Strain identifier

BacDive ID: 159720

Type strain: Yes

Species: Rhodanobacter hydrolyticus

Strain Designation: G-5-5

NCBI tax ID(s): 2250595 (species)

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General

@ref: 66621

BacDive-ID: 159720

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

description: Rhodanobacter hydrolyticus G-5-5 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 2250595
  • Matching level: species

doi: 10.13145/bacdive159720.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Rhodanobacter
  • species: Rhodanobacter hydrolyticus
  • full scientific name: Rhodanobacter hydrolyticus Dahal et al. 2018

@ref: 66621

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Rhodanobacteraceae

genus: Rhodanobacter

species: Rhodanobacter hydrolyticus

strain designation: G-5-5

type strain: yes

Morphology

cell morphology

  • @ref: 66621
  • gram stain: negative
  • cell length: 1.6-1.9 µm
  • cell width: 0.7-0.9 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 66621
  • colony size: 1-2 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 4 days
  • medium used: R2A medium

Culture and growth conditions

culture medium

@refnamegrowth
66621BHI agarno
66621LB (Luria-Bertani) agarno
66621Marine agar (MA)no
66621Mueller-Hinton agarno
66621Nutrient agar (NA)no
66621Reasoner's 2A agar (R2A)yes
66621sorbitol MacConkey agarno
66621tryptic soy agar (TSA)no
66621veal infusion agarno

culture temp

@refgrowthtypetemperaturerange
66621positivegrowth20-35
66621positiveoptimum25-30mesophilic

culture pH

@refabilitytypepHPH range
66621positivegrowth4.5-10alkaliphile
66621positiveoptimum5.5-8

Physiology and metabolism

oxygen tolerance

  • @ref: 66621
  • oxygen tolerance: aerobe

spore formation

  • @ref: 66621
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
66621NaClpositivegrowth0-0.5 %
66621NaClpositiveoptimum0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6662116024D-mannose+assimilation
6662117306maltose+assimilation
6662117634D-glucose+assimilation
6662118287L-fucose+assimilation
6662159640N-acetylglucosamine+assimilation
6662117234glucose-fermentation
666215291gelatin-hydrolysis
6662117029chitin-hydrolysis
6662117368hypoxanthine-hydrolysis
6662128017starch-hydrolysis
6662153423tween 40-hydrolysis
6662153425tween 60-hydrolysis
6662153426tween 80-hydrolysis
6662185146carboxymethylcellulose-hydrolysis
66621casein-hydrolysis
6662116991dna+hydrolysis
6662118186tyrosine+hydrolysis
66621esculin ferric citrate+hydrolysis
6662117632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6662116136hydrogen sulfideno
6662135581indoleno

enzymes

@refvalueactivityec
66621alpha-chymotrypsin-3.4.21.1
66621alpha-galactosidase-3.2.1.22
66621alpha-glucosidase-3.2.1.20
66621beta-glucosidase-3.2.1.21
66621beta-glucuronidase-3.2.1.31
66621lipase (C 14)-
66621trypsin-3.4.21.4
66621urease-3.5.1.5
66621acid phosphatase+3.1.3.2
66621alkaline phosphatase+3.1.3.1
66621alpha-fucosidase+3.2.1.51
66621alpha-mannosidase+3.2.1.24
66621beta-galactosidase+3.2.1.23
66621catalase+1.11.1.6
66621cystine arylamidase+3.4.11.3
66621cytochrome oxidase+1.9.3.1
66621esterase (C 4)+
66621esterase Lipase (C 8)+
66621leucine arylamidase+3.4.11.1
66621N-acetyl-beta-glucosaminidase+3.2.1.52
66621naphthol-AS-BI-phosphohydrolase+
66621valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    66621unknown 10.928 and/or C12:0 aldehyde0.510.928
    66621C11:0 anteiso0.1
    66621C13:0 anteiso0.1
    66621C17:0 iso 3OH0.1
    66621C17:00.2
    66621C18:00.2
    66621C13:0 iso0.2
    66621C15:0 iso 3OH0.2
    66621C16:1 iso H0.2
    66621C20:0 iso0.3
    66621C12:0 iso 3OH0.4
    66621C14:00.5
    66621C14:0 iso0.5
    66621C20:00.6
    66621C17:1 w6c0.7
    66621C19:0 iso0.7
    66621C18:0 iso1.2
    66621C16:0 iso11.8
    66621C17:0 iso15.7
    66621C15:0 iso17.8
    66621C17:0 anteiso2.3
    66621C13:0 iso 3OH2.4
    66621C17:1 iso w9c / C16:0 10-methyl21.8
    66621C16:03.3
    66621C16:1 w7c and/or C16:1 w6c3.4
    66621C11:0 iso3.6
    66621C11:0 iso 3OH4.4
    66621C15:0 anteiso5.9
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 66621
  • sample type: forest soil
  • geographic location: Kyonggi University, Suwon
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 37.3002
  • longitude: 127.039
  • enrichment culture: R2A broth
  • enrichment culture duration: 2 weeks
  • enrichment culture temperature: 28
  • isolation procedure: After placing 3 g soil into each Transwell plate, 3 ml Reasoner's 2A broth (MB Cell) was added to each insert. Then, 100 µl soil suspension (1 g soil in 9 ml distilled water; thoroughly stirred and settled) was placed into the insert. The Transwell plate was then incubated in a shaking incubator at 120 r.p.m. for 2 weeks at 28°C. After 2 weeks, the culture was serially diluted, and 100 µl of each dilution were spread onto R2A agar plates.

isolation source categories

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

Sequence information

16S sequences

  • @ref: 66621
  • description: Rhodanobacter hydrolyticus strain G-5-5 16S ribosomal RNA gene, partial sequence
  • accession: KY117469
  • length: 1478
  • database: ena
  • NCBI tax ID: 2250595

GC content

  • @ref: 66621
  • GC-content: 64.1
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 66621

culture collection no.: KEMB 9005-533, KACC 19113, NBRC 112685

literature

  • topic: Phylogeny
  • Pubmed-ID: 29952746
  • title: Rhodanobacter hydrolyticus sp. nov., a novel DNA- and tyrosine-hydrolysing gammaproteobacterium isolated from forest soil.
  • authors: Dahal RH, Chaudhary DK, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002881
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Tyrosine/metabolism, Xanthomonadaceae/*classification/growth & development/isolation & purification
  • 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
66621Ram Hari Dahal, Dhiraj Kumar Chaudhary, Jaisoo KimRhodanobacter hydrolyticus sp. nov., a novel DNA- and tyrosine-hydrolysing gammaproteobacterium isolated from forest soil10.1099/ijsem.0.002881IJSEM 68: 2580-2586 201829952746