Strain identifier

BacDive ID: 159849

Type strain: Yes

Species: Mesorhizobium ephedrae

Strain Designation: 6GN-30

Strain history: <- Lei Liu, Research Institute of Forestry, Chinese Academy of Forestry

NCBI tax ID(s): 2116701 (species)

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General

@ref: 66753

BacDive-ID: 159849

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

description: Mesorhizobium ephedrae 6GN-30 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from the root of E. przewalskii.

NCBI tax id

  • NCBI tax id: 2116701
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Lei Liu, Research Institute of Forestry, Chinese Academy of Forestry

doi: 10.13145/bacdive159849.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Phyllobacteriaceae
  • genus: Mesorhizobium
  • species: Mesorhizobium ephedrae
  • full scientific name: Mesorhizobium ephedrae Liu et al. 2018

@ref: 66753

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Phyllobacteriaceae

genus: Mesorhizobium

species: Mesorhizobium ephedrae

strain designation: 6GN-30

type strain: yes

Morphology

cell morphology

  • @ref: 66753
  • gram stain: negative
  • cell length: 0.9-2.0 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 66753
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Trypticase Soy Agar (TSA)

Culture and growth conditions

culture medium

  • @ref: 66753
  • name: tryptic soy agar (TSA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
66753positiveoptimum30mesophilic
66753positivegrowth15-45
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
66753positivegrowth6.0-9.0alkaliphile
66753positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66753aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
66753NaClpositivegrowth0-1.0 %(w/v)
66753NaClpositiveoptimum0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6675317128adipate+assimilation
6675317234glucose+assimilation
6675317306maltose+assimilation
6675322599arabinose+assimilation
6675325115malate+assimilation
6675329864mannitol+assimilation
6675332032potassium gluconate+assimilation
6675337684mannose+assimilation
6675353258citric acid+assimilation
6675359640N-acetylglucosamine+assimilation
667535291gelatin-carbon source
6675314314D-glucose 6-phosphate-carbon source
6675315588D-malate-carbon source
6675315589L-malate-carbon source
6675315748D-glucuronate-carbon source
6675316523D-serine-carbon source
6675316634raffinose-carbon source
6675316865gamma-aminobutyric acid-carbon source
6675317057cellobiose-carbon source
6675317115L-serine-carbon source
6675317164stachyose-carbon source
6675317272propionate-carbon source
6675317716lactose-carbon source
6675318183L-pyroglutamic acid-carbon source
6675318333D-arabitol-carbon source
6675326490quinate-carbon source
6675328053melibiose-carbon source
6675328066gentiobiose-carbon source
6675328800N-acetylgalactosamine-carbon source
6675329990D-aspartate-carbon source
6675330612D-glucarate-carbon source
6675335418n-acetylneuraminate-carbon source
6675348607lithium chloride-carbon source
6675353258citric acid-carbon source
6675363153N-acetyl-D-mannosamine-carbon source
6675364103sodium butyrate-carbon source
6675371321fusidate-carbon source
6675373706bromosuccinate-carbon source
66753739183-O-methyl-D-glucose-carbon source
6675375229sodium bromate-carbon source
6675375248potassium tellurite-carbon source
6675378697D-fructose 6-phosphate-carbon source
66753100147nalidixic acid-carbon source
66753161680aztreonam-carbon source
667531 % sodium lactate-carbon source
66753168102-oxoglutarate-carbon source
6675312936D-galactose+carbon source
6675313705acetoacetate+carbon source
6675315740formate+carbon source
6675315748D-glucuronate+carbon source
6675315824D-fructose+carbon source
6675315971L-histidine+carbon source
6675316024D-mannose+carbon source
6675316411acetic acid+carbon source
6675316467L-arginine+carbon source
6675316537galactarate+carbon source
6675316551D-trehalose+carbon source
6675316651(S)-lactate+carbon source
66753167632-oxobutanoate+carbon source
6675316899D-mannitol+carbon source
6675316977L-alanine+carbon source
6675317268myo-inositol+carbon source
6675317306maltose+carbon source
6675317309pectin+carbon source
6675317464L-galactonic acid gamma-lactone+carbon source
6675317596inosine+carbon source
6675317754glycerol+carbon source
6675317814salicin+carbon source
6675317924D-sorbitol+carbon source
6675317925alpha-D-glucose+carbon source
6675317992sucrose+carbon source
6675318024D-galacturonic acid+carbon source
66753181014-hydroxyphenylacetic acid+carbon source
6675318287L-fucose+carbon source
6675323652dextrin+carbon source
6675328847D-fucose+carbon source
6675329985L-glutamate+carbon source
6675329991L-aspartate+carbon source
6675332323glucuronamide+carbon source
6675332528turanose+carbon source
66753370543-hydroxybutyrate+carbon source
6675351850methyl pyruvate+carbon source
6675353423tween 40+carbon source
6675359640N-acetylglucosamine+carbon source
6675362345L-rhamnose+carbon source
6675370744glycine-proline+carbon source
6675374611methyl (R)-lactate+carbon source
66753320055methyl beta-D-glucopyranoside+carbon source
66753alpha-hydroxybutyrate+carbon source
667534853esculin-hydrolysis
6675328017starch-hydrolysis
66753casein-hydrolysis
667535291gelatin+hydrolysis
6675317632nitrate-reduction

