Strain identifier

BacDive ID: 140991

Type strain: Yes

Species: Sphingomonas silvisoli

Strain Designation: RP18

Strain history: T.-Y. Ahn; Dept. of Microbiol., Coll. of Nat. Sci., Dankook Univ., South Korea; RP18.

NCBI tax ID(s): 1795387 (species)

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General

@ref: 43878

BacDive-ID: 140991

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

description: Sphingomonas silvisoli RP18 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from forest soil in Gwang-ju, Republic of Korea.

NCBI tax id

  • NCBI tax id: 1795387
  • Matching level: species

strain history

  • @ref: 67770
  • history: T.-Y. Ahn; Dept. of Microbiol., Coll. of Nat. Sci., Dankook Univ., South Korea; RP18.

doi: 10.13145/bacdive140991.20230509.8.1

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 silvisoli
  • full scientific name: Sphingomonas silvisoli Ko et al. 2017

@ref: 43878

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas silvisoli

strain designation: RP18

type strain: yes

Morphology

cell morphology

  • @ref: 43878
  • gram stain: negative
  • cell length: 0.8-1.2 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43878
  • colony color: yellow
  • colony shape: circular
  • medium used: modified R2A agar

pigmentation

  • @ref: 43878
  • production: yes
  • name: Carotenoid pigments

Culture and growth conditions

culture medium

@refnamegrowthcomposition
43878LB (Luria-Bertani) MEDIUMno
43878MacConkey agarno
43878modified R2A agaryes1.5x concentrated; 4.5 g/L R2A broth, 15 g/L agar
43878Nutrient agar (NA)yes
43878Plate count agaryes
43878Reasoner's 2A agar (R2A)yes
43878Tryptic soy agarno

culture temp

@refgrowthtypetemperaturerange
43878positivegrowth15-30
43878positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
43878positivegrowth6.0-7.0
43878positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43878
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43878NaClpositiveoptimum0 %(w/v)
43878NaClpositivegrowth0.25 %(w/v)

observation

@refobservation
43878quinone Q-10
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4387865327D-xylose-builds acid from
4387828260galactose-builds acid from
4387828066gentiobiose-builds acid from
4387830849L-arabinose-builds acid from
4387816634raffinose-builds acid from
4387826546rhamnose-builds acid from
4387832528turanose-builds acid from
4387885146carboxymethylcellulose-hydrolysis
43878casein-hydrolysis
438785291gelatin-hydrolysis
4387817895L-tyrosine-hydrolysis
4387828017starch-hydrolysis
4387853424tween 20-hydrolysis
4387853423tween 40-hydrolysis
4387853426tween 80-hydrolysis
4387817632nitrate-reduction
4387827613amygdalin+builds acid from
4387818305arbutin+builds acid from
4387817057cellobiose+builds acid from
4387828847D-fucose+builds acid from
4387862318D-lyxose+builds acid from
438784853esculin+builds acid from
4387828757fructose+builds acid from
4387817234glucose+builds acid from
4387817716lactose+builds acid from
4387817306maltose+builds acid from
4387837684mannose+builds acid from
4387828053melibiose+builds acid from
43878320061methyl alpha-D-glucopyranoside+builds acid from
4387843943methyl alpha-D-mannoside+builds acid from
43878506227N-acetylglucosamine+builds acid from
4387817814salicin+builds acid from
4387828017starch+builds acid from
4387817992sucrose+builds acid from
4387827082trehalose+builds acid from
438784853esculin+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4387828971ampicillinyesyes10 µg (disc)
4387817698chloramphenicolyesyes50 µg (disc)
4387817833gentamicinyesyes30 µg (disc)
438786104kanamycinyesyes30 µg (disc)
4387818208penicillin gyesyes10 Unit (disc)
438788309polymyxin byesyes300 Unit (disc)
4387827902tetracyclineyesyes10 µg (disc)
4387817076streptomycinyesyes10 µg (disc)

enzymes

@refvalueactivityec
43878catalase+1.11.1.6
43878cytochrome oxidase-1.9.3.1
43878acid phosphatase+3.1.3.2
43878alkaline phosphatase+3.1.3.1
43878alpha-glucosidase+3.2.1.20
43878beta-glucosidase+3.2.1.21
43878cystine arylamidase+3.4.11.3
43878esterase (C 4)+
43878esterase Lipase (C 8)+
43878leucine arylamidase+3.4.11.1
43878naphthol-AS-BI-phosphohydrolase+
43878valine arylamidase+
43878alpha-chymotrypsin-3.4.21.1
43878alpha-galactosidase-3.2.1.22
43878beta-glucuronidase-3.2.1.31
43878lipase (C 14)-
43878N-acetyl-beta-glucosaminidase-3.2.1.52
43878trypsin-3.4.21.4
43878beta-galactosidase-3.2.1.23

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43878C14:0 2OH6.6
    43878C15:0 2OH4.4
    43878C16:015.3
    43878C16:0 2OH1.8
    43878C16:1ω7 / C16:1ω612.5
    43878C17:01.2
    43878C17:1ω6c8.8
    43878C18:01.1
    43878C18:1ω5c1
    43878C18:1ω7? / C18:1ω6?39.8
    4387811-methyl C18:1ω7c4.6
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 5
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
43878forest soil in Gwang-ju, Republic of KoreaGwang-juRepublic of KoreaKORAsiamodified R2A agar1.5x concentrated; 4.5 g/L R2A broth, 15 g/L agar5 days30
67770Forest soil in Gwang-juRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_45522.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_20363;97_25992;98_33009;99_45522&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: KU597283
  • Sequence Identity:
  • Total samples: 2204
  • soil counts: 281
  • aquatic counts: 1467
  • animal counts: 263
  • plant counts: 193

Sequence information

16S sequences

  • @ref: 43878
  • description: 16S rRNA gene sequence
  • accession: KU597283
  • database: nuccore

GC content

  • @ref: 43878
  • GC-content: 61.5
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43878

culture collection no.: KACC 18914, JCM 31801

literature

  • topic: Phylogeny
  • Pubmed-ID: 28853689
  • title: Sphingomonas silvisoli sp. nov., isolated from forest soil.
  • authors: Ko Y, Hwang WM, Kim M, Kang K, Ahn TY
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002001
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, 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
43878Yongseok Ko, Woon Mo Hwang, Minsun Kim, Keunsoo Kang, Tae-Young AhnSphingomonas silvisoli sp. nov., isolated from forest soil10.1099/ijsem.0.002001IJSEM 67: 2704-2710 201728853689
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/