Strain identifier

BacDive ID: 159185

Type strain: Yes

Species: Aerosticca soli

Strain Designation: Dysh456

Strain history: <- M. Watanabe, Inst. Low Temperature Sci., Hokkaido Univ., Sapporo, Japan; Dysh456

NCBI tax ID(s): 2010829 (species)

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General

@ref: 66008

BacDive-ID: 159185

DSM-Number: 105662

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemoorganotroph, thermophilic, Gram-negative, motile, rod-shaped

description: Aerosticca soli Dysh456 is an aerobe, chemoorganotroph, thermophilic bacterium that was isolated from crude oil-contaminated soil.

NCBI tax id

  • NCBI tax id: 2010829
  • Matching level: species

strain history

  • @ref: 66008
  • history: <- M. Watanabe, Inst. Low Temperature Sci., Hokkaido Univ., Sapporo, Japan; Dysh456

doi: 10.13145/bacdive159185.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Aerosticca
  • species: Aerosticca soli
  • full scientific name: Aerosticca soli Watanabe et al. 2020

@ref: 66008

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Rhodanobacteraceae

genus: Aerosticca

species: Aerosticca soli

full scientific name: Aerosticca soli

strain designation: Dysh456

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
68269negative2-5 µm0.8 µmrod-shapedyes
69480negative99.998

colony morphology

  • @ref: 68269
  • colony color: White
  • medium used: Reasoner's 2A agar (R2A)

multimedia

  • @ref: 66008
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_105662.jpg
  • caption: DSM 105662 on medium 830 at 45 °C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 66008
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
66008positivegrowth45thermophilic
68269positivegrowth13-48
68269positiveoptimum42-45thermophilic

culture pH

@refabilitytypepH
68269positivegrowth4.3-7.9
68269positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 68269
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 68269
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
68269no
69480no99.998
69481no100

halophily

  • @ref: 68269
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6826940585alpha-cyclodextrin+respiration
6826917925alpha-D-glucose+respiration
6826917057cellobiose+respiration
6826923652dextrin+respiration
6826915824D-fructose+respiration
6826916024D-mannose+respiration
6826917113erythritol+respiration
6826928087glycogen+respiration
6826918287L-fucose+respiration
6826917306maltose+respiration
6826959640N-acetylglucosamine+respiration
6826927082trehalose+respiration
6826932528turanose+respiration
6826951850methyl pyruvate+respiration
6826975146monomethyl succinate+respiration
682698295beta-hydroxybutyrate+respiration
6826917240itaconate+respiration
68269645522-hydroxybutyrate+respiration
68269286442-oxopentanoate+respiration
6826917272propionate+respiration
68269143136succinamate+respiration
6826921217L-alaninamide+respiration
6826916977L-alanine+respiration
6826973786L-alanylglycine+respiration
6826929991L-aspartate+respiration
6826929985L-glutamate+respiration
6826973804glycyl L-aspartic acid+respiration
6826973784glycyl-l-glutamate+respiration
6826917203L-proline+respiration
6826917115L-serine+respiration
6826917596inosine+respiration
6826916704uridine+respiration
6826928017starch+hydrolysis
6826916991dna-hydrolysis
68269skimmed milk-hydrolysis
6826985146carboxymethylcellulose-hydrolysis
6826927613amygdalin-builds acid from
6826918305arbutin-builds acid from
6826917057cellobiose-builds acid from
6826915963ribitol-builds acid from
6826917108D-arabinose-builds acid from
6826918333D-arabitol-builds acid from
6826915824D-fructose-builds acid from
6826928847D-fucose-builds acid from
6826912936D-galactose-builds acid from
6826917634D-glucose-builds acid from
6826962318D-lyxose-builds acid from
6826916899D-mannitol-builds acid from
6826916024D-mannose-builds acid from
6826916988D-ribose-builds acid from
6826917924D-sorbitol-builds acid from
6826916443D-tagatose-builds acid from
6826916813galactitol-builds acid from
6826965327D-xylose-builds acid from
6826917113erythritol-builds acid from
68269esculin ferric citrate-builds acid from
6826928066gentiobiose-builds acid from
6826917754glycerol-builds acid from
6826928087glycogen-builds acid from
6826917268myo-inositol-builds acid from
6826915443inulin-builds acid from
6826917716lactose-builds acid from
6826930849L-arabinose-builds acid from
6826918403L-arabitol-builds acid from
6826918287L-fucose-builds acid from
6826962345L-rhamnose-builds acid from
6826917266L-sorbose-builds acid from
6826965328L-xylose-builds acid from
6826917306maltose-builds acid from
682696731melezitose-builds acid from
6826928053melibiose-builds acid from
68269320061methyl alpha-D-glucopyranoside-builds acid from
6826943943methyl alpha-D-mannoside-builds acid from
6826974863methyl beta-D-xylopyranoside-builds acid from
6826959640N-acetylglucosamine-builds acid from
68269potassium 2-dehydro-D-gluconate-builds acid from
68269potassium 5-dehydro-D-gluconate-builds acid from
6826932032potassium gluconate-builds acid from
6826916634raffinose-builds acid from
6826917814salicin-builds acid from
6826928017starch-builds acid from
6826917992sucrose-builds acid from
6826927082trehalose-builds acid from
6826932528turanose-builds acid from
6826917151xylitol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6826935581indoleno
6826917997dinitrogenno

