Strain identifier

BacDive ID: 140851

Type strain: Yes

Species: Rhizobacter profundi

Strain Designation: DS48-6-5

NCBI tax ID(s): 1550730 (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 5:
version 4.1:
version 4:
version 8.1 (current version)

General

@ref: 43662

BacDive-ID: 140851

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

description: Rhizobacter profundi DS48-6-5 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from Sediment sample taken from Daechung Reservoir, 48 m depth.

NCBI tax id

  • NCBI tax id: 1550730
  • Matching level: species

doi: 10.13145/bacdive140851.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Rhizobacter
  • species: Rhizobacter profundi
  • full scientific name: Rhizobacter profundi Jin et al. 2016

@ref: 43662

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiales, not assigned to family

genus: Rhizobacter

species: Rhizobacter profundi

strain designation: DS48-6-5

type strain: yes

Morphology

cell morphology

  • @ref: 43662
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

colony morphology

  • @ref: 43662
  • colony color: Brownish
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 43662
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

  • @ref: 43662
  • growth: positive
  • type: growth
  • temperature: 8-30

culture pH

@refabilitytypepHPH range
43662positivegrowth6-9alkaliphile
43662positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43662
  • oxygen tolerance: aerobe

halophily

  • @ref: 43662
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 1-5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43662168082-dehydro-D-gluconate-builds acid from
4366215963ribitol-builds acid from
4366227613amygdalin-builds acid from
4366222605arabinitol-builds acid from
4366217057cellobiose-builds acid from
4366216813galactitol-builds acid from
4366217113erythritol-builds acid from
436624853esculin-builds acid from
4366228757fructose-builds acid from
4366228260galactose-builds acid from
4366228066gentiobiose-builds acid from
4366224265gluconate-builds acid from
4366217234glucose-builds acid from
4366217754glycerol-builds acid from
4366215443inulin-builds acid from
4366265328L-xylose-builds acid from
4366217716lactose-builds acid from
4366237684mannose-builds acid from
436626731melezitose-builds acid from
4366228053melibiose-builds acid from
4366274863methyl beta-D-xylopyranoside-builds acid from
4366226546rhamnose-builds acid from
4366233942ribose-builds acid from
4366230911sorbitol-builds acid from
4366227922sorbose-builds acid from
4366217151xylitol-builds acid from
43662168082-dehydro-D-gluconate-carbon source
43662167632-oxobutanoate-carbon source
43662286442-oxopentanoate-carbon source
43662620642,3-butanediol-carbon source
43662161933-hydroxybenzoate-carbon source
43662182404-hydroxy-L-proline-carbon source
43662178794-hydroxybenzoate-carbon source
43662181014-hydroxyphenylacetic acid-carbon source
43662581435-dehydro-D-gluconate-carbon source
4366230089acetate-carbon source
4366217128adipate-carbon source
4366215963ribitol-carbon source
4366240585alpha-cyclodextrin-carbon source
4366236219alpha-lactose-carbon source
43662645522-hydroxybutyrate-carbon source
436628295beta-hydroxybutyrate-carbon source
4366227689decanoate-carbon source
4366216383cis-aconitate-carbon source
4366216947citrate-carbon source
4366217057cellobiose-carbon source
4366215824D-fructose-carbon source
4366215895D-galactonic acid lactone-carbon source
4366212936D-galactose-carbon source
4366218024D-galacturonic acid-carbon source
436628391D-gluconate-carbon source
4366217784D-glucosaminic acid-carbon source
4366217634D-glucose-carbon source
4366214314D-glucose 6-phosphate-carbon source
4366215748D-glucuronate-carbon source
4366216024D-mannose-carbon source
4366228053melibiose-carbon source
4366227605D-psicose-carbon source
4366216634raffinose-carbon source
4366216988D-ribose-carbon source
4366233801D-saccharate-carbon source
4366216523D-serine-carbon source
4366217924D-sorbitol-carbon source
4366216551D-trehalose-carbon source
4366223652dextrin-carbon source
4366216449dl-alanine-carbon source
4366217126DL-carnitine-carbon source
4366217113erythritol-carbon source
4366216000ethanolamine-carbon source
4366216865gamma-aminobutyric acid-carbon source
43662167244-hydroxybutyrate-carbon source
4366228066gentiobiose-carbon source
4366229042glucose 1-phosphate-carbon source
4366232323glucuronamide-carbon source
4366217754glycerol-carbon source
4366214336glycerol 1-phosphate-carbon source
4366228087glycogen-carbon source
4366273804glycyl L-aspartic acid-carbon source
4366217596inosine-carbon source
4366217240itaconate-carbon source
4366221217L-alaninamide-carbon source
4366273786L-alanylglycine-carbon source
4366230849L-arabinose-carbon source
4366218403L-arabitol-carbon source
4366217196L-asparagine-carbon source
4366229991L-aspartate-carbon source
4366218287L-fucose-carbon source
4366229985L-glutamate-carbon source
4366215971L-histidine-carbon source
4366215603L-leucine-carbon source
4366215729L-ornithine-carbon source
4366217295L-phenylalanine-carbon source
4366217203L-proline-carbon source
4366218183L-pyroglutamic acid-carbon source
4366262345L-rhamnose-carbon source
4366217115L-serine-carbon source
4366216857L-threonine-carbon source
436626359lactulose-carbon source
4366225115malate-carbon source
4366215792malonate-carbon source
4366217306maltose-carbon source
4366229864mannitol-carbon source
4366237657methyl D-glucoside-carbon source
4366251850methyl pyruvate-carbon source
4366217268myo-inositol-carbon source
4366228037N-acetylgalactosamine-carbon source
43662506227N-acetylglucosamine-carbon source
4366273784glycyl-l-glutamate-carbon source
4366218401phenylacetate-carbon source
4366250048phenylethylamine-carbon source
4366217272propionate-carbon source
4366217148putrescine-carbon source
4366226490quinate-carbon source
4366217814salicin-carbon source
4366241865sebacic acid-carbon source
436629300suberic acid-carbon source
43662143136succinamate-carbon source
4366217992sucrose-carbon source
4366217748thymidine-carbon source
4366232528turanose-carbon source
4366253423tween 40-carbon source
4366253426tween 80-carbon source
4366216704uridine-carbon source
4366227248urocanic acid-carbon source
4366231011valerate-carbon source
4366217151xylitol-carbon source
436624853esculin-hydrolysis
436625291gelatin-hydrolysis
4366216443D-tagatose+builds acid from
4366232528turanose+builds acid from
4366265327D-xylose+builds acid from
4366233984fucose+builds acid from
4366217234glucose+builds acid from
4366217306maltose+builds acid from
43662potassium 5-dehydro-D-gluconate+builds acid from
4366216634raffinose+builds acid from
43662309162-oxoglutarate+carbon source
4366273706bromosuccinate+carbon source
4366215740formate+carbon source
4366224996lactate+carbon source
4366275146monomethyl succinate+carbon source
4366230031succinate+carbon source
4366217632nitrate+reduction
4366218305arbutin+/-builds acid from
4366228087glycogen+/-builds acid from
4366217268myo-inositol+/-builds acid from
4366229864mannitol+/-builds acid from
4366243943methyl alpha-D-mannoside+/-builds acid from
4366237657methyl D-glucoside+/-builds acid from
43662506227N-acetylglucosamine+/-builds acid from
4366217814salicin+/-builds acid from
4366228017starch+/-builds acid from
4366217992sucrose+/-builds acid from
4366227082trehalose+/-builds acid from
4366275146monomethyl succinate+/-carbon source
4366230031succinate+/-carbon source

