Strain identifier

BacDive ID: 140478

Type strain: Yes

Species: Bradyrhizobium mercantei

Strain Designation: U675

NCBI tax ID(s): 1904807 (species)

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

@ref: 43227

BacDive-ID: 140478

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

description: Bradyrhizobium mercantei U675 is an aerobe, mesophilic, Gram-negative bacterium that forms oval colonies and was isolated from nodules of Deguelia costata.

NCBI tax id

  • NCBI tax id: 1904807
  • Matching level: species

doi: 10.13145/bacdive140478.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Bradyrhizobium
  • species: Bradyrhizobium mercantei
  • full scientific name: Bradyrhizobium mercantei Helene et al. 2017

@ref: 43227

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Bradyrhizobiaceae

genus: Bradyrhizobium

species: Bradyrhizobium mercantei

strain designation: U675

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
43227negativerod-shaped
69480yes95.217
69480negative99.983

colony morphology

  • @ref: 43227
  • colony size: 1 mm
  • colony color: translucent
  • colony shape: oval
  • incubation period: 7 days
  • medium used: yeast extract-mannitol agar (YMA)

Culture and growth conditions

culture medium

@refnamegrowth
43227yeast extract-mannitol agar (YMA)yes
43227LB (Luria-Bertani) MEDIUMno

culture temp

@refgrowthtypetemperaturerange
43227positiveoptimum28mesophilic
43227nogrowth37mesophilic

culture pH

@refabilitytypepH
43227positivegrowth4.5
43227positivegrowth8
43227positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

  • @ref: 43227
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43227no
69481no98
69480no99.9

halophily

  • @ref: 43227
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4322717754glycerol+carbon source
4322717108D-arabinose+carbon source
4322730849L-arabinose+carbon source
4322716988D-ribose+carbon source
4322765327D-xylose+carbon source
4322765328L-xylose+carbon source
4322712936D-galactose+carbon source
4322717634D-glucose+carbon source
4322715824D-fructose+carbon source
4322716024D-mannose+carbon source
4322716899D-mannitol+carbon source
4322717924D-sorbitol+carbon source
432274853esculin+carbon source
4322728087glycogen+carbon source
4322717151xylitol+carbon source
4322762318D-lyxose+carbon source
4322728847D-fucose+carbon source
4322718287L-fucose+carbon source
4322718333D-arabitol+carbon source
4322718403L-arabitol+carbon source
4322717113erythritol+carbon source
4322715963ribitol+carbon source
4322774863methyl beta-D-xylopyranoside+carbon source
4322762345L-rhamnose+carbon source
4322716813galactitol+carbon source
4322717268myo-inositol+carbon source
4322718305arbutin+carbon source
4322717814salicin+carbon source
4322717306maltose+carbon source
4322717716lactose+carbon source
4322728017starch+carbon source
4322732528turanose+carbon source
4322717266L-sorbose-carbon source
4322743943methyl alpha-D-mannoside-carbon source
43227320061methyl alpha-D-glucopyranoside-carbon source
43227506227N-acetylglucosamine-carbon source
4322727613amygdalin-carbon source
4322717057cellobiose-carbon source
4322728053melibiose-carbon source
4322717992sucrose-carbon source
4322727082trehalose-carbon source
4322715443inulin-carbon source
432276731melezitose-carbon source
4322716634raffinose-carbon source
4322728066gentiobiose-carbon source
4322716443D-tagatose-carbon source
4322732032potassium gluconate-carbon source
43227potassium 2-dehydro-D-gluconate-carbon source
43227potassium 5-dehydro-D-gluconate-carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.
4322728971ampicillinyesyes10 µg (disc)
4322728669bacitracinyesyes0.04 Unit (disc)
432273515cefuroximeyesyes30 µg (disc)
4322717698chloramphenicolyesyes30 µg (disc)
4322748923erythromycinyesyes15 µg (disc)
43227100147nalidixic acidyesyes30 µg (disc)
432277507neomycinyesyes30 µg (disc)
4322717334penicillinyesyes10 Unit (disc)
4322717076streptomycinyesyes10 µg (disc)
4322727902tetracyclineyesyes30 µg (disc)

enzymes

  • @ref: 43227
  • value: urease
  • activity: +
  • ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 43227
  • sample type: nodules of Deguelia costata
  • geographic location: southeast Brazil
  • country: Brazil
  • origin.country: BRA
  • continent: Middle and South America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host#Plants#Tree
#Host Body-Site#Plant#Root nodule

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bradyrhizobium mercantei SEMIA 6399GCA_001982635contigncbi1904807
66792Bradyrhizobium sp. SEMIA 6399 strain SEMIA 63991904807.3wgspatric1904807
66792Bradyrhizobium mercantei SEMIA 63992876791980draftimg1904807

GC content

  • @ref: 43227
  • GC-content: 63.99
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileyes84.456no
gram-positiveno98.066yes
anaerobicno98.07no
aerobicyes91.864no
halophileno96.147no
spore-formingno93.148yes
glucose-utilyes89.134yes
flagellatedno68.824no
thermophileno99.135yes
glucose-fermentno90.446no

External links

@ref: 43227

culture collection no.: LMG 30031, BR 6010, CNPSo 1165, SEMIA 6399

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28639930Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus).Helene LCF, Delamuta JRM, Ribeiro RA, Hungria MInt J Syst Evol Microbiol10.1099/ijsem.0.0018702017Bacterial Typing Techniques, Base Composition, Bradyrhizobium/*classification/genetics/isolation & purification, Brazil, DNA, Bacterial/genetics, Fabaceae/*microbiology, Genes, Bacterial, Multilocus Sequence Typing, Nitrogen Fixation, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNATranscriptome
Genetics28883142Genome Sequence of Bradyrhizobium mercantei Strain SEMIA 6399(T), Isolated from Nodules of Deguelia costata in Brazil.Ribeiro RA, Helene LCF, Delamuta JRM, Hungria MGenome Announc10.1128/genomeA.00943-172017Phylogeny

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
43227Luisa Caroline Ferraz Helene, Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Mariangela HungriaBradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus)10.1099/ijsem.0.001870IJSEM 67: 1827-1834 201728639930
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
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