Strain identifier

BacDive ID: 166753

Type strain: Yes

Species: Pelagerythrobacter rhizovicinus

Strain Designation: AY-3R

NCBI tax ID(s): 2268576 (species)

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

@ref: 20215

BacDive-ID: 166753

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

description: Pelagerythrobacter rhizovicinus AY-3R is a Gram-negative, motile, rod-shaped bacterium that forms circular colonies and was isolated from the rhizosphere soil of a desert xerophyte H. ammodendron sampled.

NCBI tax id

  • NCBI tax id: 2268576
  • Matching level: species

doi: 10.13145/bacdive166753.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Pelagerythrobacter
  • species: Pelagerythrobacter rhizovicinus
  • full scientific name: Pelagerythrobacter rhizovicinus (Li et al. 2020) Gao et al. 2021

  • synonyms

    • @ref: 20215
    • synonym: Altererythrobacter rhizovicinus

@ref: 20215

domain: Bacteria

phylum: Pseudomonadota

class: Alphaproteobacteria

order: Sphingomonadales

family: Erythrobacteraceae

genus: Pelagerythrobacter

species: Pelagerythrobacter rhizovicinus

full scientific name: Pelagerythrobacter rhizovicinus (Li et al. 2020) Gao et al. 2021

strain designation: AY-3R

type strain: yes

Morphology

cell morphology

  • @ref: 69559
  • gram stain: negative
  • cell length: 0.9-1.3 µm
  • cell width: 0.3-0.5 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: polar

colony morphology

  • @ref: 69559
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Marine agar (MA)

pigmentation

  • @ref: 69559
  • production: yes
  • name: Methanol-soluble pigment

Culture and growth conditions

culture medium

  • @ref: 69559
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
69559positivegrowth20-42
69559positiveoptimum28-30mesophilic

culture pH

@refabilitytypepH
69559positivegrowth6.0-9.0
69559positiveoptimum6.0-7.0

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
69559NaClpositivegrowth0-8 %
69559NaClpositiveoptimum3 %

observation

@refobservation
69559The Growth of the strain was occurs on TSA, ISP 2 agar, NA and MA, weakly on PYG agar, R2A agar and LB agar, but no growth occurs on TY agar and MacConkey agar.
69559The predominant polar lipids are DPG, PC, PE, PG, SGL and one unknown polar lipid.
69559Able to grow aerobically at 20-42 °C

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6955916136hydrogen sulfide-assimilation
6955917128adipate-assimilation
6955922599arabinose-assimilation
6955917306maltose-assimilation
6955962968cellulose-hydrolysis
6955916991dna-hydrolysis
695595291gelatin-hydrolysis
6955917632nitrate-reduction
6955916947citrate+assimilation
6955924265gluconate+assimilation
6955937684mannose+assimilation
6955915824D-fructose+builds acid from
6955928847D-fucose+builds acid from
6955916024D-mannose+builds acid from
6955928066gentiobiose+builds acid from
6955917234glucose+builds acid from
6955928053melibiose+builds acid from
6955916634raffinose+builds acid from
6955917992sucrose+builds acid from
6955927082trehalose+builds acid from
6955930089acetate+carbon source
6955913705acetoacetate+carbon source
6955917925alpha-D-glucose+carbon source
695598295beta-hydroxybutyrate+carbon source
6955917057cellobiose+carbon source
6955912936D-galactose+carbon source
6955918024D-galacturonic acid+carbon source
6955916523D-serine+carbon source
6955923652dextrin+carbon source
6955970744glycyl-L-proline+carbon source
6955916977L-alanine+carbon source
6955917464L-galactonic acid gamma-lactone+carbon source
6955929985L-glutamate+carbon source
6955917115L-serine+carbon source
6955927082trehalose+carbon source
6955953423tween 40+carbon source
695594853esculin+hydrolysis
6955953426tween 80+hydrolysis

metabolite production

  • @ref: 69559
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
69559cytochrome oxidase+1.9.3.1
69559catalase+1.11.1.6
69559alkaline phosphatase+3.1.3.1
69559esterase (C 4)+
69559esterase Lipase (C 8)+
69559leucine arylamidase+3.4.11.1
69559valine arylamidase+
69559cystine arylamidase+3.4.11.3
69559alpha-chymotrypsin+3.4.21.1
69559naphthol-AS-BI-phosphohydrolase+
69559trypsin+3.4.21.4
69559alpha-glucosidase+3.2.1.20
69559beta-glucuronidase+3.2.1.31
69559lipase (C 14)-
69559acid phosphatase-3.1.3.2
69559alpha-galactosidase-3.2.1.22
69559beta-galactosidase-3.2.1.23
69559beta-glucosidase-3.2.1.21
69559N-acetyl-beta-glucosaminidase-3.2.1.52
69559alpha-mannosidase-3.2.1.24
69559alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    69559C14:0 2OH7.2
    69559C15:0 2OH5.7
    69559C16:06.9
    69559C16:0 2OH1.4
    69559C16:1 w5c2.6
    69559C16:1w7c/ C16:1w6c12.5
    69559C17:1 w6c21.4
    69559C17:1 w8c1.3
    69559C18:1 w5c1.1
    69559C18:1 w7c29.8
    69559C18:1 w7c 11-methyl5.9
    69559C19:0 cyclo w8c1.1
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine Agar
  • incubation temperature: 30
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 69559
  • sample type: the rhizosphere soil of a desert xerophyte H. ammodendron sampled
  • geographic location: Badain Jaran Desert, Alexa region Inner Mongolia
  • country: China
  • origin.country: CHN
  • continent: Asia

Sequence information

16S sequences

  • @ref: 20215
  • description: Pelagerythrobacter rhizovicinus 16S ribosomal RNA gene, partial sequence
  • accession: MH611372
  • length: 1457
  • database: ena
  • NCBI tax ID: 2268576

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pelagerythrobacter rhizovicinus AY-3RGCA_004135625contigncbi2268576
69559genome sequenceSDPV00000000ncbi2268576

GC content

  • @ref: 69559
  • GC-content: 66.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes76.755no
flagellatedno81.577no
gram-positiveno97.916no
anaerobicno99.283no
aerobicyes93.366no
halophileno88.921no
spore-formingno92.991no
thermophileno95.728no
glucose-utilyes83.395no
glucose-fermentno89.18no

External links

@ref: 20215

culture collection no.: KCTC 72280, MCCC 1K03572

literature

  • topic: Phylogeny
  • Pubmed-ID: 31675287
  • title: Altererythrobacter rhizovicinus sp. nov., isolated from rhizosphere soil of Haloxylon ammodendron.
  • authors: Li HP, Yao D, Shao KZ, Han QQ, Gou JY, Zhao Q, Zhang JL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003817
  • year: 2020
  • mesh: Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/url
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
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
69559Hui-Ping Li, Dan Yao, Kun-Zhong Shao, Qing-Qing Han, Jing-Yi Gou, Qi Zhao and Jin-Lin ZhangAltererythrobacter rhizovicinus sp. nov., isolated from rhizosphere soil of Haloxylon ammodendron10.1099/ijsem.0.003817