Strain identifier

BacDive ID: 164248

Type strain: Yes

Species: Sphingomonas edaphi

Strain Designation: DAC4

Strain history: T. Seo; Dongguk Univ., South Korea; DAC4.

NCBI tax ID(s): 2315689 (species)

« back to strain detail view
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 8.1 (current version)

General

@ref: 67770

BacDive-ID: 164248

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

description: Sphingomonas edaphi DAC4 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Soil sample collected at Ahnmok Beach.

NCBI tax id

  • NCBI tax id: 2315689
  • Matching level: species

strain history

  • @ref: 67770
  • history: T. Seo; Dongguk Univ., South Korea; DAC4.

doi: 10.13145/bacdive164248.20230509.8.1

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 edaphi
  • full scientific name: Sphingomonas edaphi Kim et al. 2020

@ref: 67770

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas edaphi

full scientific name: Sphingomonas edaphi Kim et al. 2020

strain designation: DAC4

type strain: yes

Morphology

cell morphology

  • @ref: 69545
  • gram stain: negative
  • cell length: 1.0-1.6 µm
  • cell width: 0.4-0.7 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 69545
  • colony size: 0.5-1.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 69545
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth30mesophilic
69545positivegrowth18-42
69545positiveoptimum30mesophilic

culture pH

@refabilitytypepH
69545positivegrowth6.0-9.0
69545positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 69545
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
69545NaClpositivegrowth0 %(w/v)
69545NaClpositiveoptimum0 %

observation

@refobservation
67770quinones: Q-10
69545Strain DAC4T grew on R2A, nutrient agar and Luria-Bertani agar at 30 °C, but not on MacConkey agar or marine agar.
69545The major polar lipids are diphosphatidylglycerol and sphingoglycolipids, and the predominant polyamine is HSPD.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
69545168082-dehydro-D-gluconate-assimilation
6954527613amygdalin-assimilation
6954518305arbutin-assimilation
6954517108D-arabinose-assimilation
6954518333D-arabitol-assimilation
6954517634D-fructose-assimilation
6954512936D-galactose-assimilation
6954562318D-lyxose-assimilation
6954516899D-mannitol-assimilation
6954516024D-mannose-assimilation
6954516988D-ribose-assimilation
6954517924D-sorbitol-assimilation
6954516443D-tagatose-assimilation
6954565327D-xylose-assimilation
6954527689decanoate-assimilation
6954517113erythritol-assimilation
6954516813galactitol-assimilation
6954517754glycerol-assimilation
6954515443inulin-assimilation
6954530849L-arabinose-assimilation
6954518403L-arabitol-assimilation
6954518287L-fucose-assimilation
6954562345L-rhamnose-assimilation
6954517266L-sorbose-assimilation
6954517716lactose-assimilation
6954525115malate-assimilation
6954517306maltose-assimilation
695456731melezitose-assimilation
6954528053melibiose-assimilation
69545320061methyl alpha-D-glucopyranoside-assimilation
6954543943methyl alpha-D-mannoside-assimilation
6954574863methyl beta-D-xylopyranoside-assimilation
6954517268myo-inositol-assimilation
6954518401phenylacetate-assimilation
6954516634raffinose-assimilation
6954515963ribitol-assimilation
6954517814salicin-assimilation
6954553258sodium citrate-assimilation
6954517992sucrose-assimilation
6954527082trehalose-assimilation
6954527897tryptophan-energy source
6954517057cellobiose-fermentation
6954528847D-fucose-fermentation
6954517634D-glucose-fermentation
6954528066gentiobiose-fermentation
6954517234glucose-fermentation
6954532528turanose-fermentation
695454853esculin-hydrolysis
6954517632nitrate-reduction
69545581435-dehydro-D-gluconate+assimilation
6954517128adipate+assimilation
6954517634D-glucose+assimilation
6954516899D-mannitol+assimilation
6954530849L-arabinose+assimilation
6954517306maltose+assimilation
69545506227N-acetyl-D-glucosamine+assimilation
6954532032potassium gluconate+assimilation
6954528017starch+assimilation
6954528087glycogen+fermentation
6954517151xylitol+fermentation
695455291gelatin+hydrolysis

