Strain identifier

BacDive ID: 158823

Type strain: Yes

Species: Pinisolibacter ravus

Strain Designation: E9

NCBI tax ID(s): 2172023 (species)

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General

@ref: 65587

BacDive-ID: 158823

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

description: Pinisolibacter ravus E9 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from pine forest soil.

NCBI tax id

  • NCBI tax id: 2172023
  • Matching level: species

doi: 10.13145/bacdive158823.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Ancalomicrobiaceae
  • genus: Pinisolibacter
  • species: Pinisolibacter ravus
  • full scientific name: Pinisolibacter ravus Dahal et al. 2018

@ref: 65587

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Ancalomicrobiaceae

genus: Pinisolibacter

species: Pinisolibacter ravus

strain designation: E9

type strain: yes

Morphology

cell morphology

  • @ref: 65587
  • gram stain: negative
  • cell length: 2.4-3.6 µm
  • cell width: 0.9-1.8 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 65587
  • colony size: 1-2 mm
  • colony color: straw
  • colony shape: circular
  • incubation period: 4 days
  • medium used: R2A

pigmentation

@refproductionname
65587noflexirubin type
65587nocarotenoid type

Culture and growth conditions

culture medium

@refnamegrowth
65587veal infusionyes
65587Trypticase Soy Agar (TSA)no
65587Nutrient agar (NA)no
65587Marine agar (MA)no
65587LBAno
65587BHIno
65587Reasoner's 2A agar (R2A)yes
65587PDAno

culture temp

@refgrowthtypetemperature
65587positivegrowth15-45
65587positiveoptimum28-32

culture pH

@refabilitytypepHPH range
65587positivegrowth5.0-10.0alkaliphile
65587positiveoptimum6.5-8.5

Physiology and metabolism

oxygen tolerance

  • @ref: 65587
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 65587
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentrationhalophily level
65587NaClpositivegrowth0-0.2 %
65587NaClpositiveoptimum0 %non-halophilic

observation

  • @ref: 65587
  • observation: prosthecae

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65587168082-dehydro-D-gluconate-assimilation
65587161933-hydroxybenzoate-assimilation
65587370543-hydroxybutyrate+assimilation
65587178794-hydroxybenzoate-assimilation
65587581435-dehydro-D-gluconate-assimilation
6558717128adipate-assimilation
6558727689decanoate-assimilation
6558785146carboxymethylcellulose-hydrolysis
65587casein-hydrolysis
6558717029chitin-hydrolysis
6558717634D-glucose+assimilation
6558716899D-mannitol-assimilation
6558716024D-mannose-assimilation
6558716988D-ribose-assimilation
6558717924D-sorbitol-assimilation
6558716991dna-hydrolysis
65587esculin ferric citrate+hydrolysis
655875291gelatin-hydrolysis
6558717234glucose+fermentation
6558728087glycogen-assimilation
6558717368hypoxanthine-hydrolysis
6558717268myo-inositol-assimilation
6558716977L-alanine-assimilation
6558730849L-arabinose-assimilation
6558730849L-arabinose+assimilation
6558718287L-fucose-assimilation
6558717203L-proline+assimilation
6558762345L-rhamnose-assimilation
6558724996lactate-assimilation
6558725115malate-assimilation
6558717306maltose-assimilation
6558728053melibiose-assimilation
65587506227N-acetylglucosamine-assimilation
6558717632nitrate-reduction
6558717814salicin-assimilation
6558732954sodium acetate-assimilation
6558753258sodium citrate-assimilation
6558728017starch-hydrolysis
6558717992sucrose+assimilation
6558727897tryptophan-energy source
6558753423tween 40-hydrolysis
6558753425tween 60-hydrolysis
6558753426tween 80-hydrolysis
6558718186tyrosine-hydrolysis
6558731011valerate+assimilation
6558715318xanthine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6558715688acetoinno
6558716136hydrogen sulfideno
6558735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6558715688acetoin-
6558735581indole-

enzymes

@refvalueactivityec
65587catalase-1.11.1.6
65587cytochrome oxidase+1.9.3.1
65587urease+3.5.1.5
65587tryptophan deaminase-4.1.99.1
65587alkaline phosphatase+3.1.3.1
65587esterase Lipase (C 8)+
65587leucine arylamidase+3.4.11.1
65587valine arylamidase+
65587trypsin+3.4.21.4
65587acid phosphatase+3.1.3.2
65587naphthol-AS-BI-phosphohydrolase+
65587alpha-glucosidase+3.2.1.20
65587beta-glucosidase+3.2.1.21
65587esterase (C 4)+/-
65587cystine arylamidase+/-3.4.11.3
65587lipase (C 14)-
65587alpha-chymotrypsin-3.4.21.1
65587alpha-galactosidase-3.2.1.22
65587beta-galactosidase-3.2.1.23
65587beta-glucuronidase-3.2.1.31
65587N-acetyl-beta-glucosaminidase-3.2.1.52
65587alpha-mannosidase-3.2.1.24
65587alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65587C14:00.7
    65587C16:011.5
    65587C18:02
    65587C20:00.3
    65587C20:1ω7c0.9
    65587C18:0 3OH1
    65587C12:0 aldehyde / unknown 10.9285.5
    65587C16:1ω7c / C16:1ω6c25.4
    65587C19:1ω6c / C19:0 cyclo0.4
    65587C18:1ω7c / C18:1ω6c52.3
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 65587
  • sample type: pine forest soil
  • geographic location: Kyonggi University, Suwon, Gyeonggi-Do
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • enrichment culture: R2A
  • enrichment culture duration: 14 days
  • enrichment culture temperature: 28
  • isolation procedure: six-transwell plates with 3 ml R2A broth and 3 g sample of sieved soil. 1 ml of a soil suspension (1g of soil in 9 ml R2A broth) was added.

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_25003.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_12502;97_15178;98_18798;99_25003&stattab=map
  • Last taxonomy: Pinisolibacter ravus subclade
  • 16S sequence: KY087994
  • Sequence Identity:
  • Total samples: 7333
  • soil counts: 839
  • aquatic counts: 4656
  • animal counts: 875
  • plant counts: 963

Sequence information

16S sequences

  • @ref: 65587
  • description: Pinisolibacter ravus strain E9 16S ribosomal RNA gene, partial sequence
  • accession: KY087994
  • database: nuccore

GC content

  • @ref: 65587
  • GC-content: 68.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 65587

culture collection no.: KEMB 9005-534, KACC 19120, NBRC 112686

literature

  • topic: Phylogeny
  • Pubmed-ID: 29683414
  • title: Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968.
  • authors: Dahal RH, Chaudhary DK, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002772
  • year: 2018
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Phospholipids/chemistry, *Phylogeny, *Pinus, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/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
65587Ram Hari Dahal, Dhiraj Kumar Chaudhary and Jaisoo KimPinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 196810.1099/ijsem.0.002772IJSEM 68: 1955-1962 201829683414
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/