Strain identifier

BacDive ID: 13692

Type strain: Yes

Species: Pannonibacter phragmitetus

Strain Designation: C6/19

Culture col. no.: DSM 14782, NCAIM B02025, CCUG 54624

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: gram-negative, mesophilic, chemoorganotroph, facultative anaerobe, Bacteria, 16S sequence, genome sequence, 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.

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

doi: 10.13145/bacdive13692.20201210.5

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/proteobacteria
  • domain: Bacteria
  • phylum: Proteobacteria
  • 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: Rhodobacteraceae

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5536HORIKOSHI ALKALINE (DSMZ Medium 940)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium940.pdf
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 31801GCA_001484065completencbi121719
66792Pannonibacter phragmitetus H1-4GCA_003723955chromosomencbi121719
66792Pannonibacter phragmitetus NCTC13350GCA_900454465contigncbi121719
66792Pannonibacter phragmitetus DSM 14782GCA_000382365scaffoldncbi1122929
66792Pannonibacter phragmitetus 00954GCA_003703925scaffoldncbi121719
66792Pannonibacter phragmitetus CGMCC9175GCA_001188555contigncbi121719
66792Pannonibacter phragmitetus DSM 147821122929.3wgspatric1122929
66792Pannonibacter phragmitetus strain 00954121719.23wgspatric121719
66792Pannonibacter phragmitetus strain 31801121719.10completepatric121719
66792Pannonibacter phragmitetus strain 31801121719.15plasmidpatric121719
66792Pannonibacter phragmitetus strain CGMCC9175121719.5wgspatric121719
66792Pannonibacter phragmitetus strain H1-4121719.24completepatric121719
66792Pannonibacter phragmitetus strain NCTC13350121719.18wgspatric121719
66792Pannonibacter phragmitetus DSM 147822521172637permanentimg1122929

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

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
20215D.Gleim, M.Kracht, N.Weiss et. al.http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.htmlProkaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
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 2003
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)