metabolite production

  • @ref: 43662
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43662esterase (C 4)+
43662esterase Lipase (C 8)+
43662leucine arylamidase+3.4.11.1
43662naphthol-AS-BI-phosphohydrolase+/-
43662N-acetyl-beta-glucosaminidase-3.2.1.52
43662acid phosphatase-3.1.3.2
43662alkaline phosphatase-3.1.3.1
43662alpha-chymotrypsin-3.4.21.1
43662cystine arylamidase-3.4.11.3
43662alpha-fucosidase-3.2.1.51
43662alpha-galactosidase-3.2.1.22
43662beta-galactosidase-3.2.1.23
43662alpha-glucosidase-3.2.1.20
43662beta-glucosidase-3.2.1.21
43662beta-glucuronidase-3.2.1.31
43662lipase (C 14)-
43662alpha-mannosidase-3.2.1.24
43662trypsin-3.4.21.4
43662valine arylamidase-
43662arginine dihydrolase-3.5.3.6
43662urease-3.5.1.5
43662catalase-1.11.1.6
43662cytochrome oxidase+1.9.3.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43662C15:0 anteiso1.9
    43662C15:0 3OH2.4
    43662C15:1ω6c1.1
    43662C16:02
    43662C16:0 3OH2.5
    43662C16:1ω6c / C16:1ω7c2.2
    43662C17:0 3OH1.9
    43662C17:1ω8c1.1
    43662C13:0 iso1.1
    43662C14:0 iso1.8
    43662C15:0 iso24.9
    43662C15:0 iso 3OH7.3
    43662C15:1 iso G12.6
    43662C16:0 iso6.7
    43662C16:0 iso 3OH2.5
    43662iso-C16:1G1.5
    43662C17:0 iso 3OH10.9
    43662C17:1 iso ω9c / C16:0 10-methyl12.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 5
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: 6980, Hewlett Packard
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43662
  • sample type: Sediment sample taken from Daechung Reservoir, 48 m depth
  • geographic location: Daechung Reservoir
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Container (Reservoir)
#Environmental#Aquatic#Sediment
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_111972.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_818;97_2436;98_7088;99_111972&stattab=map
  • Last taxonomy: Rhizobacter
  • 16S sequence: KM670026
  • Sequence Identity:
  • Total samples: 763
  • soil counts: 192
  • aquatic counts: 472
  • animal counts: 48
  • plant counts: 51

Sequence information

16S sequences

  • @ref: 43662
  • description: 16S rRNA gene sequence
  • accession: KM670026
  • database: nuccore

GC content

  • @ref: 43662
  • GC-content: 66.7
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43662

culture collection no.: KCTC 42645, NBRC 111169

literature

  • topic: Phylogeny
  • Pubmed-ID: 26868002
  • title: Rhizobacter profundi sp. nov., isolated from freshwater sediment.
  • authors: Jin L, Ko SR, Ahn CY, Lee HG, Oh HM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000962
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/microbiology, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Pseudomonadaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology
  • 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
43662Long Jin, So-Ra Ko, Chi-Yong Ahn, Hyung-Gwan Lee, Hee-Mock OhRhizobacter profundi sp. nov., isolated from freshwater sediment10.1099/ijsem.0.000962IJSEM 66: 1926-1931 201626868002
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/