Strain identifier
BacDive ID: 13692
Type strain:
Species: Pannonibacter phragmitetus
Strain Designation: C6/19
Strain history: CIP <- 2003, NCAIM <- A.K. Borsodi: strain C6/19
NCBI tax ID(s): 1122929 (strain), 121719 (species)
General
@ref: 5536
BacDive-ID: 13692
DSM-Number: 14782
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, chemoorganotroph, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Pannonibacter phragmitetus C6/19 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 | Matching level |
---|---|
1122929 | strain |
121719 | species |
strain history
@ref | history |
---|---|
5536 | <- A. K. Borsodi; C6/19 |
121811 | CIP <- 2003, NCAIM <- A.K. Borsodi: strain C6/19 |
doi: 10.13145/bacdive13692.20230509.8.1
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: 5536
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: C6/19
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement |
---|---|---|---|---|---|---|
43385 | negative | 2-4 µm | 0.3-0.6 µm | rod-shaped | yes | polar |
121811 | negative | rod-shaped | no |
colony morphology
@ref | colony size | colony color | colony shape | medium used |
---|---|---|---|---|
43385 | 2-4 mm | whitish-beige | circular | Horikoshi alkaline agar |
121811 |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_14782_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_14782_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_14782_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_14782_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_14782_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_14782_6.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_14782_7.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_14782_8.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5536 | 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 |
39971 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
43385 | Horikoshi alkaline agar | yes | ||
121811 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
121811 | CIP Medium 328 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5536 | positive | growth | 28 | mesophilic |
39971 | positive | growth | 30 | mesophilic |
43385 | positive | growth | 10-37 | |
43385 | positive | optimum | 22-28 | |
60266 | positive | growth | 37 | mesophilic |
121811 | positive | growth | 15-41 | |
121811 | no | growth | 5 | psychrophilic |
121811 | no | growth | 45 | thermophilic |
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 | oxygen tolerance |
---|---|
43385 | facultative anaerobe |
60266 | aerobe |
121811 | obligate aerobe |
nutrition type
- @ref: 43385
- type: chemoorganotroph
spore formation
- @ref: 43385
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43385 | NaCl | positive | growth | 0-5 %(w/v) |
121811 | NaCl | positive | growth | 0-4 % |
121811 | NaCl | no | growth | 6 % |
121811 | NaCl | no | growth | 8 % |
121811 | NaCl | no | growth | 10 % |
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 | - | hydrolysis |
43385 | 27248 | urocanic acid | + | oxidation |
121811 | 16947 | citrate | + | carbon source |
121811 | 4853 | esculin | + | hydrolysis |
121811 | 606565 | hippurate | + | hydrolysis |
121811 | 17632 | nitrate | + | builds gas from |
121811 | 17632 | nitrate | + | reduction |
121811 | 16301 | nitrite | - | builds gas from |
121811 | 16301 | nitrite | + | reduction |
121811 | 15792 | malonate | - | assimilation |
121811 | 17632 | nitrate | + | respiration |
antibiotic resistance
- @ref: 121811
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43385 | 15688 | acetoin | no |
43385 | 16136 | hydrogen sulfide | no |
43385 | 35581 | indole | no |
121811 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | methylred-test | voges-proskauer-test |
---|---|---|---|---|
43385 | 17234 | glucose | - | |
43385 | 15688 | acetoin | - | |
121811 | 15688 | acetoin | - | |
121811 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43385 | phenylalanine deaminase | - | 4.3.1.5 |
43385 | urease | + | 3.5.1.5 |
43385 | phosphatase | + | |
121811 | oxidase | + | |
121811 | beta-galactosidase | + | 3.2.1.23 |
121811 | alcohol dehydrogenase | - | 1.1.1.1 |
121811 | gelatinase | - | |
121811 | amylase | - | |
121811 | DNase | - | |
121811 | caseinase | - | 3.4.21.50 |
121811 | catalase | + | 1.11.1.6 |
121811 | tween esterase | - | |
121811 | gamma-glutamyltransferase | - | 2.3.2.2 |
121811 | lecithinase | - | |
121811 | lipase | - | |
121811 | lysine decarboxylase | - | 4.1.1.18 |
121811 | ornithine decarboxylase | - | 4.1.1.17 |
121811 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
