temp

@refgrowthtypetemperature
66592positiveoptimum33
66592nogrowth<10
66592nogrowth>37
66592positivegrowth10-37
67771positivegrowth33

culture pH

@refabilitytypepHPH range
66592positivegrowth6.5-9alkaliphile
66592positiveoptimum7.5-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66592aerobe
67771aerobe

nutrition type

  • @ref: 66592
  • type: heterotroph

spore formation

@refspore formationconfidence
66592no
69480no92.5
69481no100

halophily

@refsaltgrowthtested relationconcentration
66592NaClpositivegrowth1-8 %(w/v)
66592NaClpositiveoptimum3-4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6659253258citric acid-assimilation
6659216443D-tagatose+builds acid from
6659216988D-ribose+builds acid from
6659262318D-lyxose+builds acid from
66592potassium 5-dehydro-D-gluconate+builds acid from
6659212936D-galactose+carbon source
6659215824D-fructose+carbon source
6659216024D-mannose+carbon source
6659217716lactose+carbon source
6659212936D-galactose+energy source
6659215824D-fructose+energy source
6659216024D-mannose+energy source
6659217716lactose+energy source
665925291gelatin+hydrolysis
6659212936D-galactose+oxidation
6659215824D-fructose+oxidation
6659217164stachyose+oxidation
6659232323glucuronamide+oxidation
6659232528turanose+oxidation
6659262345L-rhamnose+oxidation

metabolite production

@refChebi-IDmetaboliteproduction
6659215688acetoinno
6659216136hydrogen sulfideno
6659235581indoleno

metabolite tests

  • @ref: 66592
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
66592arginine dihydrolase-3.5.3.6
66592beta-galactosidase-3.2.1.23
66592lysine decarboxylase-4.1.1.18
66592ornithine decarboxylase-4.1.1.17
66592tryptophan deaminase-4.1.99.1
66592urease-3.5.1.5
66592acid phosphatase+3.1.3.2
66592alkaline phosphatase+3.1.3.1
66592esterase (C 4)+
66592esterase Lipase (C 8)+
66592leucine arylamidase+3.4.11.1
66592trypsin+3.4.21.4

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66592C16:05
    66592C13:0 iso6
    66592C15:0 anteiso2.1
    66592C17:1 iso w9c4.7
    66592C15:1 iso H and/or C13:0 3OH4.8
    66592C15:0 iso46.6
    66592C17:0 iso5.2
    66592C11:0 iso5.9
    66592C16:1 w7c and/or iso-C15:0 2OH6.6
    66592C11:0 iso 3OH6.7
  • type of FA analysis: whole cell analysis
  • incubation medium: marine broth
  • incubation temperature: 33
  • incubation time: 2
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA40
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
66592marine sediment sample2015-03Weihai coast, Shandong ProvinceChinaCHNAsia36.909122.255marine agar 22165 days28The sediment sample was serially diluted to 10-4 with sterile seawater and 0.1 ml aliquots of each dilution were spread onto marine agar 2216. The isolate was grown aerobically at 28°C on MA for 5 days.
67771From marine sedimentWeihaiChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3046.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_369;96_1598;97_1906;98_2341;99_3046&stattab=map
  • Last taxonomy: Marinicella sediminis subclade
  • 16S sequence: KU647740
  • Sequence Identity:
  • Total samples: 1098
  • soil counts: 35
  • aquatic counts: 1016
  • animal counts: 21
  • plant counts: 26

Sequence information

16S sequences

  • @ref: 66592
  • description: Marinicella sediminis strain F2 16S ribosomal RNA gene, partial sequence
  • accession: KU647740
  • length: 1469
  • database: nuccore
  • NCBI tax ID: 1792834

Genome sequences

  • @ref: 66792
  • description: Marinicella sediminis F2
  • accession: GCA_002000055
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1792834

GC content

@refGC-contentmethod
6659248.1genome sequence analysis
6659248.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.5yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.398no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.443yes
69480spore-formingspore-formingAbility to form endo- or exosporesno92.5yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.455no
69480flagellatedmotile2+Ability to perform flagellated movementno70.875yes

External links

@ref: 66592

culture collection no.: KCTC 42953, MCCC 1H00149

literature

  • topic: Phylogeny
  • Pubmed-ID: 29781795
  • title: Marinicella sediminis sp. nov., isolated from marine sediment.
  • authors: Wang XQ, Li CM, Dunlap CA, Rooney AP, Du ZJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002839
  • year: 2018
  • mesh: Alcanivoraceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
66592Xiao-Qun Wang, Chang-Ming Li, Christopher A. Dunlap, Alejandro P. Rooney, Zong-Jun DuMarinicella sediminis sp. nov., isolated from marine sediment10.1099/ijsem.0.002839IJSEM 68: 2335-2339 201829781795
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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