Name: Polynucleobacter difficilis AM-8B5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2081

Type strain:

Species: Polynucleobacter difficilis

Strain Designation: AM-8B5

Culture col. no.: DSM 22349, CIP 110078

Strain history: CIP <- 2009, A. Minasyan <- M. Hahn, Austrian Academy of Science, Inst. for Limnology, Mondsee, Austria: strain AM-8B5

NCBI tax ID(s): 556054 (species)

SI-ID 379267

CIP 110078, DSM 22349

Section

Polynucleobacter difficilis AM-8B5 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from freshwater taken from a depth of 60 m close to the bottom of a eutrophic lake.

rod-shaped
aerobe
chemoorganotroph
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Polynucleobacter*
	Species	**Polynucleobacter difficilis**
	Full Scientific Name (LPSN)	Polynucleobacter difficilis Hahn et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #118935]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #118935]	Cell shape	rod-shaped
[Ref.: #23166]	Cell shape	rod-shaped

[Ref.: #23166]	Cell length	0.6-1.8 µm

[Ref.: #23166]	Cell width	0.4-0.5 µm

[Ref.: #23166]	Motility	no

[Ref.: #23166]	Colony shape	circular
[Ref.: #23166]	Cultivation medium used	NSY and R2A

[Ref.: #16306]	Incubation period	>14 days

[Ref.: #23166]	Pigment production	no
[Ref.: #23166]	Pigment name	no pigments

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16306]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #16306]

Culture medium growth

[Ref.: #16306]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16306]

Culture medium composition

expand / minimize

[Ref.: #23166]

Culture medium

NSY and R2A

[Ref.: #23166]

Culture medium growth

[Ref.: #37911]

Culture medium

MEDIUM718 - for Polynucleobacter rarum

[Ref.: #37911]

Culture medium growth

[Ref.: #118935]

Culture medium

CIP Medium 751A

[Ref.: #118935]

Culture medium growth

[Ref.: #118935]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #16306]		growth	25 °C
[Ref.: #23166]		growth	5 °C
[Ref.: #23166]	no	growth	35 °C
[Ref.: #37911]		growth	25 °C

[Ref.: #16306]	Temperature range	mesophilic
[Ref.: #23166]	Temperature range	psychrophilic
[Ref.: #23166]	Temperature range	mesophilic
[Ref.: #37911]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23166]	Oxygen tolerance	aerobe
[Ref.: #23166]	Oxygen tolerance	facultative anaerobe

[Ref.: #23166]

Nutrition type

chemoorganotroph

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23166]		NaCl		maximum	0.2	%(w/v)
[Ref.: #23166]		NaCl		growth	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23166]	4-oxopentanoate ChEBI	-	carbon source
[Ref.: #23166]	4-oxopentanoate ChEBI	-	growth
[Ref.: #23166]	acetate ChEBI	-	carbon source
[Ref.: #23166]	acetate ChEBI	-	growth
[Ref.: #23166]	betaine ChEBI	-	carbon source
[Ref.: #23166]	betaine ChEBI	-	growth
[Ref.: #23166]	citrate ChEBI	-	carbon source
[Ref.: #23166]	citrate ChEBI	-	growth
[Ref.: #23166]	D-fructose ChEBI	-	carbon source
[Ref.: #23166]	D-fructose ChEBI	-	growth
[Ref.: #23166]	D-fucose ChEBI	+	carbon source
[Ref.: #23166]	D-fucose ChEBI	+	growth
[Ref.: #23166]	D-galactose ChEBI	-	carbon source
[Ref.: #23166]	D-galactose ChEBI	-	growth
[Ref.: #23166]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #23166]	D-galacturonic acid ChEBI	+	growth
[Ref.: #23166]	D-glucose ChEBI	-	carbon source
[Ref.: #23166]	D-glucose ChEBI	-	growth
[Ref.: #23166]	D-lyxose ChEBI	+	carbon source
[Ref.: #23166]	D-lyxose ChEBI	+	growth
[Ref.: #23166]	D-mannose ChEBI	-	carbon source
[Ref.: #23166]	D-mannose ChEBI	-	growth
[Ref.: #23166]	D-sorbitol ChEBI	-	carbon source
[Ref.: #23166]	D-sorbitol ChEBI	-	growth
[Ref.: #23166]	formate ChEBI	+	carbon source
[Ref.: #23166]	formate ChEBI	+	growth
[Ref.: #23166]	fumarate ChEBI	+	carbon source
[Ref.: #23166]	fumarate ChEBI	+	growth
[Ref.: #23166]	glycolate ChEBI	-	carbon source
[Ref.: #23166]	glycolate ChEBI	-	growth
[Ref.: #23166]	glyoxylate ChEBI	-	carbon source
[Ref.: #23166]	glyoxylate ChEBI	-	growth
[Ref.: #23166]	L-alanine ChEBI	-	carbon source
[Ref.: #23166]	L-alanine ChEBI	-	growth
[Ref.: #23166]	L-asparagine ChEBI	-	carbon source
[Ref.: #23166]	L-asparagine ChEBI	-	growth
[Ref.: #23166]	L-aspartate ChEBI	-	carbon source
[Ref.: #23166]	L-aspartate ChEBI	-	growth
[Ref.: #23166]	L-cysteine ChEBI	+	carbon source
[Ref.: #23166]	L-cysteine ChEBI	+	growth
[Ref.: #23166]	L-glutamate ChEBI	-	carbon source
[Ref.: #23166]	L-glutamate ChEBI	-	growth
[Ref.: #23166]	L-serine ChEBI	-	carbon source
[Ref.: #23166]	L-serine ChEBI	-	growth
[Ref.: #23166]	malate ChEBI	+	carbon source
[Ref.: #23166]	malate ChEBI	+	growth
[Ref.: #23166]	malonate ChEBI	-	carbon source
[Ref.: #23166]	malonate ChEBI	-	growth
[Ref.: #23166]	oxalate ChEBI	-	carbon source
[Ref.: #23166]	oxalate ChEBI	-	growth
[Ref.: #23166]	oxaloacetate ChEBI	+	carbon source
[Ref.: #23166]	oxaloacetate ChEBI	+	growth
[Ref.: #23166]	propionate ChEBI	-	carbon source
[Ref.: #23166]	propionate ChEBI	-	growth
[Ref.: #23166]	pyruvate ChEBI	+	carbon source
[Ref.: #23166]	pyruvate ChEBI	+	growth
[Ref.: #23166]	succinate ChEBI	+	carbon source
[Ref.: #23166]	succinate ChEBI	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #23166]		catalase	+	1.11.1.6
[Ref.: #23166]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #16306]	Sample type/isolated from	freshwater taken from a depth of 60 m close to the bottom of a eutrophic lake
[Ref.: #16306]	Geographic location (country and/or sea, region)	Lake Sevan (40° 29' 35.50'' N 45° 11' 31.34'' E)
[Ref.: #16306]	Country	Armenia
[Ref.: #16306]	Country ISO 3 Code	ARM
[Ref.: #16306]	Continent	Asia
[Ref.: #16306]	Geographic location	40.4932°/45.1928°

