Strain identifier

BacDive ID: 141130

Type strain: Yes

Species: Devosia humi

Strain Designation: THG-MM1

NCBI tax ID(s): 1591105 (species)

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General

@ref: 44042

BacDive-ID: 141130

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

description: Devosia humi THG-MM1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil of Korean pine garden.

NCBI tax id

  • NCBI tax id: 1591105
  • Matching level: species

doi: 10.13145/bacdive141130.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Devosia
  • species: Devosia humi
  • full scientific name: Devosia humi Du et al. 2016

@ref: 44042

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Hyphomicrobiaceae

genus: Devosia

species: Devosia humi

strain designation: THG-MM1

type strain: yes

Morphology

cell morphology

  • @ref: 44042
  • gram stain: negative
  • cell length: 1.3-3.0 µm
  • cell width: 0.41-0.67 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 44042
  • colony size: 0.5-2.0 mm
  • colony color: pinkish-white
  • colony shape: circular
  • incubation period: 5 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
44042LB (Luria-Bertani) MEDIUMno
44042Marine agar (MA)no
44042MacConkey agarno
44042Nutrient agar (NA)no
44042Reasoner's 2A agar (R2A)yes
44042TSA agarno

culture temp

@refgrowthtypetemperature
44042positivegrowth18-30
44042positiveoptimum28

culture pH

@refabilitytypepH
44042positivegrowth6.0-8.0
44042positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 44042
  • oxygen tolerance: aerobe

halophily

  • @ref: 44042
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4404217128adipate-carbon source
4404227689decanoate-carbon source
4404216899D-mannitol-carbon source
4404216024D-mannose-carbon source
4404217234glucose-carbon source
4404230849L-arabinose-carbon source
4404225115malate-carbon source
4404217306maltose-carbon source
44042506227N-acetylglucosamine-carbon source
4404218401phenylacetate-carbon source
4404232032potassium gluconate-carbon source
4404253258sodium citrate-carbon source
4404216991dna-hydrolysis
440425291gelatin-hydrolysis
4404217895L-tyrosine-hydrolysis
4404228017starch-hydrolysis
4404253424tween 20-hydrolysis
4404253426tween 80-hydrolysis
4404217632nitrate-reduction

metabolite production

  • @ref: 44042
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44042catalase+1.11.1.6
44042cytochrome oxidase+1.9.3.1
44042esterase (C 4)+
44042esterase Lipase (C 8)+
44042leucine arylamidase+3.4.11.1
44042valine arylamidase+
44042naphthol-AS-BI-phosphohydrolase+
44042beta-galactosidase+3.2.1.23
44042N-acetyl-beta-glucosaminidase+3.2.1.52
44042alpha-mannosidase+3.2.1.24
44042lipase (C 14)+/-
44042beta-glucosidase+/-3.2.1.21
44042acid phosphatase+/-3.1.3.2
44042alkaline phosphatase-3.1.3.1
44042cystine arylamidase-3.4.11.3
44042trypsin-3.4.21.4
44042alpha-chymotrypsin-3.4.21.1
44042beta-glucuronidase-3.2.1.31
44042alpha-galactosidase-3.2.1.22
44042alpha-glucosidase-3.2.1.20
44042alpha-fucosidase-3.2.1.51
44042arginine dihydrolase-3.5.3.6
44042urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    4404211-methyl-C18:1ω7c8.1
    44042C15:0 anteiso1.3
    44042C10:0 3OH8.4
    44042C16:027.8
    44042C18:011
    44042C18:1ω7c / C18:1ω6c12.8
    44042C18:1ω9c1.6
    44042C18:3ω6c(6,9,12)2.2
    44042C19:0-cyclo-ω8c1.6
    44042iso-C11:0-3-OH9.9
    44042C17:0 iso9.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 44042
  • sample type: soil of Korean pine (Pinus koraiensis) garden
  • geographic location: Kyung Hee University, Yongin City, Gyeonggi-Do
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 37.2408
  • longitude: 127.177
  • enrichment culture: R2A agar
  • enrichment culture duration: 5 days
  • enrichment culture temperature: 28

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Garden
#Environmental#Terrestrial#Soil
#Host#Plants#Tree

Sequence information

16S sequences

  • @ref: 44042
  • description: Devosia humi 16S ribosomal RNA gene, partial sequence
  • accession: KM598259
  • database: nuccore

GC content

  • @ref: 44042
  • GC-content: 63.7
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 44042

culture collection no.: KACC 18281, CCTCC AB 2015121

literature

  • topic: Phylogeny
  • Pubmed-ID: 26514816
  • title: Devosia humi sp. nov., isolated from soil of a Korean pine (Pinus koraiensis) garden.
  • authors: Du J, Kook M, Akter S, Singh H, Won K, Ngo HTT, Yi TH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000724
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pinus/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
  • topic2: Genetics

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
44042Juan Du, MooChang Kook, Shahina Akter, Hina Singh, KyungHwa Won, Hien T. T. Ngo and Tae-Hoo YiDevosia humi sp. nov., isolated from soil of a Korean pine (Pinus koraiensis) garden10.1099/ijsem.0.000724IJSEM 66: 341-346 201626514816