Strain identifier

BacDive ID: 13692

Type strain: Yes

Species: Pannonibacter phragmitetus

Strain Designation: C6/19

Strain history: CIP <- 2003, NCAIM <- A.K. Borsodi: strain 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: genome sequence, 16S sequence, Bacteria, facultative anaerobe, chemoorganotroph, Gram-negative, motile, rod-shaped, colony-forming

description: Pannonibacter phragmitetus C6/19 is a facultative anaerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from surface of decomposing reed rhizomes.

NCBI tax id

NCBI tax idMatching level
1122929strain
121719species

strain history

@refhistory
5536<- A. K. Borsodi; C6/19
121811CIP <- 2003, NCAIM <- A.K. Borsodi: strain C6/19

doi: 10.13145/bacdive13692.20240510.9

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

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43385negative2-4 µm0.3-0.6 µmrod-shapedyespolar
69480negative98.868
121811negativerod-shapedno

colony morphology

@refcolony sizecolony colorcolony shapemedium used
433852-4 mmwhitish-beigecircularHorikoshi alkaline agar
121811

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://mediadive.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
121811CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121811CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
5536positivegrowth28
39971positivegrowth30
43385positivegrowth10-37
43385positiveoptimum22-28
60266positivegrowth37
121811positivegrowth15-41
121811nogrowth5
121811nogrowth45

culture pH

@refabilitytypepHPH range
43385positivegrowth7-11alkaliphile
43385positiveoptimum9-10

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43385facultative anaerobe
60266aerobe
121811obligate aerobe

nutrition type

  • @ref: 43385
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
43385no
69480no95.311

halophily

@refsaltgrowthtested relationconcentration
43385NaClpositivegrowth0-5 %(w/v)
121811NaClpositivegrowth0-4 %
121811NaClnogrowth6 %
121811NaClnogrowth8 %
121811NaClnogrowth10 %

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
12181116947citrate+carbon source
1218114853esculin+hydrolysis
121811606565hippurate+hydrolysis
12181117632nitrate+builds gas from
12181117632nitrate+reduction
12181116301nitrite-builds gas from
12181116301nitrite+reduction
12181115792malonate-assimilation
12181117632nitrate+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

@refChebi-IDmetaboliteproduction
4338515688acetoinno
4338516136hydrogen sulfideno
4338535581indoleno
12181135581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4338517234glucose-
4338515688acetoin-
12181115688acetoin-
12181117234glucose-

enzymes

@refvalueactivityec
43385phenylalanine deaminase-4.3.1.5
43385urease+3.5.1.5
43385phosphatase+
121811oxidase+
121811beta-galactosidase+3.2.1.23
121811alcohol dehydrogenase-1.1.1.1
121811gelatinase-
121811amylase-
121811DNase-
121811caseinase-3.4.21.50
121811catalase+1.11.1.6
121811tween esterase-
121811gamma-glutamyltransferase-2.3.2.2
121811lecithinase-
121811lipase-
121811lysine decarboxylase-4.1.1.18
121811ornithine decarboxylase-4.1.1.17
121811phenylalanine ammonia-lyase-4.3.1.24
121811tryptophan deaminase-
121811urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121811-+++-+--+-++++-+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121811+++++-+-------++++++-++++------++---------------+-----++++-----++--------+++------------+------+---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5536surface of decomposing reed rhizomesLake FertóHungaryHUNEurope
43385surface of decomposing reed rhizomes from Lake FertöLake FertöHungaryHUNEurope
60266Surface of decomposing reed rhizomesLake FertöHungaryHUNEurope
121811Surface of decomposing reed rhizomesHungaryHUNEurope1998

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
55361Risk group (German classification)
1218111Risk 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: nuccore
  • NCBI tax ID: 121719

Genome sequences

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

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.324yes
flagellatedyes71.77yes
gram-positiveno98.868yes
anaerobicno97.469no
aerobicyes83.897no
halophileno73.093no
spore-formingno95.311yes
thermophileno95.631yes
glucose-utilyes89.296no
glucose-fermentno89.913yes

External links

@ref: 5536

culture collection no.: DSM 14782, NCAIM B02025, CCUG 54624, CIP 107962

straininfo link

  • @ref: 82876
  • straininfo: 100841

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
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
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
82876Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100841.1StrainInfo: A central database for resolving microbial strain identifiers
121811Curators of the CIPCollection of Institut Pasteur (CIP 107962)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107962