Strain identifier

BacDive ID: 140469

Type strain: Yes

Species: Rhodanobacter humi

Strain Designation: RS22

NCBI tax ID(s): 1888173 (species)

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General

@ref: 43208

BacDive-ID: 140469

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

description: Rhodanobacter humi RS22 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 1888173
  • Matching level: species

doi: 10.13145/bacdive140469.20230509.8.1

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 humi
  • full scientific name: Rhodanobacter humi Dahal and Kim 2017

@ref: 43208

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Rhodanobacteraceae

genus: Rhodanobacter

species: Rhodanobacter humi

strain designation: RS22

type strain: yes

Morphology

cell morphology

  • @ref: 43208
  • gram stain: negative
  • cell length: 1.8-2.9 µm
  • cell width: 0.8-1.2 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43208
  • colony size: 2-3 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 4 days
  • medium used: tryptic soy agar (TSA)

Culture and growth conditions

culture medium

@refnamegrowth
43208tryptic soy agar (TSA)yes
43208Reasoner's 2A agar (R2A)yes
43208nutritient agar (NA)yes
43208LBAyes
43208BHIyes
43208veal infusion agaryes
43208marine ager (MA)no
43208MacConkey agarno
43208potato dextrose agarno

culture temp

@refgrowthtypetemperaturerange
43208positiveoptimum25-30mesophilic
43208positivegrowth15-35

culture pH

@refabilitytypepHPH range
43208positivegrowth4.5-11.0alkaliphile
43208positiveoptimum6.5-9.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43208
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43208
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43208NaClpositivegrowth0-4 %(w/v)
43208NaClpositiveoptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4320817234glucose+fermentation
43208esculin ferric citrate+hydrolysis
4320853425tween 60+hydrolysis
4320853423tween 40+hydrolysis
4320818186tyrosine+hydrolysis
4320816991dna+hydrolysis
432085291gelatin-hydrolysis
43208casein-hydrolysis
4320828017starch-hydrolysis
4320885146carboxymethylcellulose-hydrolysis
4320817029chitin-hydrolysis
4320815318xanthine-hydrolysis
4320817368hypoxanthine-hydrolysis
4320853426tween 80-hydrolysis
4320835581indole-hydrolysis
4320827897tryptophan-energy source
4320817632nitrate-reduction
4320817634D-glucose+assimilation
43208506227N-acetylglucosamine+assimilation
4320817306maltose+assimilation
4320830849L-arabinose-assimilation
4320816024D-mannose-assimilation
4320816899D-mannitol-assimilation
4320832032potassium gluconate-assimilation
4320827689decanoate-assimilation
4320817128adipate-assimilation
4320825115malate-assimilation
4320853258sodium citrate-assimilation
4320818401phenylacetate-assimilation
4320832954sodium acetate+assimilation
4320824996lactate+assimilation
43208161933-hydroxybenzoate+assimilation
4320817115L-serine+assimilation
4320818287L-fucose+assimilation
4320817203L-proline+assimilation
43208370543-hydroxybutyrate+assimilation
4320862345L-rhamnose-assimilation
4320816988D-ribose-assimilation
4320817268myo-inositol-assimilation
4320817992sucrose-assimilation
4320817240itaconate-assimilation
432089300suberic acid-assimilation
4320862983sodium malonate-assimilation
4320816977L-alanine-assimilation
43208581435-dehydro-D-gluconate-assimilation
4320828087glycogen-assimilation
4320817814salicin-assimilation
4320828053melibiose-assimilation
4320817924D-sorbitol-assimilation
4320817272propionate-assimilation
4320831011valerate-assimilation
4320815971L-histidine-assimilation
43208168082-dehydro-D-gluconate-assimilation
43208178794-hydroxybenzoate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
4320816136hydrogen sulfideno
4320835581indoleno

metabolite tests

  • @ref: 43208
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
43208catalase+1.11.1.6
43208cytochrome oxidase+1.9.3.1
43208urease-3.5.1.5
43208DNase+
43208alkaline phosphatase+3.1.3.1
43208esterase (C 4)+
43208esterase Lipase (C 8)+
43208leucine arylamidase+3.4.11.1
43208valine arylamidase+
43208alpha-chymotrypsin+3.4.21.1
43208acid phosphatase+3.1.3.2
43208naphthol-AS-BI-phosphohydrolase+
43208beta-galactosidase+3.2.1.23
43208alpha-glucosidase+3.2.1.20
43208beta-glucosidase+3.2.1.21
43208N-acetyl-beta-glucosaminidase+3.2.1.52
43208alpha-mannosidase+3.2.1.24
43208alpha-fucosidase+3.2.1.51
43208cystine arylamidase+3.4.11.3
43208alpha-galactosidase+3.2.1.22
43208lipase (C 14)-
43208trypsin-3.4.21.4
43208beta-glucuronidase-3.2.1.31
43208tryptophan deaminase-4.1.99.1

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43208C16:05.3
    43208C17:1ω6c1
    43208C11:0 iso4.8
    43208C15:0 iso20.7
    43208C16:0 iso8.4
    43208C17:0 iso13.7
    43208C15:0 anteiso6
    43208C11:0 iso 3OH4.3
    43208C13:0 iso 3OH2.4
    43208C16:1ω7c / C16:1ω6c3.8
    43208C17:1 iso ω9c / C16:0 10-methyl25.7
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy agar (TSA)
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.0B
  • system: MIS MIDI
  • instrument: HP 6890, Hewlett Packard
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43208
  • sample type: forest soil
  • geographic location: Kyonggi University, Suwon
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 37
  • longitude: 127
  • enrichment culture: R2A broth

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7022.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_114;96_316;97_352;98_5158;99_7022&stattab=map
  • Last taxonomy: Rhodanobacter humi
  • 16S sequence: KX674374
  • Sequence Identity:
  • Total samples: 1408
  • soil counts: 976
  • aquatic counts: 106
  • animal counts: 104
  • plant counts: 222

Sequence information

16S sequences

  • @ref: 43208
  • description: Rhodanobacter humi strain RS22 16S ribosomal RNA gene, partial sequence
  • accession: KX674374
  • length: 1479
  • database: nuccore
  • NCBI tax ID: 1888173

GC content

  • @ref: 43208
  • GC-content: 63.2
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43208

culture collection no.: KEMB 9005-480, KACC 19048, NBRC 112473

literature

  • topic: Phylogeny
  • Pubmed-ID: 28073405
  • title: Rhodanobacter humi sp. nov., an acid-tolerant and alkalitolerant gammaproteobacterium isolated from forest soil.
  • authors: Dahal RH, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001786
  • year: 2017
  • 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, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/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
43208Ram Hari Dahal, Jaisoo KimRhodanobacter humi sp. nov., an acid-tolerant and alkalitolerant gammaproteobacterium isolated from forest soil10.1099/ijsem.0.001786IJSEM 67: 1185-1190 201728073405
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/