enzymes

@refvalueactivityec
68269cytochrome oxidase+1.9.3.1
68269catalase-1.11.1.6
68269arginine dihydrolase+3.5.3.6
68269alkaline phosphatase+3.1.3.1
68269acid phosphatase+3.1.3.2
68269esterase Lipase (C 8)+
68269beta-glucosidase+3.2.1.21
68269leucine arylamidase+3.4.11.1
68269valine arylamidase+
68269lipase (C 14)+
68269cystine arylamidase+3.4.11.3
68269urease-3.5.1.5
68269nitrate reductase-1.7.99.4
68269trypsin-3.4.21.4
68269chymotrypsin-3.4.4.5
68269alpha-galactosidase-3.2.1.22
68269beta-glucuronidase-3.2.1.31
68269alpha-mannosidase-3.2.1.24
68269alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68269C15:0 iso42.5
    68269C17:0 iso15.3
    68269C17:1 iso w9c / C16:0 10-methyl13.7
    68269C13:0 iso5
    68269C15:0 anteiso4.4
    68269C16:0 iso3
    68269C11:0 iso2.6
    68269C11:0 iso 3-OH2.4
    68269C13:0 iso 3OH2.1
    68269C16:1 w6c/C16:1 w7c1.8
    68269C16:01.5
    68269C17:0 anteiso0.8
    68269C14:0 iso0.7
    68269C18:00.7
    68269C15:1 iso G0.7
    68269C18:1 w9c0.6
    68269C17:0 iso 3OH0.5
    68269C13:0 anteiso0.4
    68269C18:1 w5c0.3
    68269C14:00.3
    68269C15:1 iso H / C13:0 3OH0.3
    68269C17:0 cyclo0.3
    68269C18:2 w6,9c / C18:0 anteiso0.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • incubation temperature: 45
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateenrichment cultureenrichment culture durationenrichment culture temperature
66008crude oil-contaminated soilIshikari oil field, Hokkaido (43° 28' N, 141° 48' E)JapanJPNAsia43.4667141.8
68269crude oil-contaminated soil from an oil filedIshikari oil field on HokkaidoJapanJPNAsia43.4667141.82016-11-01R2A broth4 days45

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Engineered#Industrial#Oil reservoir
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 66008
  • description: Aerosticca soli gene for 16S ribosomal RNA, partial sequence
  • accession: LC276682
  • length: 1483
  • database: ena
  • NCBI tax ID: 2010829

Genome sequences

  • @ref: 68269
  • description: Aerosticca soli Dysh456
  • accession: GCA_003967035
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2010829

GC content

  • @ref: 68269
  • GC-content: 68
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.596yes
flagellatedno84.343no
gram-positiveno98.852yes
anaerobicno98.904no
aerobicyes81.366no
halophileno94.921yes
spore-formingno94.062yes
thermophileyes65.302yes
glucose-utilyes86.954yes
glucose-fermentno89.433no

External links

@ref: 66008

culture collection no.: DSM 105662, NBRC 112897

straininfo link

  • @ref: 111688
  • straininfo: 402228

literature

  • topic: Phylogeny
  • Pubmed-ID: 32020244
  • title: Aerosticca soli gen. nov., sp. nov., an aerobic gammaproteobacterium isolated from crude oil-contaminated soil.
  • authors: Watanabe M, Kojima H, Fukui M
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-020-01819-w
  • year: 2020
  • mesh: Bacterial Typing Techniques, Base Composition/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/genetics, Petroleum/*microbiology, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology, Ubiquinone/analysis, Xanthomonadaceae/*classification/genetics/*isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
66008Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105662Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105662)
68269Miho Watanabe, Hisaya Kojima & Manabu FukuAerosticca soli gen. nov., sp. nov., an aerobic gammaproteobacterium isolated from crude oil-contaminated soil10.1007/s00203-020-01819-wArch Microbiol 202: 1069-1076 2020
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111688Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID402228.1