Strain identifier

BacDive ID: 140831

Type strain: Yes

Species: Variovorax humicola

NCBI tax ID(s): 1769758 (species)

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General

@ref: 43629

BacDive-ID: 140831

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

description: Variovorax humicola KACC 18501 is an aerobe, chemoautolithotroph, Gram-negative bacterium that forms irregular colonies and was isolated from forest topsoil.

NCBI tax id

  • NCBI tax id: 1769758
  • Matching level: species

doi: 10.13145/bacdive140831.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Variovorax
  • species: Variovorax humicola
  • full scientific name: Variovorax humicola Nguyen and Kim 2016

@ref: 43629

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Variovorax

species: Variovorax humicola

type strain: yes

Morphology

cell morphology

  • @ref: 43629
  • gram stain: negative
  • cell length: 1.5-2 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: gliding

colony morphology

  • @ref: 43629
  • colony color: pale yellowish
  • colony shape: irregular
  • medium used: R2A agar plates

Culture and growth conditions

culture medium

  • @ref: 43629
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43629positivegrowth4-35
43629positiveoptimum25-30mesophilic

culture pH

@refabilitytypepHPH range
43629positivegrowth4-9alkaliphile
43629positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

  • @ref: 43629
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 43629
  • type: chemoautolithotroph

spore formation

  • @ref: 43629
  • spore formation: no

halophily

  • @ref: 43629
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
436293557154-nitrophenyl beta-D-galactopyranoside-assimilation
4362917128adipate-assimilation
4362927689decanoate-assimilation
4362916024D-mannose-assimilation
4362916988D-ribose-assimilation
436294853esculin-assimilation
436295291gelatin-assimilation
4362928087glycogen-assimilation
4362917268myo-inositol-assimilation
4362917240itaconate-assimilation
4362916977L-alanine-assimilation
4362930849L-arabinose-assimilation
4362916467L-arginine-assimilation
4362918287L-fucose-assimilation
4362915971L-histidine-assimilation
4362917203L-proline-assimilation
4362917115L-serine-assimilation
4362916828L-tryptophan-assimilation
4362917306maltose-assimilation
4362928053melibiose-assimilation
43629506227N-acetylglucosamine-assimilation
43629potassium 2-dehydro-D-gluconate-assimilation
43629potassium 5-dehydro-D-gluconate-assimilation
4362932032potassium gluconate-assimilation
4362917272propionate-assimilation
4362917814salicin-assimilation
4362932954sodium acetate-assimilation
4362953258sodium citrate-assimilation
4362962983sodium malonate-assimilation
436299300suberic acid-assimilation
4362917992sucrose-assimilation
4362916199urea-assimilation
4362931011valerate-assimilation
436294853esculin-hydrolysis
43629milk-hydrolysis
4362928017starch-hydrolysis
4362953425tween 60-hydrolysis
4362916199urea-hydrolysis
43629161933-hydroxybenzoate+assimilation
43629370543-hydroxybutyrate+assimilation
43629178794-hydroxybenzoate+assimilation
4362917634D-glucose+assimilation
4362916899D-mannitol+assimilation
4362917924D-sorbitol+assimilation
4362924996lactate+assimilation
4362925115malate+assimilation
4362917634D-glucose+builds acid from
4362916991dna+hydrolysis
4362953426tween 80+hydrolysis
4362962345L-rhamnose+/-assimilation
4362918401phenylacetate+/-assimilation
4362953423tween 40+/-hydrolysis
4362917632nitrate+/-reduction

metabolite production

@refChebi-IDmetaboliteproduction
4362916136hydrogen sulfideno
4362935581indoleno

enzymes

@refvalueactivityec
43629catalase+1.11.1.6
43629cytochrome oxidase+1.9.3.1
43629alkaline phosphatase+3.1.3.1
43629leucine arylamidase+3.4.11.1
43629acid phosphatase+3.1.3.2
43629naphthol-AS-BI-phosphohydrolase+
43629cystine arylamidase+/-3.4.11.3
43629alpha-glucosidase+/-3.2.1.20
43629esterase (C 4)-
43629esterase Lipase (C 8)-
43629valine arylamidase-
43629beta-glucosidase-3.2.1.21
43629lipase (C 14)-
43629trypsin-3.4.21.4
43629alpha-chymotrypsin-3.4.21.1
43629alpha-galactosidase-3.2.1.22
43629beta-galactosidase-3.2.1.23
43629N-acetyl-beta-glucosaminidase-3.2.1.52
43629alpha-mannosidase-3.2.1.24
43629alpha-fucosidase-3.2.1.51
43629urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43629C15:0 anteiso1.4
    43629C16:02.2
    43629C16:1ω5c3.8
    43629C16:1ω7c / C15:0 iso 2OH17
    43629C15:0 iso25.5
    43629C17:0 iso3.1
    43629iso-C17:1 / anteiso-C17:11.4
    43629C17:1 iso ω9c34.9
    43629Unknown C13.5652.5
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.08
  • library/peak naming table: TSBA6 6.21
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43629
  • sample type: forest topsoil
  • geographic location: Kyonggi University campus, Suwon, Gyeonggi-Do province
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

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

Sequence information

16S sequences

  • @ref: 43629
  • description: 16S rRNA gene sequence
  • accession: KT301941
  • database: nuccore

GC content

  • @ref: 43629
  • GC-content: 66.2
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43629

culture collection no.: KACC 18501, NBRC 111520, UC 38

literature

  • topic: Phylogeny
  • Pubmed-ID: 27082126
  • title: Description of Variovorax humicola sp. nov., isolated from a forest topsoil.
  • authors: Nguyen TM, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001082
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
  • 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
43629Tuan Manh Nguyen, Jaisoo KimDescription of Variovorax humicola sp. nov., isolated from a forest topsoil10.1099/ijsem.0.001082IJSEM 66: 2520-2527 201627082126