[Ref.: #118935]	Sample type/isolated from	Environment, Freshwater
[Ref.: #118935]	Geographic location (country and/or sea, region)	Gosh lake
[Ref.: #118935]	Country	Armenia
[Ref.: #118935]	Country ISO 3 Code	ARM
[Ref.: #118935]	Continent	Asia
[Ref.: #118935]	Isolation date	2006
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)

What are isolation sources categories?

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

[Ref.: #16306]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118935]	Biosafety level	1	Risk group (French classification)

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.: #16306]	Polynucleobacter difficilis 16S rRNA gene (partial), IGS and 23S rRNA gene (partial), type strain AM-8B5T	FM208181	2103	ENA	556054 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Polynucleobacter difficilis AM-8B5	GCA_003065365	complete	GenBank	556054 tax ID	*
[Ref.: #66792]	Polynucleobacter difficilis AM-8B5	2808606694	complete	JGI IMG/M	556054 tax ID	*

[Ref.: #16306]	GC-content	49.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #23166]	GC-content	49.4 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Polynucleobacter difficilis AM-8B5 NCBI: GCA_003065365.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Polynucleobacter difficilis AM-8B5 NCBI: GCA_003065365.1
[Ref.: #69480]	flagellated	no	67.73	yes
[Ref.: #69480]	gram-positive	no	98.771	no
[Ref.: #69480]	anaerobic	no	95.446	yes
[Ref.: #69480]	halophile	no	90.688	yes
[Ref.: #69480]	spore-forming	no	95.017	no
[Ref.: #69480]	glucose-util	no	82.081	no
[Ref.: #69480]	aerobic	yes	72.231	no
[Ref.: #69480]	thermophile	no	87.43	yes
[Ref.: #69480]	motile	yes	64.508	yes
[Ref.: #69480]	glucose-ferment	no	91.794	no

Availability in culture collections External links

[Ref.: #16306]

Culture collection no.

DSM 22349, CIP 110078

[Ref.: #71728]

SI-ID 379267

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter.	Hahn MW, Minasyan A, Lang E, Koll U, Sproer C	Int J Syst Evol Microbiol	10.1099/ijs.0.031393-0	2011	*

References

#16306

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22349

#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 )

#23166

Martin W. Hahn, Arevik Minasyan, Elke Lang, Ulrike Koll, Catrin Spröer: Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter. IJSEM 62: 376 - 383 2012 ( DOI 10.1099/ijs.0.031393-0 , PubMed 21441373 )

#37911 ; Curators of the CIP;

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#71728

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID379267.1 )

#118935 Collection of Institut Pasteur ; Curators of the CIP; CIP 110078
* These data were automatically processed and therefore are not curated

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