Strain identifier

BacDive ID: 140978

Type strain: Yes

Species: Sphingomonas limnosediminicola

Strain Designation: 03SUJ6

Strain history: <- CN Seong, Sunchon Natl. Univ.

NCBI tax ID(s): 940133 (species)

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General

@ref: 43868

BacDive-ID: 140978

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

description: Sphingomonas limnosediminicola 03SUJ6 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from freshwater sediment of an artificial lake, Juam reservoir, Republic of Korea.

NCBI tax id

  • NCBI tax id: 940133
  • Matching level: species

strain history

@refhistory
67770C. N. Seong 03SUJ6.
67771<- CN Seong, Sunchon Natl. Univ.

doi: 10.13145/bacdive140978.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas limnosediminicola
  • full scientific name: Sphingomonas limnosediminicola Lee et al. 2017

@ref: 43868

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas limnosediminicola

strain designation: 03SUJ6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
43868negative0.6-1.0 µm0.2-0.4 µmrod-shapedyesgliding
67771negative

colony morphology

  • @ref: 43868
  • colony size: 1.5-2.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: R2A agar

pigmentation

@refproductionname
43868noFelxirubin-type pigments
43868yesCarotenoid pigment

Culture and growth conditions

culture medium

@refnamegrowth
43868LB (Luria-Bertani) MEDIUMno
43868Marine agar (MA)no
43868Nutrient agar (NA)yes
43868Plate count agaryes
43868Reasoner's 2A agar (R2A)yes
43868Tryptic soy agarno

culture temp

@refgrowthtypetemperaturerange
43868positivegrowth15-37
43868positiveoptimum25-30mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
43868positivegrowth6.0-8.0
43868positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43868aerobe
67771aerobe

spore formation

  • @ref: 43868
  • spore formation: no

halophily

  • @ref: 43868
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0 %(w/v)

observation

  • @ref: 43868
  • observation: quinone Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4386817128adipate-assimilation
4386822599arabinose-assimilation
4386827689decanoate-assimilation
4386817234glucose-assimilation
4386825115malate-assimilation
43868maltose hydrate-assimilation
4386829864mannitol-assimilation
4386837684mannose-assimilation
43868506227N-acetylglucosamine-assimilation
4386818401phenylacetate-assimilation
4386832032potassium gluconate-assimilation
4386828757fructose-builds acid from
4386828260galactose-builds acid from
4386817234glucose-builds acid from
4386817716lactose-builds acid from
4386817306maltose-builds acid from
4386829864mannitol-builds acid from
4386837684mannose-builds acid from
4386826546rhamnose-builds acid from
4386817992sucrose-builds acid from
4386827082trehalose-builds acid from
4386818222xylose-builds acid from
4386816947citrate-carbon source
4386817234glucose-fermentation
4386829016arginine-hydrolysis
4386885146carboxymethylcellulose-hydrolysis
43868casein-hydrolysis
4386817029chitin-hydrolysis
4386816991dna-hydrolysis
438685291gelatin-hydrolysis
4386828017starch-hydrolysis
4386853424tween 20-hydrolysis
4386853426tween 80-hydrolysis
4386816199urea-hydrolysis
4386815318xanthine-hydrolysis
4386817632nitrate-reduction
43868309162-oxoglutarate+assimilation
4386817203L-proline+assimilation
4386873784glycyl-l-glutamate+assimilation
438684853esculin+hydrolysis
4386817925alpha-D-glucose+/-assimilation
4386873706bromosuccinate+/-assimilation
4386816383cis-aconitate+/-assimilation
4386833801D-saccharate+/-assimilation
43868167244-hydroxybutyrate+/-assimilation
4386829042glucose 1-phosphate+/-assimilation
4386828087glycogen+/-assimilation
43868L-alanine 4-nitroanilide+/-assimilation
4386873786L-alanylglycine+/-assimilation
4386829985L-glutamate+/-assimilation
4386826490quinate+/-assimilation
4386830031succinate+/-assimilation
4386827082trehalose+/-assimilation
4386832528turanose+/-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
438682637amikacinyesyes30 µg (disc)
4386817698chloramphenicolyesyes30 µg (disc)
4386848923erythromycinyesyes15 µg (disc)
4386827902tetracyclineyesyes30 µg (disc)
4386828001vancomycinyesyes30 µg (disc)
4386828971ampicillinyesyes10 µg (disc)
4386817833gentamicinyesyes10 µg (disc)
43868100147nalidixic acidyesyes30 µg (disc)
4386817334penicillinyesyes10 Unit (disc)
4386817076streptomycinyesyes10 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4386815688acetoinno
4386816136hydrogen sulfideno
4386835581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4386817234glucose-
4386815688acetoin-

enzymes

@refvalueactivityec
43868catalase+1.11.1.6
43868cytochrome oxidase+1.9.3.1
43868urease-3.5.1.5
43868esterase Lipase (C 8)+
43868leucine arylamidase+3.4.11.1
43868acid phosphatase+/-3.1.3.2
43868alkaline phosphatase+/-3.1.3.1
43868esterase (C 4)+/-
43868valine arylamidase+/-
43868naphthol-AS-BI-phosphohydrolase+/-
43868alpha-chymotrypsin-3.4.21.1
43868cystine arylamidase-3.4.11.3
43868alpha-fucosidase-3.2.1.51
43868alpha-galactosidase-3.2.1.22
43868beta-galactosidase-3.2.1.23
43868N-acetyl-beta-glucosaminidase-3.2.1.52
43868alpha-glucosidase-3.2.1.20
43868beta-glucosidase-3.2.1.21
43868beta-glucuronidase-3.2.1.31
43868lipase (C 14)-
43868alpha-mannosidase-3.2.1.24
43868trypsin-3.4.21.4

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43868C14:02.6
    43868C14:0 2OH1.6
    43868C16:026.9
    43868C16:1ω5c1.2
    43868C16:1ω7c / C16:1ω6c2.9
    43868C17:01.2
    43868C17:1ω6c7.3
    43868C18:08.1
    43868C18:1 2OH5.4
    43868C18:1ω7c / C18:1ω6c38.4
    4386811-methyl C18:1ω7c1.3
    43868C18:1ω9c3.1
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
43868freshwater sediment of an artificial lake, Juam reservoir, Republic of KoreaJuam reservoirRepublic of KoreaKORAsia35127.167R2A agar7 days25
67770Freshwater sediment of Juam reservoirRepublic of KoreaKORAsia
67771From fresh waterWoopoRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

Sequence information

16S sequences

  • @ref: 43868
  • description: 16S rRNA gene sequence
  • accession: HQ436498
  • database: nuccore

GC content

  • @ref: 43868
  • GC-content: 65
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 43868

culture collection no.: KCTC 23331, JCM 17543

literature

  • topic: Phylogeny
  • Pubmed-ID: 28820093
  • title: Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments.
  • authors: Lee JH, Kim DI, Choe HN, Lee SD, Seong CN
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002029
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistry
  • 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
43868Ji Hee Lee, Dae In Kim, Han Na Choe, Soon Dong Lee, Chi Nam SeongSphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments10.1099/ijsem.0.002029IJSEM 67: 2834-2841 201728820093
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc