Strain identifier

BacDive ID: 140971

Type strain: Yes

Species: Arenimonas soli

Strain Designation: Y3L17

Strain history: <- SUN, Ji-Quan, Peking Univ.

NCBI tax ID(s): 2269504 (species)

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General

@ref: 43863

BacDive-ID: 140971

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

description: Arenimonas soli Y3L17 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from saline-alkaline soil from farmland in Hangjin Banner, Ordos, Inner Mongolia, northern China.

NCBI tax id

  • NCBI tax id: 2269504
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- SUN, Ji-Quan, Peking Univ.

doi: 10.13145/bacdive140971.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Arenimonas
  • species: Arenimonas soli
  • full scientific name: Arenimonas soli Xu et al. 2017

@ref: 43863

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Lysobacteraceae

genus: Arenimonas

species: Arenimonas soli

strain designation: Y3L17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43863negative0.8-1.3 µm0.3-0.4 µmrod-shapedno
69480negative99.979

colony morphology

  • @ref: 43863
  • colony size: 1 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: Luria-Bertani agar

Culture and growth conditions

culture medium

@refnamegrowth
43863LB (Luria-Bertani) MEDIUMyes
43863Tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
43863positivegrowth15-45
43863positiveoptimum35mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43863positivegrowth6.0-10.0alkaliphile
43863positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43863aerobe
67771aerobe

spore formation

@refspore formationconfidence
43863no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
43863NaClpositivegrowth0-4 %(w/v)
43863NaClpositiveoptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4386315589L-malate-assimilation
4386330089acetate-assimilation
4386317128adipate-assimilation
4386335391aspartate-assimilation
4386328885butanol-assimilation
4386327689decanoate-assimilation
4386316947citrate-assimilation
4386316919creatine-assimilation
4386317634D-glucose-assimilation
4386365327D-xylose-assimilation
4386316236ethanol-assimilation
4386317268myo-inositol-assimilation
4386330849L-arabinose-assimilation
4386316467L-arginine-assimilation
4386329985L-glutamate-assimilation
4386315603L-leucine-assimilation
4386317295L-phenylalanine-assimilation
4386317115L-serine-assimilation
4386317716lactose-assimilation
4386315792malonate-assimilation
4386317306maltose-assimilation
4386317790methanol-assimilation
43863506227N-acetylglucosamine-assimilation
4386318401phenylacetate-assimilation
4386332032potassium gluconate-assimilation
4386353258sodium citrate-assimilation
4386317632nitrate-reduction
4386315824D-fructose+assimilation
4386316024D-mannose+assimilation
4386317234glucose+assimilation
4386317203L-proline+assimilation
4386362345L-rhamnose+assimilation
4386317992sucrose+assimilation
4386317234glucose+fermentation
438635291gelatin+hydrolysis

metabolite production

  • @ref: 43863
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43863cytochrome oxidase+1.9.3.1
43863catalase-1.11.1.6
43863leucine arylamidase+3.4.11.1
43863arginine dihydrolase+3.5.3.6
43863urease+3.5.1.5
43863alkaline phosphatase+3.1.3.1
43863esterase (C 4)+
43863esterase Lipase (C 8)+
43863alpha-chymotrypsin+3.4.21.1
43863acid phosphatase+3.1.3.2
43863valine arylamidase-
43863cystine arylamidase-3.4.11.3
43863trypsin-3.4.21.4
43863naphthol-AS-BI-phosphohydrolase-
43863beta-galactosidase-3.2.1.23
43863alpha-glucosidase-3.2.1.20
43863beta-glucosidase-3.2.1.21
43863lipase (C 14)-
43863alpha-galactosidase-3.2.1.22
43863N-acetyl-beta-glucosaminidase-3.2.1.52
43863beta-glucuronidase-3.2.1.31
43863alpha-mannosidase-3.2.1.24
43863alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture
43863saline-alkaline soil from farmland in Hangjin Banner, Ordos, Inner Mongolia, northern ChinaHangjin Banner, Ordos, Inner MongoliaChinaCHNAsia40.07107.823Luria-Bertani agar
67771From saline-alkaline soil, Farmland soilOrdos, Inner MongoliaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Condition#Alkaline
#Condition#Saline
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 43863
  • description: 16S rRNA gene sequence
  • accession: KX756571
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arenimonas soli CGMCC 1.15905GCA_014643775contigncbi2269504
66792Arenimonas soli strain CGMCC 1.159052269504.3wgspatric2269504

GC content

  • @ref: 43863
  • GC-content: 65.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno84.917yes
gram-positiveno98.46no
anaerobicno98.629yes
aerobicyes90.435yes
halophileno87.176no
spore-formingno98.178no
glucose-utilyes78.583no
flagellatedno93.124no
thermophileno97.896yes
glucose-fermentno88.139yes

External links

@ref: 43863

culture collection no.: CGMCC 1.15905, KCTC 52420

literature

  • topic: Phylogeny
  • Pubmed-ID: 28853685
  • title: Arenimonas soli sp. nov., isolated from saline-alkaline soil.
  • authors: Xu L, Sun JQ, Liu X, Liu XZ, Qiao MQ, Wu XL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002026
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification
  • 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
43863Lian Xu, Ji-Quan Sun, Xia Liu, Xiao Zhen Liu, Ming-Quan Qiao, Xiao-Lei WuArenimonas soli sp. nov., isolated from saline–alkaline soil10.1099/ijsem.0.002026IJSEM 67: 2829-2833 201728853685
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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