Strain identifier

BacDive ID: 141112

Type strain: Yes

Species: Ramlibacter alkalitolerans

Strain Designation: CJ661

Strain history: C.-J. Cha; Chung-Ang Univ., South Korea; CJ661.

NCBI tax ID(s): 2039631 (species)

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General

@ref: 44020

BacDive-ID: 141112

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

description: Ramlibacter alkalitolerans CJ661 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from ginseng soil.

NCBI tax id

  • NCBI tax id: 2039631
  • Matching level: species

strain history

  • @ref: 67770
  • history: C.-J. Cha; Chung-Ang Univ., South Korea; CJ661.

doi: 10.13145/bacdive141112.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Ramlibacter
  • species: Ramlibacter alkalitolerans
  • full scientific name: Ramlibacter alkalitolerans Lee and Cha 2017

@ref: 44020

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Ramlibacter

species: Ramlibacter alkalitolerans

strain designation: CJ661

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
44020negative2 µm1 µmrod-shapedno
69480yes98.11
69480negative99.998

colony morphology

  • @ref: 44020
  • colony color: white, become red-brown with aging
  • colony shape: circular
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 44020
  • name: Reasoners 2A agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
44020positivegrowth25-37mesophilic
44020positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
44020positivegrowth5.0-10.0alkaliphile
44020positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 44020
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.984

halophily

  • @ref: 44020
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

@refobservation
44020orange fluorescence typical for the Nile red complex with PHA appears
44020the isoprenoid quinone is Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4402017128adipate-assimilation
4402027689decanoate-assimilation
4402027613amygdalin-builds acid from
4402018305arbutin-builds acid from
4402017108D-arabinose-builds acid from
4402018333D-arabitol-builds acid from
4402017057cellobiose-builds acid from
4402028847D-fucose-builds acid from
4402062318D-lyxose-builds acid from
4402016899D-mannitol-builds acid from
4402017924D-sorbitol-builds acid from
4402016443D-tagatose-builds acid from
4402016813galactitol-builds acid from
4402017113erythritol-builds acid from
4402028066gentiobiose-builds acid from
4402017754glycerol-builds acid from
4402028087glycogen-builds acid from
4402017268myo-inositol-builds acid from
4402015443inulin-builds acid from
4402018403L-arabitol-builds acid from
4402018287L-fucose-builds acid from
4402017266L-sorbose-builds acid from
4402065328L-xylose-builds acid from
4402017716lactose-builds acid from
4402017306maltose-builds acid from
440206731melezitose-builds acid from
4402028053melibiose-builds acid from
4402043943methyl alpha-D-mannoside-builds acid from
4402074863methyl beta-D-xylopyranoside-builds acid from
44020potassium 2-dehydro-D-gluconate-builds acid from
4402032032potassium gluconate-builds acid from
4402016634raffinose-builds acid from
4402017814salicin-builds acid from
4402028017starch-builds acid from
4402017992sucrose-builds acid from
4402027082trehalose-builds acid from
4402032528turanose-builds acid from
4402017151xylitol-builds acid from
4402062968cellulose-hydrolysis
4402028017starch-hydrolysis
4402017634D-glucose+assimilation
4402016899D-mannitol+assimilation
4402016024D-mannose+assimilation
4402030849L-arabinose+assimilation
4402025115malate+assimilation
4402017306maltose+assimilation
44020506227N-acetylglucosamine+assimilation
4402018401phenylacetate+assimilation
4402032032potassium gluconate+assimilation
4402053258sodium citrate+assimilation
4402015963ribitol+builds acid from
4402015824D-fructose+builds acid from
4402012936D-galactose+builds acid from
4402017634D-glucose+builds acid from
4402016024D-mannose+builds acid from
4402016988D-ribose+builds acid from
4402065327D-xylose+builds acid from
44020esculin ferric citrate+builds acid from
4402030849L-arabinose+builds acid from
4402062345L-rhamnose+builds acid from
44020506227N-acetylglucosamine+builds acid from
44020potassium 5-dehydro-D-gluconate+builds acid from
44020181014-hydroxyphenylacetic acid+carbon source
4402015963ribitol+carbon source
4402017925alpha-D-glucose+carbon source
4402017665alpha-D-glucose 6-phosphate+carbon source
440208295beta-hydroxybutyrate+carbon source
4402017057cellobiose+carbon source
4402016383cis-aconitate+carbon source
4402016947citrate+carbon source
4402015570D-alanine+carbon source
4402017108D-arabinose+carbon source
4402015824D-fructose+carbon source
4402015895D-galactonic acid lactone+carbon source
4402018024D-galacturonic acid+carbon source
440208391D-gluconate+carbon source
4402015748D-glucuronate+carbon source
4402016899D-mannitol+carbon source
4402016024D-mannose+carbon source
4402027605D-psicose+carbon source
4402033801D-saccharate+carbon source
4402017924D-sorbitol+carbon source
4402023652dextrin+carbon source
4402028066gentiobiose+carbon source
4402029042glucose 1-phosphate+carbon source
4402017754glycerol+carbon source
4402028087glycogen+carbon source
4402017596inosine+carbon source
44020L-alanine 4-nitroanilide+carbon source
4402073786L-alanylglycine+carbon source
4402030849L-arabinose+carbon source
4402017196L-asparagine+carbon source
4402029991L-aspartate+carbon source
4402018287L-fucose+carbon source
4402029985L-glutamate+carbon source
4402062345L-rhamnose+carbon source
4402024996lactate+carbon source
4402017716lactose+carbon source
440206359lactulose+carbon source
4402017306maltose+carbon source
44020320061methyl alpha-D-glucopyranoside+carbon source
4402051850methyl pyruvate+carbon source
44020506227N-acetylglucosamine+carbon source
4402017272propionate+carbon source
4402017822serine+carbon source
44020143136succinamate+carbon source
4402017992sucrose+carbon source
4402063528thymidine 5'-monophosphate+carbon source
4402032528turanose+carbon source
4402053423tween 40+carbon source
4402053426tween 80+carbon source
4402027248urocanic acid+carbon source
44020casein+hydrolysis
440204853esculin+hydrolysis
440205291gelatin+hydrolysis
4402017632nitrate+reduction