metabolite production

  • @ref: 66753
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 66753
  • Chebi-ID: 35581
  • metabolite: indole
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
66753alpha-chymotrypsin-3.4.21.1
66753alpha-fucosidase-3.2.1.51
66753alpha-galactosidase-3.2.1.22
66753alpha-glucosidase-3.2.1.20
66753alpha-mannosidase-3.2.1.24
66753arginine dihydrolase-3.5.3.6
66753beta-galactosidase-3.2.1.23
66753beta-glucosidase-3.2.1.21
66753beta-glucuronidase-3.2.1.31
66753cystine arylamidase-3.4.11.3
66753leucine aminopeptidase-3.4.1.1
66753lipase (C 14)-
66753N-acetyl-beta-glucosaminidase-3.2.1.52
66753tryptophan deaminase-4.1.99.1
66753urease-3.5.1.5
66753acid phosphatase+3.1.3.2
66753alkaline phosphatase+3.1.3.1
66753catalase+1.11.1.6
66753cytochrome oxidase+1.9.3.1
66753esterase (C 4)+
66753esterase Lipase (C 8)+
66753leucine arylamidase+3.4.11.1
66753naphthol-AS-BI-phosphohydrolase+
66753trypsin+3.4.21.4
66753valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
66753the root of E. przewalskiiEphedra przewalskiiKumtag Desert, XinjiangChinaCHNAsianutrient agar plates and R2A agar5-7 days30The roots of E. przewalskii were collected from the Kumtag Desert, Xinjiang, PR China. The root surface was sterilized as previously described, with some modifications. Samples were washed with tap water and sterilized with 70 % ethanol for 30 s, then immersed in 2.0 % sodium hypochlorite solution for 10-15 min, followed by three or four rinses with sterile distilled water. Sterilized roots (1 g) were ground with a sterile mortar and pestle and serially diluted in sterile distilled water, then incubated on nutrient agar plates and R2A agar plates at 30°C for 5-7 days.
67771From Ephedra sinica, Kumtag desertChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

Sequence information

16S sequences

  • @ref: 66753
  • description: Mesorhizobium sp. strain 6GN-30 16S ribosomal RNA gene, partial sequence
  • accession: MH105075
  • length: 1406
  • database: ena
  • NCBI tax ID: 1871066

Genome sequences

  • @ref: 66792
  • description: Mesorhizobium ephedrae 6GN-30
  • accession: GCA_003012745
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2116701

GC content

  • @ref: 66753
  • GC-content: 66.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno86.625no
gram-positiveno97.444no
anaerobicno97.622no
aerobicyes92.114yes
halophileno91.868yes
spore-formingno95.068no
glucose-utilyes89.683yes
thermophileno97.307yes
motileyes89.237yes
glucose-fermentno89.058no

External links

@ref: 66753

culture collection no.: ACCC 60073, KCTC 62410

literature

  • topic: Phylogeny
  • Pubmed-ID: 30272540
  • title: Mesorhizobium ephedrae sp. nov. isolated from the roots of Ephedra przewalskii in Kumtag desert.
  • authors: Liu L, Liang LX, Zhang XX, Li LB, Sun QW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003044
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Desert Climate, Ephedra/*microbiology, Fatty Acids/chemistry, Mesorhizobium/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • 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
66753Lei Liu, Li-xiong Liang, Xiao-xia Zhang, Lu-bin Li, Qi-wu SunMesorhizobium ephedrae sp. nov. isolated from the roots of Ephedra przewalskii in Kumtag desert10.1099/ijsem.0.003044IJSEM 68: 3615-3620 201830272540
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