Strain identifier
BacDive ID: 130599
Type strain: 
Species: Rhizobium paknamense
Strain Designation: L6-8
Strain history: <- NBRC <- C. Thawai, King Mongkut's Institute of Technology, Thailand; L6-8
NCBI tax ID(s): 1206817 (species)
version 8.1 (current version)
General
@ref: 21931
BacDive-ID: 130599
DSM-Number: 100301
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, motile, rod-shaped
description: Rhizobium paknamense L6-8 is a mesophilic, Gram-negative, motile bacterium that was isolated from whole fresh plants of lesser duckweed Lemna aequinoctialis.
NCBI tax id
- NCBI tax id: 1206817
- Matching level: species
strain history
- @ref: 21931
- history: <- NBRC <- C. Thawai, King Mongkut's Institute of Technology, Thailand; L6-8
doi: 10.13145/bacdive130599.20230509.8.1
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 paknamense
- full scientific name: Rhizobium paknamense Kittiwongwattana and Thawai 2013
synonyms
- @ref: 20215
- synonym: Allorhizobium paknamense
@ref: 21931
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhizobiaceae
genus: Rhizobium
species: Rhizobium paknamense
full scientific name: Rhizobium paknamense Kittiwongwattana and Thawai 2013
strain designation: L6-8
type strain: yes
Morphology
cell morphology
- @ref: 31093
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
colony morphology
- @ref: 21931
- incubation period: 1-2 days
pigmentation
- @ref: 31093
- production: yes
Culture and growth conditions
culture medium
- @ref: 21931
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 21931 | positive | growth | 30 | mesophilic |
| 31093 | positive | growth | 20-45 | |
| 31093 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31093 | positive | growth | 4.0-9.0 | alkaliphile |
| 31093 | positive | optimum | 6.5 |
Physiology and metabolism
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31093 | NaCl | positive | growth | 0-2 % |
| 31093 | NaCl | positive | optimum | 1 % |
observation
- @ref: 31093
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31093 | 28053 | melibiose | + | carbon source |
| 31093 | 26546 | rhamnose | + | carbon source |
| 31093 | 27082 | trehalose | + | carbon source |
| 31093 | 16296 | D-tryptophan | + | carbon source |
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 17306 | maltose | + | assimilation |
| 68369 | 59640 | N-acetylglucosamine | + | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 16024 | D-mannose | + | assimilation |
| 68369 | 30849 | L-arabinose | + | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | + | hydrolysis |
| 68369 | 16199 | urea | + | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31093 | urease | + | 3.5.1.5 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | + | 3.2.1.21 |
| 68369 | urease | + | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21931 | - | - | - | - | + | + | - | + | + | + | + | + | + | + | + | - | - | + | + | - |
Isolation, sampling and environmental information
isolation
- @ref: 21931
- sample type: whole fresh plants of lesser duckweed Lemna aequinoctialis
- host species: Lemna aequinoctialis
- country: Thailand
- origin.country: THA
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Aquatic plant
taxonmaps
- @ref: 69479
- File name: preview.99_99861.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1787;97_51780;98_68295;99_99861&stattab=map
- Last taxonomy: Rhizobium paknamense subclade
- 16S sequence: AB733647
- Sequence Identity:
- Total samples: 52
- soil counts: 12
- aquatic counts: 29
- animal counts: 8
- plant counts: 3
Safety information
risk assessment
- @ref: 21931
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21931
- description: Rhizobium paknamense gene for 16S ribosomal RNA, partial sequence
- accession: AB733647
- length: 1413
- database: ena
- NCBI tax ID: 1206817
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhizobium paknamense DSM 100301 | 2928424016 | draft | img | 1401443 |
| 66792 | Rhizobium paknamense DSM 100301 | 2738541325 | draft | img | 1401443 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 31093 | 60.4 | |
| 21931 | 60.4 | thermal denaturation, midpoint method (Tm) |
External links
@ref: 21931
culture collection no.: DSM 100301, BCC 55142, NBRC 109338
straininfo link
- @ref: 89114
- straininfo: 407377
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23687054 | Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis). | Kittiwongwattana C, Thawai C | Int J Syst Evol Microbiol | 10.1099/ijs.0.051888-0 | 2013 | Araceae/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Thailand, *Water Microbiology | Genetics |
| Phylogeny | 25555455 | Rhizobium capsici sp. nov., isolated from root tumor of a green bell pepper (Capsicum annuum var. grossum) plant. | Lin SY, Hung MH, Hameed A, Liu YC, Hsu YH, Wen CZ, Arun AB, Busse HJ, Glaeser SP, Kampfer P, Young CC | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0371-5 | 2015 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Capsicum/*microbiology, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Rhizobium/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Taiwan, Temperature, Transcription Factors/genetics | Genetics |
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | 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 | |||
| 21931 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100301 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100301) | |||
| 31093 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27422 | 28776041 | |
| 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 | |||
| 68369 | Automatically annotated from API 20NE | |||||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 89114 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID407377.1 |