metabolite production

  • @ref: 44020
  • Chebi-ID: 16301
  • metabolite: nitrite
  • production: yes

enzymes

@refvalueactivityec
44020esterase (C 4)+
44020esterase Lipase (C 8)+
44020lipase (C 14)+
44020valine arylamidase+
44020naphthol-AS-BI-phosphohydrolase+
44020alpha-galactosidase+3.2.1.22
44020arginine dihydrolase-3.5.3.6
44020urease-3.5.1.5
44020alkaline phosphatase-3.1.3.1
44020trypsin-3.4.21.4
44020alpha-chymotrypsin-3.4.21.1
44020acid phosphatase-3.1.3.2
44020beta-galactosidase-3.2.1.23
44020beta-glucuronidase-3.2.1.31
44020alpha-glucosidase-3.2.1.20
44020beta-glucosidase-3.2.1.21
44020N-acetyl-beta-glucosaminidase-3.2.1.52
44020alpha-mannosidase-3.2.1.24
44020beta-D-fucosidase-3.2.1.38

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44020C15:0 anteiso0.7
    44020C10:0 3OH4.4
    44020C12:03.1
    44020C14:04.4
    44020C14:1ω5c1.1
    44020C16:032.1
    44020C16:1ω6c and/or C16:1ω7c44.4
    44020C17:0 cyclo1
    44020C18:1ω7c and/or C18:1ω6c7.3
    44020C17:1 iso ω5c0.9
  • type of FA analysis: whole cell analysis
  • incubation temperature: 30
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6 6.10
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture durationenrichment culture temperatureisolation procedure
44020ginseng soilAnseongRepublic of KoreaKORAsia37.99931273 days30R2A agar (BD) and preserved with glycerol suspension (30 %, v/v)
67770Soil of ginseng in AnseongRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_47440.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_5619;97_6770;98_28588;99_47440&stattab=map
  • Last taxonomy: Ramlibacter
  • 16S sequence: KF740333
  • Sequence Identity:
  • Total samples: 227
  • soil counts: 143
  • aquatic counts: 13
  • animal counts: 8
  • plant counts: 63

Sequence information

16S sequences

  • @ref: 44020
  • description: 16S rRNA gene sequence
  • accession: KF740333
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ramlibacter alkalitolerans KACC 19305GCA_016722765contigncbi2039631
66792Ramlibacter alkalitolerans strain KACC 193052039631.3wgspatric2039631

GC content

  • @ref: 44020
  • GC-content: 65.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes83.264no
gram-positiveno98.933yes
anaerobicno98.032yes
aerobicyes81.058yes
halophileno95.256yes
spore-formingno94.947no
glucose-utilno63.393no
flagellatedno63.518yes
thermophileno96.707yes
glucose-fermentno89.338no

External links

@ref: 44020

culture collection no.: KACC 19305, JCM 32081

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28920850Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng.Lee DH, Cha CJInt J Syst Evol Microbiol10.1099/ijsem.0.0023422017Alkalies, Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny35305190Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea.Dahal RH, Kim J, Chaudhary DK, Le TTN, Kim DU, Jang H, Kim JAntonie Van Leeuwenhoek10.1007/s10482-022-01721-z2022Agriculture, Bacterial Typing Techniques, *Comamonadaceae, DNA, Bacterial/genetics, Fatty Acids, Humans, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Soil MicrobiologyPathogenicity

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
44020Do-Hoon Lee, Chang-Jun ChaRamlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng10.1099/ijsem.0.002342IJSEM 67: 4619-4623 201728920850
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/
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