Strain identifier

BacDive ID: 166117

Type strain: Yes

Species: Neorhizobium deserti

Strain Designation: SPY-1

NCBI tax ID(s): 2547961 (species)

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General

@ref: 68063

BacDive-ID: 166117

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

description: Neorhizobium deserti SPY-1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from biological soil crusts.

NCBI tax id

  • NCBI tax id: 2547961
  • Matching level: species

doi: 10.13145/bacdive166117.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Neorhizobium
  • species: Neorhizobium deserti
  • full scientific name: Neorhizobium deserti (Liu et al. 2020) Ma et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Rhizobium deserti

@ref: 68063

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhizobiaceae

genus: Rhizobium

species: Rhizobium deserti

strain designation: SPY-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
68063negative0.7-2.0 µm0.3-0.7 µmrod-shapedno
69480negative97.833

colony morphology

  • @ref: 68063
  • colony size: 2.0-3.0 mm
  • colony color: milky
  • colony shape: circular
  • incubation period: 2 days
  • medium used: YMA

Culture and growth conditions

culture temp

@refgrowthtypetemperature
68063positivegrowth15-37
68063positiveoptimum30

culture pH

@refabilitytypepHPH range
68063positivegrowth6.0-9.0alkaliphile
68063positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 68063
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
68063NaClpositivegrowth0.0-2.0 %(w/v)
68063NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 68063
  • observation: the common genes required for legume nodulation, nodACD and nifH, are absent from the genome

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6806317315D-glucosamine+carbon source
68063495056gamma-cyclodextrin+carbon source
6806363154N-acetyl-beta-D-mannosamine+carbon source
6806317925alpha-D-glucose+carbon source
6806316024D-mannose+carbon source
6806315824D-fructose+carbon source
6806312936D-galactose+carbon source
6806328847D-fucose+carbon source
6806342548alpha-L-fucose+carbon source
6806362345L-rhamnose+carbon source
6806316899D-mannitol+carbon source
6806318333D-arabitol+carbon source
6806317268myo-inositol+carbon source
6806317754glycerol+carbon source
6806370744glycyl-L-proline+carbon source
68063L-alanine 4-nitroanilide+carbon source
6806329991L-aspartate+carbon source
6806329985L-glutamate+carbon source
6806318024D-galacturonic acid+carbon source
6806324265gluconate+carbon source
6806324297glucuronate+carbon source
6806332323glucuronamide+carbon source
680632-oxogluconate+carbon source
6806325115malate+carbon source
6806315589L-malate+carbon source
6806373706bromosuccinate+carbon source
6806353423tween 40+carbon source
680638295beta-hydroxybutyrate+carbon source
6806313705acetoacetate+carbon source
6806316411acetic acid+carbon source
680634853esculin+hydrolysis
680635291gelatin+/-hydrolysis
6806328017starch-hydrolysis
68063casein-hydrolysis
6806337684mannose+assimilation
68063506227N-acetyl-D-glucosamine+assimilation
6806317306maltose+assimilation
6806316947citrate+assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6806316136hydrogen sulfideno
6806335581indoleno

enzymes

@refvalueactivityec
68063urease-3.5.1.5
68063alkaline phosphatase+3.1.3.1
68063esterase (C 4)+
68063esterase Lipase (C 8)+
68063leucine arylamidase+3.4.11.1
68063acid phosphatase+3.1.3.2
68063naphthol-AS-BI-phosphohydrolase+
68063beta-glucosidase+3.2.1.21

Isolation, sampling and environmental information

isolation

  • @ref: 68063
  • sample type: biological soil crusts
  • geographic location: Mu Us Sandy Land in the Erdos Wushenqi areas of Inner Mongolia
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 38.1589
  • longitude: 108.641

Sequence information

16S sequences

  • @ref: 68063
  • description: Rhizobium deserti 16S ribosomal RNA gene, partial sequence
  • accession: MK685279.1
  • length: 1469
  • database: nuccore
  • NCBI tax ID: 2547961

Genome sequences

  • @ref: 66792
  • description: Rhizobium deserti SPY-1
  • accession: GCA_004358025
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2547961

GC content

  • @ref: 68063
  • GC-content: 60
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.833yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.08yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes83.846yes
69480spore-formingspore-formingAbility to form endo- or exosporesno86.713no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.514yes
69480flagellatedmotile2+Ability to perform flagellated movementyes67.697no

External links

@ref: 68063

culture collection no.: ACCC 61627, JCM 33732

literature

  • topic: Phylogeny
  • Pubmed-ID: 31820041
  • title: Rhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China.
  • authors: Liu L, Liang L, Xu L, Chi M, Zhang X, Li L
  • journal: Curr Microbiol
  • DOI: 10.1007/s00284-019-01831-4
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/isolation & purification, Sand/microbiology, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
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
68063Lei Liu, Lixiong Liang, Lijun Xu, Miao Chi, Xiaoxia Zhang, Lubin LiRhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China10.1007/s00284-019-01831-4Curr Microbiol 77: 327-333 2020
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