Strain identifier
BacDive ID: 13690
Type strain:
Species: Pannonibacter phragmitetus
Strain Designation: C6/8
Strain history: <- A. K. Borsodi; C6/8
NCBI tax ID(s): 121719 (species)
General
@ref: 5534
BacDive-ID: 13690
DSM-Number: 14780
keywords: 16S sequence, Bacteria, facultative anaerobe, chemoorganotroph, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Pannonibacter phragmitetus C6/8 is a facultative anaerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies and was isolated from surface of decomposing reed rhizomes.
NCBI tax id
- NCBI tax id: 121719
- Matching level: species
strain history
- @ref: 5534
- history: <- A. K. Borsodi; C6/8
doi: 10.13145/bacdive13690.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Stappiaceae
- genus: Pannonibacter
- species: Pannonibacter phragmitetus
- full scientific name: Pannonibacter phragmitetus Borsodi et al. 2003
@ref: 5534
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Stappiaceae
genus: Pannonibacter
species: Pannonibacter phragmitetus
full scientific name: Pannonibacter phragmitetus Borsodi et al. 2003
strain designation: C6/8
type strain: no
Morphology
cell morphology
- @ref: 43385
- gram stain: negative
- cell length: 2-4 µm
- cell width: 0.3-0.6 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: polar
colony morphology
- @ref: 43385
- colony size: 2-4 mm
- colony color: whitish-beige
- colony shape: circular
- medium used: Horikoshi alkaline agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5534 | HORIKOSHI ALKALINE (DSMZ Medium 940) | yes | https://mediadive.dsmz.de/medium/940 | Name: HORIKOSHI ALKALINE (DSMZ Medium 940) Composition: Agar 15.0 g/l D-Glucose 10.0 g/l Na2CO3 5.0 g/l Yeast extract 5.0 g/l Peptone 5.0 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Distilled water |
43385 | Horikoshi alkaline agar | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5534 | positive | growth | 28 | mesophilic |
43385 | positive | growth | 10-37 | |
43385 | positive | optimum | 22-28 |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43385 | positive | growth | 7-11 | alkaliphile |
43385 | positive | optimum | 9-10 |
Physiology and metabolism
oxygen tolerance
- @ref: 43385
- oxygen tolerance: facultative anaerobe
nutrition type
- @ref: 43385
- type: chemoorganotroph
spore formation
- @ref: 43385
- spore formation: no
halophily
- @ref: 43385
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-5 %(w/v)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43385 | 16763 | 2-oxobutanoate | + | oxidation |
43385 | 30916 | 2-oxoglutarate | + | oxidation |
43385 | 17925 | alpha-D-glucose | + | oxidation |
43385 | 29016 | arginine | + | hydrolysis |
43385 | 8295 | beta-hydroxybutyrate | + | oxidation |
43385 | 73706 | bromosuccinate | + | oxidation |
43385 | casein | - | hydrolysis | |
43385 | 17057 | cellobiose | + | oxidation |
43385 | 62968 | cellulose | - | hydrolysis |
43385 | 16383 | cis-aconitate | + | oxidation |
43385 | 16947 | citrate | + | carbon source |
43385 | 16947 | citrate | + | oxidation |
43385 | 15824 | D-fructose | + | oxidation |
43385 | 28847 | D-fucose | + | builds acid from |
43385 | 12936 | D-galactose | + | oxidation |
43385 | 15748 | D-glucuronate | + | oxidation |
43385 | 28053 | melibiose | + | oxidation |
43385 | 16551 | D-trehalose | + | oxidation |
43385 | 65327 | D-xylose | + | builds acid from |
43385 | 23652 | dextrin | + | oxidation |
43385 | 24996 | lactate | + | oxidation |
43385 | 4853 | esculin | - | hydrolysis |
43385 | 4853 | esculin | + | builds acid from |
43385 | 15740 | formate | + | oxidation |
43385 | 16724 | 4-hydroxybutyrate | + | oxidation |
43385 | 5291 | gelatin | - | hydrolysis |
43385 | 28066 | gentiobiose | + | oxidation |
43385 | 17234 | glucose | - | fermentation |
43385 | 17754 | glycerol | + | oxidation |
43385 | 28087 | glycogen | + | oxidation |
43385 | 606565 | hippurate | - | hydrolysis |
43385 | 30849 | L-arabinose | + | oxidation |
43385 | 30849 | L-arabinose | + | builds acid from |
43385 | 17196 | L-asparagine | + | oxidation |
43385 | 18287 | L-fucose | + | oxidation |
43385 | 18287 | L-fucose | + | builds acid from |
43385 | 29985 | L-glutamate | + | oxidation |
43385 | 18183 | L-pyroglutamic acid | + | oxidation |
43385 | 62345 | L-rhamnose | + | oxidation |
43385 | 6359 | lactulose | + | oxidation |
43385 | 17306 | maltose | + | oxidation |
43385 | 75146 | monomethyl succinate | + | oxidation |
43385 | 17268 | myo-inositol | + | oxidation |
43385 | 26490 | quinate | + | oxidation |
43385 | 28017 | starch | - | hydrolysis |
43385 | 30031 | succinate | + | oxidation |
43385 | 17992 | sucrose | + | oxidation |
43385 | 32528 | turanose | + | oxidation |
43385 | 53426 | tween 80 | - | |
43385 | 27248 | urocanic acid | + | oxidation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43385 | 15688 | acetoin | no |
43385 | 16136 | hydrogen sulfide | no |
43385 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | methylred-test | voges-proskauer-test |
---|---|---|---|---|
43385 | 17234 | glucose | - | |
43385 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43385 | phenylalanine deaminase | - | 4.3.1.5 |
43385 | urease | + | 3.5.1.5 |
43385 | phosphatase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5534 | surface of decomposing reed rhizomes | Lake Fertó | Hungary | HUN | Europe |
43385 | surface of decomposing reed rhizomes from Lake Fertö | Lake Fertö | Hungary | HUN | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Decomposing plant |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_5252.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2552;97_3118;98_3917;99_5252&stattab=map
- Last taxonomy: Pannonibacter
- 16S sequence: AJ314748
- Sequence Identity:
- Total samples: 12794
- soil counts: 2317
- aquatic counts: 5053
- animal counts: 4774
- plant counts: 650
Safety information
risk assessment
- @ref: 5534
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5534
- description: Pannonibacter phragmitetus partial 16S rRNA gene, strain C6/8
- accession: AJ314748
- length: 1454
- database: ena
- NCBI tax ID: 121719
External links
@ref: 5534
culture collection no.: DSM 14780, NCAIM B02027
straininfo link
- @ref: 82873
- straininfo: 276264
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5534 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14780) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14780 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
43385 | Andrea K. Borsodi, Adrienn Micsinai, Gábor Kovács, Erika Tóth, Peter Schumann, Attila L. Kovács, Béla Böddi and Károly Márialigeti | 10.1099/ijs.0.02356-0 | Pannonibacter phragmitetus gen. nov., sp. nov., a novel alkalitolerant bacterium isolated from decomposing reed rhizomes in a Hungarian soda lake | IJSEM 53: 555-561 2003 | 12710626 | |
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
82873 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID276264.1 | StrainInfo: A central database for resolving microbial strain identifiers |