Strain identifier

BacDive ID: 7630

Type strain: Yes

Species: Arthrobacter cupressi

Strain Designation: D48

Strain history: CIP <- 2013, DSMZ <- Y. Ma, Beijing Forestry Univ., China: strain D48

NCBI tax ID(s): 1045773 (species)

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General

@ref: 17726

BacDive-ID: 7630

DSM-Number: 24664

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, ovoid-shaped

description: Arthrobacter cupressi D48 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rhizosphere soil, cypress tree .

NCBI tax id

  • NCBI tax id: 1045773
  • Matching level: species

strain history

@refhistory
17726<- Y. Ma, Beijing Forestry Univ., College Biological Scs. and Biotechnol., China; D48 <- Y. Ma and J. Zhang
67770CGMCC 1.10783 <-- J. Zhang et al. D48.
118819CIP <- 2013, DSMZ <- Y. Ma, Beijing Forestry Univ., China: strain D48

doi: 10.13145/bacdive7630.20230509.8.1

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 cupressi
  • full scientific name: Arthrobacter cupressi Zhang et al. 2012

@ref: 17726

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter cupressi

full scientific name: Arthrobacter cupressi Zhang et al. 2012 emend. Nouioui et al. 2018

strain designation: D48

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30474positiveovoid-shapedno
69480positive100
118819positiverod-shapedno

pigmentation

  • @ref: 30474
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41616MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
17726TRYPTICASE 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
118819CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
17726positivegrowth28mesophilic
30474positivegrowth12-37
30474positiveoptimum28mesophilic
41616positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30474positivegrowth5.5-9alkaliphile
30474positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30474
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30474no
69480no99.916

halophily

@refsaltgrowthtested relationconcentration
30474NaClpositivegrowth0-2 %
30474NaClpositiveoptimum0.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-7(H2), MK-10(H2), MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3047430089acetate+carbon source
3047416449alanine+carbon source
3047422653asparagine+carbon source
3047423652dextrin+carbon source
3047428757fructose+carbon source
3047428260galactose+carbon source
3047424265gluconate+carbon source
3047417234glucose+carbon source
3047429987glutamate+carbon source
3047417754glycerol+carbon source
3047417596inosine+carbon source
3047425115malate+carbon source
3047417306maltose+carbon source
3047429864mannitol+carbon source
3047437684mannose+carbon source
3047428053melibiose+carbon source
3047415361pyruvate+carbon source
3047451850methyl pyruvate+carbon source
3047416634raffinose+carbon source
3047417822serine+carbon source
3047417992sucrose+carbon source
3047453423tween 40+carbon source
3047453426tween 80+carbon source
304744853esculin+hydrolysis

enzymes

@refvalueactivityec
30474acid phosphatase+3.1.3.2
30474alkaline phosphatase+3.1.3.1
30474alpha-galactosidase+3.2.1.22
30474catalase+1.11.1.6
30474gelatinase+
30474urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
17726rhizosphere soil, cypress tree (Cupressus sempervirens)Cupressus sempervirensSichuan province, MianyangChinaCHNAsia
67770Rhizosphere soil of a cypress tree (Cupressus sempervirens)Cupressus sempervirensMianyang, Sichuan ProvinceChinaCHNAsia
118819Environment, Rhizosphere soil, cypress tree, Cupressus sempervirensSichuan Province, Mianyang, ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Tree
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
177261Risk group (German classification)
1188191Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17726
  • description: Arthrobacter cupressi strain D48 16S ribosomal RNA gene, partial sequence
  • accession: HQ657321
  • length: 1491
  • database: ena
  • NCBI tax ID: 1045773

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter cupressi strain CGMCC 1.107831045773.8wgspatric1045773
66792Arthrobacter cupressi strain DSM 246641045773.10wgspatric1045773
66792Arthrobacter cupressi DSM 246642844849076draftimg1045773
66792Arthrobacter cupressi CGMCC 1.107832663762744draftimg1045773
67770Arthrobacter cupressi CGMCC 1.10783GCA_900099975scaffoldncbi1045773
67770Arthrobacter cupressi DSM 24664GCA_013409905contigncbi1045773

GC content

@refGC-contentmethod
1772665.0thermal denaturation, midpoint method (Tm)
3047465
6777065thermal denaturation, midpoint method (Tm)
6777067genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
motileno93.291no
flagellatedno96.008no
gram-positiveyes91.195yes
anaerobicno99.606yes
aerobicyes97.048yes
halophileno91.687yes
spore-formingno89.967yes
thermophileno96.795yes
glucose-utilyes85.579yes
glucose-fermentno86.193no

External links

@ref: 17726

culture collection no.: DSM 24664, CGMCC 1.10783, CIP 110640, JCM 19662

straininfo link

  • @ref: 77074
  • straininfo: 398746

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22228666Arthrobacter cupressi sp. nov., an actinomycete isolated from the rhizosphere soil of Cupressus sempervirens.Zhang J, Ma Y, Yu HInt J Syst Evol Microbiol10.1099/ijs.0.036889-02012Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, Cupressus/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny30351271Arthrobacter silvisoli sp. nov., isolated from forest soil.Yan R, Fu Y, Liu D, Jiang S, Ju H, Guo X, Guo X, Wang X, Zhang J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0030852018Arthrobacter/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31329533Arthrobacter celericrescens sp. nov., isolated from forest soil.Yan R, Liu D, Fu Y, Zhang Y, Ju H, Zhao J, Wang X, Zhang J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0035972019Arthrobacter/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17726Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24664)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24664
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
30474Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2680928776041
41616Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30444
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
77074Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398746.1StrainInfo: A central database for resolving microbial strain identifiers
118819Curators of the CIPCollection of Institut Pasteur (CIP 110640)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110640