Strain identifier

BacDive ID: 132518

Type strain: Yes

Species: Arthrobacter deserti

Strain history: <- W. Li, YIM; YIM CS25 <- Z. Yan

NCBI tax ID(s): 1742687 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24307

BacDive-ID: 132518

DSM-Number: 29935

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive

description: Arthrobacter deserti DSM 29935 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from desert soil.

NCBI tax id

  • NCBI tax id: 1742687
  • Matching level: species

strain history

  • @ref: 24307
  • history: <- W. Li, YIM; YIM CS25 <- Z. Yan

doi: 10.13145/bacdive132518.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Arthrobacter
  • species: Arthrobacter deserti
  • full scientific name: Arthrobacter deserti Hu et al. 2016

@ref: 24307

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter deserti

full scientific name: Arthrobacter deserti Hu et al. 2016

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
43967positiveno
69480positive100

colony morphology

  • @ref: 43967
  • colony color: white
  • medium used: T5 agar

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
43967T5 agaryes0.05 % tryptone, 0.1 % glucose, 0.2 % yeast extract, 0.1 % CaCO3, 0.1 % trace salt, 1.5 % agar, pH 7.0
24307TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/92

culture temp

@refgrowthtypetemperaturerange
43967positivegrowth15-40
24307positivegrowth28mesophilic

culture pH

  • @ref: 43967
  • ability: positive
  • type: growth
  • pH: 6.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43967
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes100
69480no99.997

halophily

  • @ref: 43967
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4396717234glucose-builds acid from
4396728017starch-hydrolysis
4396753424tween 20-hydrolysis
4396753425tween 60-hydrolysis
4396753426tween 80-hydrolysis
4396717632nitrate-reduction
4396717128adipate+assimilation
4396727613amygdalin+assimilation
4396718305arbutin+assimilation
4396716947citrate+assimilation
4396717113erythritol+assimilation
4396724265gluconate+assimilation
4396725115malate+assimilation
4396728053melibiose+assimilation
4396718401phenylacetate+assimilation
4396715588D-malate+carbon source
4396715589L-malate+carbon source
43967739183-O-methyl-D-glucose+carbon source
4396730089acetate+carbon source
4396713705acetoacetate+carbon source
4396717925alpha-D-glucose+carbon source
4396773706bromosuccinate+carbon source
4396717057cellobiose+carbon source
4396716947citrate+carbon source
4396718333D-arabitol+carbon source
4396715824D-fructose+carbon source
4396778697D-fructose 6-phosphate+carbon source
4396712936D-galactose+carbon source
439678391D-gluconate+carbon source
4396714314D-glucose 6-phosphate+carbon source
4396716899D-mannitol+carbon source
4396716024D-mannose+carbon source
4396723652dextrin+carbon source
4396717754glycerol+carbon source
43967L-alanine 4-nitroanilide+carbon source
4396730849L-arabinose+carbon source
4396716467L-arginine+carbon source
4396729985L-glutamate+carbon source
4396717115L-serine+carbon source
4396717306maltose+carbon source
43967320061methyl alpha-D-glucopyranoside+carbon source
4396743943methyl alpha-D-mannoside+carbon source
43967506227N-acetylglucosamine+carbon source
4396717309pectin+carbon source
4396717272propionate+carbon source
4396726490quinate+carbon source
4396716634raffinose+carbon source
4396717992sucrose+carbon source
4396733954tagatose+carbon source
4396727082trehalose+carbon source
4396732528turanose+carbon source
439674853esculin+hydrolysis
439675291gelatin+hydrolysis
4396753423tween 40+hydrolysis

metabolite production

  • @ref: 43967
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43967catalase+1.11.1.6
43967cytochrome oxidase-1.9.3.1
43967urease-3.5.1.5
43967arginine dihydrolase-3.5.3.6
43967alkaline phosphatase+3.1.3.1
43967esterase (C 4)+
43967esterase Lipase (C 8)+
43967phosphatase+
43967naphthol-AS-BI-phosphohydrolase+
43967alpha-glucosidase+3.2.1.20

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43967C13:0 anteiso0.1
    43967C15:0 anteiso51.4
    43967C17:0 anteiso8.7
    43967C17:1 anteiso ω9c4.3
    43967C14:00.5
    43967C14:1ω5c0.1
    43967C15:1ω6c0.3
    43967C16:01.1
    43967C16:1ω7c / C16:1ω7c1.7
    43967C18:00.1
    43967C18:1ω9c0.1
    43967C14:0 iso0.5
    43967C15:0 iso18.9
    43967iso-C15:1 H / C15:1 iH / C13:3 OH0.9
    43967C16:0 iso5
    43967C16:1 iso H1.8
    43967C17:0 iso2.8
    43967C17:1 iso ω9c / C16:0 10-methyl2
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: ACTINO
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
24307desert soilXinjiang Uyghur Autonomous Region, Turpan desert (42° 12' 33'' N 89° 17' 47'' E)ChinaCHNAsia42.209289.2964
43967soil sample collected from Turpan desert in Xinjiang Uyghur Autonomous Region, north-western Chinadesert in Xinjiang Uyghur Autonomous RegionChinaCHNAsia42.209289.2964Tryptic soy agarsupplemeted with 100 mg/L nyastatin2 weeks28

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil
#Condition#Xerophilic

Safety information

risk assessment

  • @ref: 24307
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24307
  • description: Arthrobacter sp. YIM CS25 16S ribosomal RNA gene, partial sequence
  • accession: KT946776
  • length: 1491
  • database: ena
  • NCBI tax ID: 1742687

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter deserti CGMCC 1.15091GCA_012395865scaffoldncbi1742687
66792Arthrobacter deserti strain CGMCC 1.150911742687.3wgspatric1742687
66792Arthrobacter deserti CGMCC 1.150912903049818draftimg1742687

GC content

@refGC-contentmethod
4396768.3thermal denaturation, midpoint method (Tm)
2430768.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno72.546yes
flagellatedno93.855no
gram-positiveyes90.592no
anaerobicno98.846yes
aerobicyes94.133no
halophileno58.218no
spore-formingno95.665no
glucose-utilyes85.1yes
thermophileno97.982no
glucose-fermentno89.656no

External links

@ref: 24307

culture collection no.: DSM 29935, CGMCC 1.15091, KCTC 39544, YIM CS25

straininfo link

  • @ref: 90844
  • straininfo: 400969

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26908080Arthrobacter deserti sp. nov., isolated from a desert soil sample.Hu QW, Chu X, Xiao M, Li CT, Yan ZF, Hozzein WN, Kim CJ, Zhi XY, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0009862016Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32886595Arthrobacter mobilis sp. nov., a novel actinobacterium isolated from Cholistan desert soil.Ye JJ, Liu SW, Lu QP, Cheema MT, Abbas M, Sajid I, Huang DL, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0044312020Arthrobacter/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Pakistan, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24307Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29935Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29935)
43967Qing-Wen Hu, Xiao Chu, Min Xiao, Chang-Tian Li, Zheng-Fei Yan, Wael N. Hozzein, Chang-Jin Kim, Xiao-Yang Zhi, Wen-Jun LiArthrobacter deserti sp. nov., isolated from a desert soil sample10.1099/ijsem.0.000986IJSEM 66: 2035-2040 201626908080
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
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
90844Reimer, 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-ID400969.1