121811 | tryptophan deaminase | - | |
121811 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121811 | - | + | + | + | - | + | - | - | + | - | + | + | + | + | - | + | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121811 | + | + | + | + | + | - | + | - | - | - | - | - | - | - | + | + | + | + | + | + | - | + | + | + | + | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | + | + | + | + | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
5536 | surface of decomposing reed rhizomes | Lake Fertó | Hungary | HUN | Europe | |
43385 | surface of decomposing reed rhizomes from Lake Fertö | Lake Fertö | Hungary | HUN | Europe | |
60266 | Surface of decomposing reed rhizomes | Lake Fertö | Hungary | HUN | Europe | |
121811 | Surface of decomposing reed rhizomes | Hungary | HUN | Europe | 1998 |
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: AJ400704
- Sequence Identity:
- Total samples: 12794
- soil counts: 2317
- aquatic counts: 5053
- animal counts: 4774
- plant counts: 650
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5536 | 1 | Risk group (German classification) |
121811 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5536
- description: Pannonibacter phragmitetus partial 16S rRNA gene, type strain C6-19T
- accession: AJ400704
- length: 1475
- database: ena
- NCBI tax ID: 121719
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pannonibacter phragmitetus DSM 14782 | GCA_000382365 | scaffold | ncbi | 1122929 |
66792 | Pannonibacter phragmitetus DSM 14782 | 1122929.3 | wgs | patric | 1122929 |
66792 | Pannonibacter phragmitetus DSM 14782 | 2521172637 | draft | img | 1122929 |
GC content
@ref | GC-content | method |
---|---|---|
5536 | 64.6 | |
43385 | 64.6 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 87.324 | yes |
flagellated | yes | 71.77 | yes |
gram-positive | no | 98.868 | yes |
anaerobic | no | 97.469 | no |
aerobic | yes | 83.897 | no |
halophile | no | 73.093 | no |
spore-forming | no | 95.311 | yes |
thermophile | no | 95.631 | yes |
glucose-util | yes | 89.296 | no |
glucose-ferment | no | 89.913 | yes |
External links
@ref: 5536
culture collection no.: DSM 14782, NCAIM B02025, CCUG 54624, CIP 107962
straininfo link
- @ref: 82876
- straininfo: 100841
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12710626 | Pannonibacter phragmitetus gen. nov., sp. nov., a novel alkalitolerant bacterium isolated from decomposing reed rhizomes in a Hungarian soda lake. | Borsodi AK, Micsinai A, Kovacs G, Toth E, Schumann P, Kovacs AL, Boddi B, Marialigeti K | Int J Syst Evol Microbiol | 10.1099/ijs.0.02356-0 | 2003 | Alkalies/*metabolism, Alphaproteobacteria/*classification/genetics/growth & development/metabolism, Bacteria, Anaerobic, Base Composition, Cell Wall/*chemistry, Hungary, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizome/microbiology, Sequence Analysis, DNA, Sodium Chloride/*pharmacology, *Water Microbiology | Metabolism |
Phylogeny | 22940883 | Pannonibacter indica sp. nov., a highly arsenate-tolerant bacterium isolated from a hot spring in India. | Bandyopadhyay S, Schumann P, Das SK | Arch Microbiol | 10.1007/s00203-012-0840-z | 2012 | Arsenates/pharmacology, Base Composition, Geologic Sediments/microbiology, Hot Springs/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/drug effects/genetics/ultrastructure | Genetics |
Phylogeny | 29693544 | Pannonibacter carbonis sp. nov., isolated from coal mine water. | Xi L, Qiao N, Liu D, Li J, Zhang J, Liu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002794 | 2018 | Bacterial Typing Techniques, Base Composition, China, *Coal, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, *Water Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5536 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14782) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14782 | |||
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 | |||
39971 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5531 | ||||
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 | |
60266 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 54624) | https://www.ccug.se/strain?id=54624 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
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 | |
68382 | Automatically annotated from API zym | |||||
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 | |||
82876 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100841.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121811 | Curators of the CIP | Collection of Institut Pasteur (CIP 107962) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107962 |