Strain identifier
BacDive ID: 140478
Type strain:
Species: Bradyrhizobium mercantei
Strain Designation: U675
NCBI tax ID(s): 1904807 (species)
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
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
43227 | negative | rod-shaped | ||
69480 | yes | 95.217 | ||
69480 | negative | 99.983 |
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
@ref | name | growth |
---|---|---|
43227 | yeast extract-mannitol agar (YMA) | yes |
43227 | LB (Luria-Bertani) MEDIUM | no |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43227 | positive | optimum | 28 | mesophilic |
43227 | no | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
43227 | positive | growth | 4.5 |
43227 | positive | growth | 8 |
43227 | positive | optimum | 6.8 |
Physiology and metabolism
oxygen tolerance
- @ref: 43227
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
43227 | no | |
69481 | no | 98 |
69480 | no | 99.9 |
halophily
- @ref: 43227
- salt: NaCl
- growth: no
- tested relation: growth
- concentration: 1 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43227 | 17754 | glycerol | + | carbon source |
43227 | 17108 | D-arabinose | + | carbon source |
43227 | 30849 | L-arabinose | + | carbon source |
43227 | 16988 | D-ribose | + | carbon source |
43227 | 65327 | D-xylose | + | carbon source |
43227 | 65328 | L-xylose | + | carbon source |
43227 | 12936 | D-galactose | + | carbon source |
43227 | 17634 | D-glucose | + | carbon source |
43227 | 15824 | D-fructose | + | carbon source |
43227 | 16024 | D-mannose | + | carbon source |
43227 | 16899 | D-mannitol | + | carbon source |
43227 | 17924 | D-sorbitol | + | carbon source |
43227 | 4853 | esculin | + | carbon source |
43227 | 28087 | glycogen | + | carbon source |
43227 | 17151 | xylitol | + | carbon source |
43227 | 62318 | D-lyxose | + | carbon source |
43227 | 28847 | D-fucose | + | carbon source |
43227 | 18287 | L-fucose | + | carbon source |
43227 | 18333 | D-arabitol | + | carbon source |
43227 | 18403 | L-arabitol | + | carbon source |
43227 | 17113 | erythritol | + | carbon source |
43227 | 15963 | ribitol | + | carbon source |
43227 | 74863 | methyl beta-D-xylopyranoside | + | carbon source |
43227 | 62345 | L-rhamnose | + | carbon source |
43227 | 16813 | galactitol | + | carbon source |
43227 | 17268 | myo-inositol | + | carbon source |
43227 | 18305 | arbutin | + | carbon source |
43227 | 17814 | salicin | + | carbon source |
43227 | 17306 | maltose | + | carbon source |
43227 | 17716 | lactose | + | carbon source |
43227 | 28017 | starch | + | carbon source |
43227 | 32528 | turanose | + | carbon source |
43227 | 17266 | L-sorbose | - | carbon source |
43227 | 43943 | methyl alpha-D-mannoside | - | carbon source |
43227 | 320061 | methyl alpha-D-glucopyranoside | - | carbon source |
43227 | 506227 | N-acetylglucosamine | - | carbon source |
43227 | 27613 | amygdalin | - | carbon source |
43227 | 17057 | cellobiose | - | carbon source |
43227 | 28053 | melibiose | - | carbon source |
43227 | 17992 | sucrose | - | carbon source |
43227 | 27082 | trehalose | - | carbon source |
43227 | 15443 | inulin | - | carbon source |
43227 | 6731 | melezitose | - | carbon source |
43227 | 16634 | raffinose | - | carbon source |
43227 | 28066 | gentiobiose | - | carbon source |
43227 | 16443 | D-tagatose | - | carbon source |
43227 | 32032 | potassium gluconate | - | carbon source |
43227 | potassium 2-dehydro-D-gluconate | - | carbon source | |
43227 | potassium 5-dehydro-D-gluconate | - | carbon source |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. |
---|---|---|---|---|---|
43227 | 28971 | ampicillin | yes | yes | 10 µg (disc) |
43227 | 28669 | bacitracin | yes | yes | 0.04 Unit (disc) |
43227 | 3515 | cefuroxime | yes | yes | 30 µg (disc) |
43227 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) |
43227 | 48923 | erythromycin | yes | yes | 15 µg (disc) |
43227 | 100147 | nalidixic acid | yes | yes | 30 µg (disc) |
43227 | 7507 | neomycin | yes | yes | 30 µg (disc) |
43227 | 17334 | penicillin | yes | yes | 10 Unit (disc) |
43227 | 17076 | streptomycin | yes | yes | 10 µg (disc) |
43227 | 27902 | tetracycline | yes | yes | 30 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Shrub (Scrub) |
#Host | #Plants | #Tree |
#Host Body-Site | #Plant | #Root nodule |
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bradyrhizobium mercantei SEMIA 6399 | GCA_001982635 | contig | ncbi | 1904807 |
66792 | Bradyrhizobium sp. SEMIA 6399 strain SEMIA 6399 | 1904807.3 | wgs | patric | 1904807 |
66792 | Bradyrhizobium mercantei SEMIA 6399 | 2876791980 | draft | img | 1904807 |
GC content
- @ref: 43227
- GC-content: 63.99
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 98 | no |
motile | yes | 84.456 | no |
gram-positive | no | 98.066 | yes |
anaerobic | no | 98.07 | no |
aerobic | yes | 91.864 | no |
halophile | no | 96.147 | no |
spore-forming | no | 93.148 | yes |
glucose-util | yes | 89.134 | yes |
flagellated | no | 68.824 | no |
thermophile | no | 99.135 | yes |
glucose-ferment | no | 90.446 | no |
External links
@ref: 43227
culture collection no.: LMG 30031, BR 6010, CNPSo 1165, SEMIA 6399
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 28639930 | Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus). | Helene LCF, Delamuta JRM, Ribeiro RA, Hungria M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001870 | 2017 | Bacterial 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, DNA | Transcriptome |
Genetics | 28883142 | Genome Sequence of Bradyrhizobium mercantei Strain SEMIA 6399(T), Isolated from Nodules of Deguelia costata in Brazil. | Ribeiro RA, Helene LCF, Delamuta JRM, Hungria M | Genome Announc | 10.1128/genomeA.00943-17 | 2017 | Phylogeny |
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | ||
43227 | Luisa Caroline Ferraz Helene, Jakeline Renata Marçon Delamuta, Renan Augusto Ribeiro, Mariangela Hungria | Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus) | 10.1099/ijsem.0.001870 | IJSEM 67: 1827-1834 2017 | 28639930 |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | ||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 |