metabolite production

  • @ref: 69545
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 69545
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
69545catalase+1.11.1.6
69545cytochrome oxidase+1.9.3.1
69545alkaline phosphatase+3.1.3.1
69545esterase (C 4)+
69545esterase Lipase (C 8)+
69545lipase (C 14)+
69545leucine arylamidase+3.4.11.1
69545valine arylamidase+
69545cystine arylamidase+3.4.11.3
69545trypsin+3.4.21.4
69545acid phosphatase+3.1.3.2
69545naphthol-AS-BI-phosphohydrolase+
69545alpha-glucosidase+3.2.1.20
69545alpha-chymotrypsin-3.4.21.1
69545alpha-galactosidase-3.2.1.22
69545beta-galactosidase-3.2.1.23
69545beta-glucuronidase-3.2.1.31
69545beta-glucosidase-3.2.1.21
69545N-acetyl-beta-glucosaminidase-3.2.1.52
69545alpha-mannosidase-3.2.1.24
69545alpha-fucosidase-3.2.1.51
69545tryptophan deaminase-4.1.99.1
69545arginine dihydrolase-3.5.3.6
69545urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    69545ante-C 18 :0/C18 :2 w6 ,9c1
    69545C14:00.5
    69545C14:0 2OH0.6
    69545C14:1 w5c0.4
    69545C15:01.5
    69545C15:1 H/C13:0 3OH0.4
    69545C16 :1 w7c/C16 :1 w6c29.5
    69545C16:011.7
    69545C16:1 w5c3.3
    69545C17:01.1
    69545C17:1 w6c7.4
    69545C17:1 w8c1.3
    69545C18:00.6
    69545C18:1 2OH5.9
    69545C18:1 w5c0.5
    69545C18:1 w7c29.7
    69545C18:1 w7c 11-methyl4.3
    69545C8:0 3OH0.3
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.01
  • library/peak naming table: TSBA6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
67770Soil sample collected at Ahnmok BeachBusanRepublic of KoreaKORAsia
69545soil sample collected at Ahnmok Beach, BusanAhnmok Beach, BusanRepublic of KoreaKORAsia

Sequence information

16S sequences

  • @ref: 67770
  • description: Sphingomonas sp. strain DAC4 16S ribosomal RNA gene, partial sequence
  • accession: MF503624
  • length: 1416
  • database: ena
  • NCBI tax ID: 2315689

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
67770Sphingomonas edaphi DAC4GCA_003583725contigncbi2315689
69545genome sequenceQXTF00000000ncbi2315689

GC content

  • @ref: 67770
  • GC-content: 62.16
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno79.664no
flagellatedno96.729no
gram-positiveno96.537no
anaerobicno98.902no
aerobicyes89.395no
halophileno89.879no
spore-formingno96.041no
thermophileno96.07yes
glucose-utilyes73.802no
glucose-fermentno89.455no

External links

@ref: 67770

culture collection no.: JCM 32377, KCTC 62107

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny31596192Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea.Kim H, Chhetri G, Seo TInt J Syst Evol Microbiol10.1099/ijsem.0.0037802020Bacterial Typing Techniques, Base Composition, *Bathing Beaches, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny33146742Sphingomonas xanthus sp. nov., Isolated from Beach Soil.Kim H, Chhetri G, Seo TCurr Microbiol10.1007/s00284-020-02273-z2020Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology, *Sphingomonas/geneticsTranscriptome

Reference

@idauthorstitledoi/url
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69545Hyungdong Kim, Geeta Chhetri and Taegun SeoSphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea10.1099/ijsem.0.003780