Strain identifier

BacDive ID: 133409

Type strain: Yes

Species: Chthonobacter albigriseus

Strain Designation: ED7

Strain history: <- Taeyoung Ahn, Dankook Univ.

NCBI tax ID(s): 1683161 (species)

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General

@ref: 25245

BacDive-ID: 133409

keywords: genome sequence, 16S sequence, Bacteria, aerobe, oligotroph, Gram-negative, rod-shaped

description: Chthonobacter albigriseus ED7 is an aerobe, oligotroph, Gram-negative bacterium that was isolated from grass-field soil near a stream.

NCBI tax id

  • NCBI tax id: 1683161
  • Matching level: species

strain history

@refhistory
67770T.-Y. Ahn; Dankook Univ., South Korea; ED7.
67771<- Taeyoung Ahn, Dankook Univ.

doi: 10.13145/bacdive133409.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Pleomorphomonadaceae
  • genus: Chthonobacter
  • species: Chthonobacter albigriseus
  • full scientific name: Chthonobacter albigriseus Kim et al. 2017

@ref: 25245

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Methylocystaceae

genus: Chthonobacter

species: Chthonobacter albigriseus

strain designation: ED7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25245negative1.0-1.8 µm0.8-1.0 µmrod-shapedno
69480yes94.451
69480negative99.996

colony morphology

  • @ref: 25245
  • colony color: greyish-white
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthcomposition
25245Reasoner's 2A agar (R2A)yes
25245minimal medium Kyessupplemented with methylamine or methanol
25245tryptic soy agar (TSA)yes
25245nutritient agar (NA)yes

culture temp

@refgrowthtypetemperaturerange
25245positivegrowth20-42
25245positiveoptimum30-35mesophilic
25245nogrowth4psychrophilic
25245nogrowth45thermophilic
67770positivegrowth30mesophilic
67771positivegrowth28mesophilic

culture pH

  • @ref: 25245
  • ability: positive
  • type: optimum
  • pH: 7.5-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25245aerobe
67771aerobe

nutrition type

  • @ref: 25245
  • type: oligotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.964

halophily

  • @ref: 25245
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 0 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2524518305arbutin-assimilation
2524585146carboxymethylcellulose-degradation
25245casein-degradation
2524515963ribitol-assimilation
2524518333D-arabitol-assimilation
252456731melezitose-assimilation
2524516443D-tagatose-assimilation
2524532528turanose-assimilation
2524516991dna-degradation
2524517113erythritol-assimilation
2524516813galactitol-assimilation
2524528066gentiobiose-assimilation
2524517754glycerol-assimilation
2524517268myo-inositol-assimilation
2524515443inulin-assimilation
2524518403L-arabitol-assimilation
2524517266L-sorbose-assimilation
2524517716lactose-assimilation
2524528053melibiose-assimilation
25245320061methyl alpha-D-glucopyranoside-assimilation
2524543943methyl alpha-D-mannoside-assimilation
25245506227N-acetylglucosamine-assimilation
25245potassium 2-dehydro-D-gluconate-assimilation
2524532032potassium gluconate-assimilation
2524516634raffinose-assimilation
2524528017starch-degradation
2524517992sucrose-assimilation
2524527082trehalose-assimilation
2524553426tween 80-degradation
2524517151xylitol-assimilation
252452511agarose+degradation
2524517057cellobiose+assimilation
2524517108D-arabinose+assimilation
2524515824D-fructose+assimilation
2524528847D-fucose+assimilation
2524512936D-galactose+assimilation
2524517634D-glucose+assimilation
2524562318D-lyxose+assimilation
2524516024D-mannose+assimilation
2524516988D-ribose+assimilation
2524517924D-sorbitol+assimilation
2524565327D-xylose+assimilation
252454853esculin+hydrolysis
252454853esculin+assimilation
2524530849L-arabinose+assimilation
2524518287L-fucose+assimilation
2524562345L-rhamnose+assimilation
2524565328L-xylose+assimilation
2524525115malate+assimilation
2524517306maltose+assimilation
25245potassium 5-dehydro-D-gluconate+assimilation
2524517814salicin+assimilation

