Strain identifier

BacDive ID: 159664

Type strain: Yes

Species: Allorhizocola rhizosphaerae

Strain history: <- Yu-Qin Zhang, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

NCBI tax ID(s): 1872709 (species)

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General

@ref: 66514

BacDive-ID: 159664

DSM-Number: 102292

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

description: Allorhizocola rhizosphaerae DSM 102292 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1872709
  • Matching level: species

strain history

@refhistory
66514<- C. F. Zhang, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; CPCC 204380
67771<- Yu-Qin Zhang, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

doi: 10.13145/bacdive159664.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Allorhizocola
  • species: Allorhizocola rhizosphaerae
  • full scientific name: Allorhizocola rhizosphaerae Sun et al. 2019

@ref: 66514

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micromonosporales

family: Micromonosporaceae

genus: Allorhizocola

species: Allorhizocola rhizosphaerae

full scientific name: Allorhizocola rhizosphaerae Sun et al. 2019

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91
6948090.365positive

colony morphology

@refcolony colormedium used
69251Beige (1001)ISP 2
69251Ivory (1014)ISP 4
69251Ivory (1014)ISP 6
69251Ivory (1014), light ivory (1015)ISP 3
69251Ivory (1014), light ivory (1015)ISP 5
69251Light ivory (1015)ISP 7
69251Olive yellow (1020)suter with tyrosine
69251Olive yellow (1020)suter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69251noAerial myceliumISP 2
69251noAerial myceliumISP 3
69251noAerial myceliumISP 4
69251noAerial myceliumISP 5
69251noAerial myceliumISP 6
69251noAerial myceliumISP 7
69251noAerial myceliumsuter with tyrosine
69251noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69251noMelanin
69251nosoluble pigment

Culture and growth conditions

culture medium

  • @ref: 66514
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
66514positivegrowth28
67771positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 97

halophily

  • @ref: 69251
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6925122599arabinose+growth
6925162968cellulose+/-growth
6925128757fructose-growth
6925117234glucose+growth
6925117268inositol-growth
6925137684mannose-growth
6925116634raffinose+/-growth
6925126546rhamnose+growth
6925117992sucrose-growth
6925118222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382naphthol-AS-BI-phosphohydrolase-
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69251---+-++---+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69251++/-+/-+/-++/---++/--+/-+-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
66514soilXinjiang, Yili ValleyChinaCHNAsia81.216742.5667
67771From soil sampleXinjiang Province China.ChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Sequence information

16S sequences

  • @ref: 66514
  • description: Allorhizocola rhizosphaerae strain CPCC 204380 16S ribosomal RNA gene, partial sequence
  • accession: KX128909
  • length: 1536
  • database: nuccore
  • NCBI tax ID: 1872709

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Allorhizocola rhizosphaerae CPCC 204380GCA_003426775contigncbi1872709
66792Micromonosporaceae bacterium CPCC 2043801872709.3wgspatric1872709
66792Allorhizocola rhizosphaerae CPCC 2043802866347563draftimg1872709

GC content

  • @ref: 66514
  • GC-content: 64.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes97no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.365no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.28no
69480spore-formingspore-formingAbility to form endo- or exosporesyes87.126no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes87.897yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.4no
69480flagellatedmotile2+Ability to perform flagellated movementno91no

External links

@ref: 66514

culture collection no.: DSM 102292, KCTC 39746, CPCC 204380

straininfo link

  • @ref: 112138
  • straininfo: 404393

literature

  • topic: Phylogeny
  • Pubmed-ID: 30444473
  • title: Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum.
  • authors: Sun Y, Jiang ZM, Zhao LL, Su J, Yu LY, Tian YQ, Zhang YQ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003114
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, Polygonaceae/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcatalogue
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
66514Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102292Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102292)
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69251Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%20102292.pdf
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
112138Reimer, 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-ID404393.1