Strain identifier

BacDive ID: 133322

Type strain: Yes

Species: Microvirga soli

Strain Designation: R491

NCBI tax ID(s): 1854496 (species)

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General

@ref: 25157

BacDive-ID: 133322

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

description: Microvirga soli R491 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil from reclaimed grassland.

NCBI tax id

  • NCBI tax id: 1854496
  • Matching level: species

doi: 10.13145/bacdive133322.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Microvirga
  • species: Microvirga soli
  • full scientific name: Microvirga soli Dahal and Kim 2017

@ref: 25157

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Methylobacteriaceae

genus: Microvirga

species: Microvirga soli

strain designation: R491

type strain: yes

Morphology

cell morphology

  • @ref: 25157
  • 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: 25157
  • colony size: 1.0-2.0 mm
  • colony color: light pink
  • colony shape: circular
  • incubation period: 4 days
  • medium used: R2A

pigmentation

  • @ref: 25157
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

@refnamegrowth
25157Reasoner's 2A agar (R2A)yes
25157nutrient agar (NA)yes
25157tryptic soy agar (TSA)yes
25157LBAyes
25157BHIyes
25157marine agar (MA)no
25157MHAno
25157veal infusion agarno
25157MacConkey agarno

culture temp

@refgrowthtypetemperaturerange
25157positivegrowth15.0-40.0
25157positiveoptimum25.0-35.0mesophilic

culture pH

@refabilitytypepHPH range
25157positivegrowth6.0-10.5alkaliphile
25157positiveoptimum7.0-8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 25157
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25157
  • spore formation: no

halophily

@refsalttested relationconcentration
25157NaCloptimum0 %
25157NaClmaximum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2515785146carboxymethylcellulose-hydrolysis
25157casein-hydrolysis
2515717029chitin-hydrolysis
251575291gelatin-hydrolysis
2515717368hypoxanthine-hydrolysis
2515728017starch-hydrolysis
2515727897tryptophan-energy source
2515753423tween 40-hydrolysis
2515753426tween 80-hydrolysis
2515718186tyrosine-hydrolysis
2515715318xanthine-hydrolysis
2515717632nitrate+reduction
2515753425tween 60+hydrolysis

metabolite production

  • @ref: 25157
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25157
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25157acid phosphatase+3.1.3.2
25157alkaline phosphatase+3.1.3.1
25157alpha-chymotrypsin-3.4.21.1
25157alpha-fucosidase-3.2.1.51
25157alpha-galactosidase-3.2.1.22
25157alpha-glucosidase-3.2.1.20
25157alpha-mannosidase-3.2.1.24
25157beta-galactosidase-3.2.1.23
25157beta-glucosidase-3.2.1.21
25157beta-glucuronidase-3.2.1.31
25157catalase+1.11.1.6
25157cystine arylamidase+3.4.11.3
25157cytochrome oxidase-1.9.3.1
25157esterase (C 4)+
25157esterase Lipase (C 8)+
25157leucine arylamidase+3.4.11.1
25157lipase (C 14)+
25157N-acetyl-beta-glucosaminidase-3.2.1.52
25157naphthol-AS-BI-phosphohydrolase+
25157trypsin+3.4.21.4
25157tryptophan deaminase-4.1.99.1
25157valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    2515710-Methyl C19:01
    25157aldehyde C12:02.411
    25157C10:00.3
    25157C14:01.7
    25157C16:012
    25157C16:1ω7c / C16:1ω6c4.7
    25157C17:00.4
    25157C18:04.2
    25157C18:1ω7c / C18:1ω6c71.2
    25157Cyclo C19:0ω8c2.1
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 25157
  • sample type: soil from reclaimed grassland
  • geographic location: Hwaseong,Gyeonggi-Do
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 37.193
  • longitude: 126.838
  • enrichment culture: R2A
  • enrichment culture duration: 14 days
  • enrichment culture temperature: 28
  • isolation procedure: modified culture method using transwell plates (Corning);placing 3 g of soil into each transwell plate;3 ml R2A medium (MB Cell) was added to each transwell insert. 100 µl soil suspension (1 g soil in 9 ml distilled water) placed into the insert;shaking incubator at 120 r.p.m.

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 25157
  • description: Microvirga soli strain R491 16S ribosomal RNA gene, partial sequence
  • accession: KX247636
  • length: 1433
  • database: nuccore
  • NCBI tax ID: 1854496

Genome sequences

  • @ref: 66792
  • description: Microvirga soli R491
  • accession: GCA_016734765
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1854496

GC content

  • @ref: 25157
  • GC-content: 61.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno78.016no
gram-positiveno98.097no
anaerobicno97.792yes
aerobicyes91.874yes
halophileno90.075no
spore-formingno93.868yes
thermophileno94.54yes
glucose-utilyes86.738no
motileyes56.963yes
glucose-fermentno90.891no

External links

@ref: 25157

culture collection no.: KEMB 9005-408, KACC 18969, NBRC 112417

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902203Microvirga soli sp. nov., an alphaproteobacterium isolated from soil.Dahal RH, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0015822017Bacterial Typing Techniques, Base Composition, Bradyrhizobiaceae/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Methylobacteriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny35666677Microvirga roseola sp. nov. and Microvirga lenta sp. nov., isolated from Taklamakan Desert soil.Du X, Ran Q, Wang J, Jiang H, Wang J, Li YZInt J Syst Evol Microbiol10.1099/ijsem.0.0054092022Bacterial Typing Techniques, Base Composition, *Bradyrhizobiaceae/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Soil MicrobiologyTranscriptome

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
25157R. H. K. Dahal, J.Microvirga soli sp. nov., an alphaproteobacterium isolated from soil10.1099/ijsem.0.001582IJSEM 67: 127-132 201727902203
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes