Name: Pannonibacter phragmitetus C6/8
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13690

Type strain:

Species: Pannonibacter phragmitetus

Strain Designation: C6/8

Culture col. no.: DSM 14780, NCAIM B02027

Strain history: <- A. K. Borsodi; C6/8

NCBI tax ID(s): 121719 (species)

Other strains from Pannonibacter phragmitetus

P. phragmitetus C6/19, DSM 14782, NCAIM B02025, ... (type strain)
P. phragmitetus C6/17, DSM 14781, NCAIM B02026
P. phragmitetus CCUG 24693, LMG 5431
P. phragmitetus CCUG 30180

Section

Pannonibacter phragmitetus C6/8 is a facultative anaerobe, chemoorganotroph, mesophilic bacterium that forms circular colonies and was isolated from surface of decomposing reed rhizomes.

colony-forming
Gram-negative
motile
rod-shaped
chemoorganotroph
facultative anaerobe
mesophilic
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Stappiaceae*
	Genus	*Pannonibacter*
	Species	**Pannonibacter phragmitetus**
	Full Scientific Name (PNU)	Pannonibacter phragmitetus Borsodi et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #43385]	Gram stain	negative
[Ref.: #43385]	Cell length	2-4 µm
[Ref.: #43385]	Cell width	0.3-0.6 µm
[Ref.: #43385]	Cell shape	rod-shaped
[Ref.: #43385]	Motility	yes
[Ref.: #43385]	Flagellum arrangement	polar

[Ref.: #43385]	Colony size	2-4 mm
[Ref.: #43385]	Colony color	whitish-beige
[Ref.: #43385]	Colony shape	circular
[Ref.: #43385]	Cultivation medium used	Horikoshi alkaline agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5534]

Culture medium

HORIKOSHI ALKALINE (DSMZ Medium 940)

[Ref.: #5534]

Culture medium growth

[Ref.: #5534]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #5534]

Culture medium composition

expand / minimize

[Ref.: #43385]

Culture medium

Horikoshi alkaline agar

[Ref.: #43385]

Culture medium growth

		Temperature
[Ref.: #5534]	growth	28 °C
[Ref.: #43385]	growth	10-37 °C
[Ref.: #43385]	optimum	22-28 °C

[Ref.: #5534]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #43385]			optimum	9-10
[Ref.: #43385]			growth	7-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43385]

Oxygen tolerance

facultative anaerobe

[Ref.: #43385]

Nutrition type

chemoorganotroph

[Ref.: #43385]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43385]		NaCl		growth	0-5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43385]	2-oxobutanoate ChEBI	+	oxidation
[Ref.: #43385]	2-oxoglutarate ChEBI	+	oxidation
[Ref.: #43385]	4-hydroxybutyrate ChEBI	+	oxidation
[Ref.: #43385]	alpha-D-glucose ChEBI	+	oxidation
[Ref.: #43385]	arginine ChEBI	+	hydrolysis
[Ref.: #43385]	beta-hydroxybutyrate ChEBI	+	oxidation
[Ref.: #43385]	bromosuccinate ChEBI	+	oxidation
[Ref.: #43385]	casein	-	hydrolysis
[Ref.: #43385]	cellobiose ChEBI	+	oxidation
[Ref.: #43385]	cellulose ChEBI	-	hydrolysis
[Ref.: #43385]	cis-aconitate ChEBI	+	oxidation
[Ref.: #43385]	citrate ChEBI	+	carbon source
[Ref.: #43385]	citrate ChEBI	+	oxidation
[Ref.: #43385]	D-fructose ChEBI	+	oxidation
[Ref.: #43385]	D-fucose ChEBI	+	builds acid from
[Ref.: #43385]	D-galactose ChEBI	+	oxidation
[Ref.: #43385]	D-glucuronate ChEBI	+	oxidation
[Ref.: #43385]	D-trehalose ChEBI	+	oxidation
[Ref.: #43385]	D-xylose ChEBI	+	builds acid from
[Ref.: #43385]	dextrin ChEBI	+	oxidation
[Ref.: #43385]	esculin ChEBI	-	hydrolysis
[Ref.: #43385]	esculin ChEBI	+	builds acid from
[Ref.: #43385]	formate ChEBI	+	oxidation
[Ref.: #43385]	gelatin ChEBI	-	hydrolysis
[Ref.: #43385]	gentiobiose ChEBI	+	oxidation
[Ref.: #43385]	glucose ChEBI	-	fermentation
[Ref.: #43385]	glycerol ChEBI	+	oxidation
[Ref.: #43385]	glycogen ChEBI	+	oxidation
[Ref.: #43385]	hippurate ChEBI	-	hydrolysis
[Ref.: #43385]	L-arabinose ChEBI	+	oxidation
[Ref.: #43385]	L-arabinose ChEBI	+	builds acid from
[Ref.: #43385]	L-asparagine ChEBI	+	oxidation
[Ref.: #43385]	L-fucose ChEBI	+	oxidation
[Ref.: #43385]	L-fucose ChEBI	+	builds acid from
[Ref.: #43385]	L-glutamate ChEBI	+	oxidation
[Ref.: #43385]	L-pyroglutamic acid ChEBI	+	oxidation
[Ref.: #43385]	L-rhamnose ChEBI	+	oxidation
[Ref.: #43385]	lactate ChEBI	+	oxidation
[Ref.: #43385]	lactulose ChEBI	+	oxidation
[Ref.: #43385]	maltose ChEBI	+	oxidation
[Ref.: #43385]	melibiose ChEBI	+	oxidation
[Ref.: #43385]	monomethyl succinate ChEBI	+	oxidation
[Ref.: #43385]	myo-inositol ChEBI	+	oxidation
[Ref.: #43385]	quinate ChEBI	+	oxidation
[Ref.: #43385]	starch ChEBI	-	hydrolysis
[Ref.: #43385]	succinate ChEBI	+	oxidation
[Ref.: #43385]	sucrose ChEBI	+	oxidation
[Ref.: #43385]	turanose ChEBI	+	oxidation
[Ref.: #43385]	tween 80 ChEBI	-
[Ref.: #43385]	urocanic acid ChEBI	+	oxidation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #43385]		acetoin ChEBI
[Ref.: #43385]		hydrogen sulfide ChEBI
[Ref.: #43385]		indole ChEBI

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #43385]		acetoin ChEBI	-
[Ref.: #43385]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #43385]	phenylalanine deaminase	-	4.3.1.5
[Ref.: #43385]	phosphatase	+
[Ref.: #43385]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	vitamin B12 metabolism	91.18	31 of 34
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	4-hydroxyphenylacetate degradation	90	9 of 10
[Ref.: #66794]	alanine metabolism	89.66	26 of 29
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	ketogluconate metabolism	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	degradation of sugar acids	84	21 of 25
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	phenol degradation	80	16 of 20
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	degradation of pentoses	78.57	22 of 28
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	oxidative phosphorylation	76.92	70 of 91
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	3-phenylpropionate degradation	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	69.23	9 of 13
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	androgen and estrogen metabolism	62.5	10 of 16
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ascorbate metabolism	50	11 of 22
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #5534]	Sample type/isolated from	surface of decomposing reed rhizomes
[Ref.: #5534]	Geographic location (country and/or sea, region)	Lake Fertó
[Ref.: #5534]	Country	Hungary
[Ref.: #5534]	Country ISO 3 Code	HUN
[Ref.: #5534]	Continent	Europe

[Ref.: #43385]	Sample type/isolated from	surface of decomposing reed rhizomes from Lake Fertö
[Ref.: #43385]	Geographic location (country and/or sea, region)	Lake Fertö
[Ref.: #43385]	Country	Hungary
[Ref.: #43385]	Country ISO 3 Code	HUN
[Ref.: #43385]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ314748 (>99% sequence identity) for Pannonibacter from Microbeatlas

Aquatic Samples	5053
Soil Samples	2317
Animal Samples	4774
Plant Samples	650
Total Samples	12794

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #5534]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #5534]	Pannonibacter phragmitetus partial 16S rRNA gene, strain C6/8	AJ314748	1454	ENA	121719 tax ID

Availability in culture collections External links

[Ref.: #5534]

Culture collection no.

DSM 14780, NCAIM B02027

[Ref.: #20218]

Associated Passport(s) in StrainInfo

340515, 340516

References

#5534

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14780

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#43385

Andrea K. Borsodi, Adrienn Micsinai, Gábor Kovács, Erika Tóth, Peter Schumann, Attila L. Kovács, Béla Böddi and Károly Márialigeti: 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 ( DOI 10.1099/ijs.0.02356-0 , PubMed 12710626 )

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 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.: MicrobeAtlas 1.0 beta .

* These data were automatically processed and therefore are not curated

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