Strain identifier

BacDive ID: 140545

Type strain: Yes

Species: Rhizobium zeae

Strain Designation: CRZM18R

NCBI tax ID(s): 1905846 (species)

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General

@ref: 43333

BacDive-ID: 140545

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

description: Rhizobium zeae CRZM18R is an aerobe, thermophilic, Gram-negative bacterium that forms circular colonies and was isolated from surface disinfected roots of Zea mays plants growing in a soil from Ciudad Rodrigo, Salamanca, Spain.

NCBI tax id

  • NCBI tax id: 1905846
  • Matching level: species

doi: 10.13145/bacdive140545.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Rhizobium
  • species: Rhizobium zeae
  • full scientific name: Rhizobium zeae Celador-Lera et al. 2017

@ref: 43333

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium zeae

strain designation: CRZM18R

type strain: yes

Morphology

cell morphology

  • @ref: 43333
  • gram stain: negative
  • cell length: 2.0-3.0 µm
  • cell width: 0.6-0.9 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 43333
  • colony color: pearl-white
  • colony shape: circular
  • medium used: YMA

Culture and growth conditions

culture medium

  • @ref: 43333
  • name: YMA
  • growth: yes
  • composition: 0.4 % yeast extract, 1 % mannitol, 0.02 % K2HPO4, 0.02 % KH2PO4, 0.02 % Mg2SO4.7H2O, 0.01 % NaCl and 2 % agar

culture temp

@refgrowthtypetemperaturerange
43333nogrowth40thermophilic
43333positivegrowth15-35
43333positiveoptimum28mesophilic

culture pH

@refabilitytypepH
43333positiveoptimum7-7.5
43333positivegrowth6-8
43333nogrowth5

Physiology and metabolism

oxygen tolerance

  • @ref: 43333
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43333
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43333NaClpositiveoptimum1 %(w/v)
43333NaClpositivegrowth3.5 %(w/v)
43333NaClnogrowth4 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4333317632nitrate+reduction
4333316301nitrite+reduction
4333317234glucose-fermentation
433334853esculin+hydrolysis
4333337684mannose+carbon source
4333362345L-rhamnose+carbon source
43333506227N-acetylglucosamine+carbon source
4333333942ribose+carbon source
4333317268myo-inositol+carbon source
4333317992sucrose+carbon source
4333317306maltose+carbon source
4333329864mannitol+carbon source
4333317234glucose+carbon source
4333328053melibiose+carbon source
4333318287L-fucose+carbon source
4333317266L-sorbose+carbon source
4333330849L-arabinose+carbon source
4333330089acetate+carbon source
4333316651(S)-lactate+carbon source
4333316004(R)-lactate+carbon source
4333324265gluconate+carbon source
4333325115malate+carbon source
43333L-alanine 4-nitroanilide+carbon source
43333168082-dehydro-D-gluconate+carbon source
43333581435-dehydro-D-gluconate+carbon source
43333161933-hydroxybenzoate+carbon source
4333317203L-proline+carbon source
4333317115L-serine+/-carbon source
4333317240itaconate-carbon source
433339300suberic acid-carbon source
4333315792malonate-carbon source
4333328087glycogen-carbon source
43333161933-hydroxybenzoate-carbon source
4333317814salicin-carbon source
4333317272propionate-carbon source
4333327689decanoate-carbon source
4333331011valerate-carbon source
4333316947citrate-carbon source
4333317128adipate-carbon source
4333315971L-histidine-carbon source
43333370543-hydroxybutyrate-carbon source
4333337684mannose+builds acid from
4333317268myo-inositol+builds acid from
4333317234glucose+builds acid from
4333330849L-arabinose+builds acid from
4333362345L-rhamnose+builds acid from
4333316988D-ribose+builds acid from
4333316024D-mannose+builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.is sensitivesensitivity conc.
4333328971ampicillinyesyes2 µg (disc)
433333515cefuroximeyesyes30 µg (disc)
43333100241ciprofloxacinyesyes5 µg (disc)
4333349566cloxacillinyesyes1 µg (disc)
4333348923erythromycinyesyes2 µg (disc)
4333317833gentamicinyesyes10 µg (disc)
433337507neomycinyesyes5 µg (disc)
4333317334penicillinyesyes10 Unit (disc)
433338309polymyxin byesyes300 Unit (disc)
4333327902tetracyclineyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4333335581indoleno
4333316136hydrogen sulfideno
4333328017starchno

enzymes

@refvalueactivityec
43333catalase+1.11.1.6
43333cytochrome oxidase+1.9.3.1
43333urease+3.5.1.5
43333arginine dihydrolase-3.5.3.6
43333caseinase-3.4.21.50
43333gelatinase-
43333alpha-glucosidase+3.2.1.20
43333beta-glucosidase+3.2.1.21
43333alpha-galactosidase+3.2.1.22
43333beta-galactosidase+3.2.1.23
43333alpha-arabinosidase+3.2.1.55
43333beta-D-fucosidase+3.2.1.38
43333lactosidase+
43333beta-maltosidase+
43333beta-cellobiase+
43333beta-xylosidase+
43333alkaline phosphatase+3.1.3.1
43333acid phosphatase+/-3.1.3.2
43333beta-L-arabinosidase-3.2.1.88
43333alpha-fucosidase-3.2.1.51
43333alpha-mannosidase-3.2.1.24
43333beta-mannosidase-3.2.1.25
43333alpha-maltosidase-
43333alpha-L-rhamnosidase-3.2.1.40
43333alpha-xylosidase-
43333galacturonidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43333C16:011.9
    43333C17:00.1
    43333C18:01
    43333C16:0 3OH2.5
    43333C18:0 3OH0.3
    43333C18:1ω7c 11-methyl1.1
    43333C19:0 cyclo ω8c5.3
    43333C14:0 3OH / C16:1 iso I4.1
    43333C16:1ω7c / C16:1ω6c3.3
    43333C18:1ω7c / C18:1ω6c68.6
  • type of FA analysis: whole cell analysis
  • incubation medium: TY
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 6.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43333
  • sample type: surface disinfected roots of Zea mays (maize) plants growing in a soil from Ciudad Rodrigo, Salamanca, Spain
  • geographic location: Ciudad Rodrigo, Salamanca
  • country: Spain
  • origin.country: ESP
  • continent: Europe
  • latitude: 40
  • longitude: -6
  • enrichment culture: yeast mannitol agar (YMA)
  • enrichment culture composition: 0.4 % yeast extract, 1 % mannitol, 0.02 % K2HPO4, 0.02 % KH2PO4, 0.02 % Mg2SO4.7H2O, 0.01 % NaCl and 2 % agar
  • enrichment culture duration: 4
  • enrichment culture temperature: 28

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Sequence information

16S sequences

  • @ref: 43333
  • description: 16S rRNA gene sequence
  • accession: KX932068
  • database: nuccore

GC content

  • @ref: 43333
  • GC-content: 62.7
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 43333

culture collection no.: LMG 29735, CECT 9169

literature

  • topic: Phylogeny
  • Pubmed-ID: 28699873
  • title: Rhizobium zeae sp. nov., isolated from maize (Zea mays L.) roots.
  • authors: Celador-Lera L, Menendez E, Peix A, Igual JM, Velazquez E, Rivas R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001944
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Spain, Zea mays/*microbiology
  • 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
43333Lorena Celador-Lera, Esther Menéndez, Alvaro Peix, José M. Igual, Encarna Velázquez, Raúl RivasRhizobium zeae sp. nov., isolated from maize (Zea mays L.) roots10.1099/ijsem.0.001944IJSEM 67: 2306-2311 201728699873