enzymes

@refvalueactivityec
25245acid phosphatase-3.1.3.2
25245alkaline phosphatase-3.1.3.1
25245alpha-chymotrypsin-3.4.21.1
25245alpha-fucosidase-3.2.1.51
25245alpha-galactosidase+3.2.1.22
25245alpha-glucosidase-3.2.1.20
25245alpha-mannosidase-3.2.1.24
25245beta-galactosidase+3.2.1.23
25245beta-glucosidase-3.2.1.21
25245beta-glucuronidase-3.2.1.31
25245cystine arylamidase-3.4.11.3
25245esterase (C 4)+
25245esterase Lipase (C 8)-
25245leucine arylamidase+3.4.11.1
25245lipase (C 14)-
25245N-acetyl-beta-glucosaminidase-3.2.1.52
25245naphthol-AS-BI-phosphohydrolase+
25245trypsin+3.4.21.4
25245urease+3.5.1.5
25245valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25245C15:0 anteiso1.5
    25245C12:01.3
    25245C14:0 3OH / C16:1 iso I11.1
    25245C16:03.8
    25245C16:0 3OH6.4
    25245C18:04.3
    25245C18:0 3OH2
    25245C18:1ω7c / C18:1ω6c57.5
    25245C18:1ω7c 11-methyl6.5
    25245C18:1ω9c1.8
    25245C18:0 iso3.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • system: MIS MIDI
  • method/protocol: Sasser 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
25245grass-field soil near a streamCheonanRepublic of KoreaKORAsia36.8167127.167R2A agar0.5 g/l yeast extract, 0.5 g/l meat peptone, 0.5 g/l casamino acids, 0.5 g/l glucose, 0.5 g/l starch, 0.3 g/l dipotassium hydrogen phosphate, 0.05 g/l magnesium sulphate, 0.3 g/l sodium pyruvate3 days30standard dilution plating technique
67770Grass-field soil in CheonanRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_90036.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2225;97_4171;98_55610;99_90036&stattab=map
  • Last taxonomy: Chthonobacter albigriseus subclade
  • 16S sequence: KP289282
  • Sequence Identity:
  • Total samples: 414
  • soil counts: 116
  • aquatic counts: 158
  • animal counts: 24
  • plant counts: 116

Sequence information

16S sequences

  • @ref: 25245
  • description: Methylocystaceae bacterium ED7 16S ribosomal RNA gene, partial sequence
  • accession: KP289282
  • length: 1404
  • database: nuccore
  • NCBI tax ID: 1683161

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chthonobacter albigriseus strain KCTC 424501683161.3wgspatric1683161
67770Chthonobacter albigriseus KCTC 42450GCA_013839445scaffoldncbi1683161

GC content

  • @ref: 67770
  • GC-content: 71.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes80.873yes
gram-positiveno98.617yes
anaerobicno98.139yes
aerobicyes90.078no
halophileno90.003yes
spore-formingno95.964no
glucose-utilyes94.393yes
flagellatedno71.88yes
thermophileno95.278no
glucose-fermentno90.987no

External links

@ref: 25245

culture collection no.: JCM 30603, KCTC 42450

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28475028Chthonobacter albigriseus gen. nov., sp. nov., isolated from grass-field soil.Kim D, Kang K, Ahn TYInt J Syst Evol Microbiol10.1099/ijsem.0.0016952017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Methylocystaceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny33655406Chthonobacter rhizosphaerae sp. nov., a bacterium isolated from rhizosphere soil of Citrus sinenesis.Liu XM, Zhou XK, Li YD, Jiang JX, Dong LM, Fang BZ, Li WJ, Duan YQArch Microbiol10.1007/s00203-021-02217-62021Bacterial Typing Techniques, Base Composition/genetics, Citrus sinensis/*microbiology, DNA, Bacterial/genetics, Methylocystaceae/*classification/*genetics/isolation & purification, Phospholipids/analysis/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

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
25245D. K. Kim, K.,Ahn, T. Y.Chthonobacter albigriseus gen. nov., sp. nov., isolated from grass-field soil10.1099/ijsem.0.001695IJSEM 67: 883-888 201728475028
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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