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Strain identifier

BacDive ID: 13692

Type strain: Yes

Species: Pannonibacter phragmitetus

Strain Designation: C6/19

Strain history: <- A. K. Borsodi; C6/19

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

@ref: 5536

BacDive-ID: 13692

DSM-Number: 14782

keywords: mesophilic, chemoorganotroph, facultative anaerobe, Bacteria, 16S sequence, genome sequence, 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 idMatching level
121719species
1122929strain

strain history: <- A. K. Borsodi; C6/19

doi: 10.13145/bacdive13692.20220920.7

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: 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

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_14782_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14782_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14782_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14782_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14782_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14782_6.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14782_7.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_14782_8.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5536HORIKOSHI ALKALINE (DSMZ Medium 940)yeshttps://bacmedia.dsmz.de/medium/940Name: 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
39971MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
43385Horikoshi alkaline agaryes

culture temp

@refgrowthtypetemperaturerange
5536positivegrowth28mesophilic
39971positivegrowth30mesophilic
43385positivegrowth10-37
43385positiveoptimum22-28
60266positivegrowth37mesophilic

culture pH

@refabilitytypepH
43385positivegrowth7-11
43385positiveoptimum9-10

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43385facultative anaerobe
60266aerobe

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

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43385167632-oxobutanoate+oxidation
43385309162-oxoglutarate+oxidation
4338517925alpha-D-glucose+oxidation
4338529016arginine+hydrolysis
433858295beta-hydroxybutyrate+oxidation
4338573706bromosuccinate+oxidation
43385casein-hydrolysis
4338517057cellobiose+oxidation
4338562968cellulose-hydrolysis
4338516383cis-aconitate+oxidation
4338516947citrate+carbon source
4338516947citrate+oxidation
4338515824D-fructose+oxidation
4338528847D-fucose+builds acid from
4338512936D-galactose+oxidation
4338515748D-glucuronate+oxidation
4338528053melibiose+oxidation
4338516551D-trehalose+oxidation
4338565327D-xylose+builds acid from
4338523652dextrin+oxidation
4338524996lactate+oxidation
433854853esculin-hydrolysis
433854853esculin+builds acid from
4338515740formate+oxidation
43385167244-hydroxybutyrate+oxidation
433855291gelatin-hydrolysis
4338528066gentiobiose+oxidation
4338517234glucose-fermentation
4338517754glycerol+oxidation
4338528087glycogen+oxidation
43385606565hippurate-hydrolysis
4338530849L-arabinose+oxidation
4338530849L-arabinose+builds acid from
4338517196L-asparagine+oxidation
4338518287L-fucose+oxidation
4338518287L-fucose+builds acid from
4338529985L-glutamate+oxidation
4338518183L-pyroglutamic acid+oxidation
4338562345L-rhamnose+oxidation
433856359lactulose+oxidation
4338517306maltose+oxidation
4338575146monomethyl succinate+oxidation
4338517268myo-inositol+oxidation
4338526490quinate+oxidation
4338528017starch-hydrolysis
4338530031succinate+oxidation
4338517992sucrose+oxidation
4338532528turanose+oxidation
4338553426tween 80-hydrolysis
4338527248urocanic acid+oxidation

metabolite production

@refChebi-IDmetaboliteproduction
4338515688acetoinno
4338516136hydrogen sulfideno
4338535581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4338517234glucose-
4338515688acetoin-

enzymes

@refvalueactivityec
43385phenylalanine deaminase-4.3.1.5
43385urease+3.5.1.5
43385phosphatase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5536surface of decomposing reed rhizomesLake FertóHungaryHUNEurope
43385surface of decomposing reed rhizomes from Lake FertöLake FertöHungaryHUNEurope
60266Surface of decomposing reed rhizomesLake FertöHungaryHUNEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pannonibacter phragmitetus DSM 14782 DSM 14782GCA_000382365scaffoldncbi1122929
66792Pannonibacter phragmitetus DSM 147821122929.3wgspatric1122929
66792Pannonibacter phragmitetus DSM 147822521172637draftimg1122929

GC content

@refGC-contentmethod
553664.6
4338564.6high performance liquid chromatography (HPLC)

External links

@ref: 5536

culture collection no.: DSM 14782, NCAIM B02025, CCUG 54624

straininfo link

  • @ref: 20218
  • passport: http://www.straininfo.net/strains/303359

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710626Pannonibacter 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 KInt J Syst Evol Microbiol10.1099/ijs.0.02356-02003Alkalies/*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 MicrobiologyMetabolism
Phylogeny22940883Pannonibacter indica sp. nov., a highly arsenate-tolerant bacterium isolated from a hot spring in India.Bandyopadhyay S, Schumann P, Das SKArch Microbiol10.1007/s00203-012-0840-z2012Arsenates/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/ultrastructureGenetics
Phylogeny29693544Pannonibacter carbonis sp. nov., isolated from coal mine water.Xi L, Qiao N, Liu D, Li J, Zhang J, Liu JInt J Syst Evol Microbiol10.1099/ijsem.0.0027942018Bacterial 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 MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5536Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14782)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14782
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
39971Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5531
43385Andrea K. Borsodi, Adrienn Micsinai, Gábor Kovács, Erika Tóth, Peter Schumann, Attila L. Kovács, Béla Böddi and Károly Márialigeti10.1099/ijs.0.02356-0Pannonibacter phragmitetus gen. nov., sp. nov., a novel alkalitolerant bacterium isolated from decomposing reed rhizomes in a Hungarian soda lakeIJSEM 53: 555-561 200312710626
60266Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54624)https://www.ccug.se/strain?id=54624
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880