Polynucleobacter rarus (DSM 21648, CIP 109928, MT-CBb6A5)

Name: Polynucleobacter rarus (DSM 21648, CIP 109928, MT-CBb6A5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2080

Type strain

Strain Designation MT-CBb6A5

Culture col. no. DSM 21648 CIP 109928 MT-CBb6A5

NCBI tax ID(s) 556055

Special Collections DSMZ CIP Literature strains

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Polynucleobacter rarus MT-CBb6A5 is an aerobe, chemoorganotroph, mesophilic prokaryote that was isolated from water from the pelagic zone of an acidic lake.

rod-shaped aerobe chemoorganotroph mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 371503

CIP 109928,DSM 21648

@ref 20215

Last LPSN update 2025-12-16 09:47:15

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Polynucleobacter

Species Polynucleobacter rarus

Full scientific name Polynucleobacter rarus Hahn et al. 2011

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape
23165	0.8-1.8 µm	0.6-0.8 µm	rod-shaped
122139			rod-shaped
125439
125438

Colony morphology

@ref	Incubation period
15865	8-14 days
23165

Pigmentation

@ref	Production	Name
23165		no pigments

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15865	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
23165	NSY and R2A
37883	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
122139	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15865	positive	growth	28	mesophilic
23165	negative	growth	5
23165	negative	growth	35
37883	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
23165	aerobe
23165	facultative anaerobe
125439	obligate aerobe

Nutrition type

23165

Typechemoorganotroph

Spore formation

@ref	Spore formation	Confidence
125439		96.9
125438		92.95

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23165	NaCl	positive	maximum	0.3 %(w/v)
23165	NaCl	positive	maximum	0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23165	39150 ChEBI	4-oxopentanoate	+	carbon source
23165	39150 ChEBI	4-oxopentanoate	+	growth
23165	30089 ChEBI	acetate	+	carbon source
23165	30089 ChEBI	acetate	+	growth
23165	17750 ChEBI	betaine	-	carbon source
23165	17750 ChEBI	betaine	-	growth
23165	16947 ChEBI	citrate	-	carbon source
23165	16947 ChEBI	citrate	-	growth
23165	15824 ChEBI	D-fructose	+	carbon source
23165	15824 ChEBI	D-fructose	+	growth
23165	28847 ChEBI	D-fucose	+	carbon source
23165	28847 ChEBI	D-fucose	+	growth
23165	12936 ChEBI	D-galactose	-	carbon source
23165	12936 ChEBI	D-galactose	-	growth
23165	18024 ChEBI	D-galacturonic acid	+	carbon source
23165	18024 ChEBI	D-galacturonic acid	+	growth
23165	17634 ChEBI	D-glucose	-	carbon source
23165	17634 ChEBI	D-glucose	-	growth
23165	62318 ChEBI	D-lyxose	+	carbon source
23165	62318 ChEBI	D-lyxose	+	growth
23165	16024 ChEBI	D-mannose	+	carbon source
23165	16024 ChEBI	D-mannose	+	growth
23165	17924 ChEBI	D-sorbitol	-	carbon source
23165	17924 ChEBI	D-sorbitol	-	growth
23165	15740 ChEBI	formate	-	carbon source
23165	15740 ChEBI	formate	-	growth
23165	29806 ChEBI	fumarate	+	carbon source
23165	29806 ChEBI	fumarate	+	growth
23165	29805 ChEBI	glycolate	+	carbon source
23165	29805 ChEBI	glycolate	+	growth
23165	36655 ChEBI	glyoxylate	+	carbon source
23165	36655 ChEBI	glyoxylate	+	growth
23165	16977 ChEBI	L-alanine	-	carbon source
23165	16977 ChEBI	L-alanine	-	growth
23165	17196 ChEBI	L-asparagine	-	carbon source
23165	17196 ChEBI	L-asparagine	-	growth
23165	29991 ChEBI	L-aspartate	-	carbon source
23165	29991 ChEBI	L-aspartate	-	growth
23165	17561 ChEBI	L-cysteine	+	carbon source
23165	17561 ChEBI	L-cysteine	+	growth
23165	29985 ChEBI	L-glutamate	-	carbon source
23165	29985 ChEBI	L-glutamate	-	growth
23165	17115 ChEBI	L-serine	-	carbon source
23165	25115 ChEBI	malate	+	carbon source
23165	25115 ChEBI	malate	+	growth
23165	15792 ChEBI	malonate	-	carbon source
23165	15792 ChEBI	malonate	-	growth
23165	30623 ChEBI	oxalate	-	growth
23165	30623 ChEBI	oxalate	+	carbon source
23165	16452 ChEBI	oxaloacetate	-	carbon source
23165	16452 ChEBI	oxaloacetate	-	growth
23165	17272 ChEBI	propionate	-	carbon source
23165	17272 ChEBI	propionate	-	growth
23165	15361 ChEBI	pyruvate	+	carbon source
23165	30031 ChEBI	succinate	+	carbon source
23165	30031 ChEBI	succinate	+	growth
23165	16094 ChEBI	thiosulfate	-	growth
23165	16199 ChEBI	urea	-	growth

Enzymes

@ref	Value	Activity	Ec
23165	catalase	+	1.11.1.6
122139	catalase	+	1.11.1.6
23165	cytochrome oxidase	+	1.9.3.1
122139	oxidase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Condition	#Acidic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15865	water from the pelagic zone of an acidic lake	Crystal Bog Lake, Wisconsin	USA	USA	North America
122139	Environment, Freshwater lake	Crystal Bog lake, Wisconsin	United States of America	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence FM208182 (>99% sequence identity) for Polynucleobacter rarus subclade from Microbeatlas

Aquatic Samples	1074
Soil Samples	65
Animal Samples	35
Plant Samples	3
Total Samples	1177

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15865	1	Risk group (German classification) According to TRBA 466
122139	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM307250v1 assembly for Polynucleobacter rarus MT-CBb6A5	scaffold	GCA_003072505	556055.3	2645728114	556055	61.99

Genome browser: GCA_003072505

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15865	Polynucleobacter rarus 16S rRNA gene (partial), IGS and 23S rRNA gene (partial), strain MT-CBb6A5	FM208182	2134		556055

GC content

@ref	GC-content (mol%)	Method
15865	40.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Polynucleobacter rarus MT-CBb6A5
NCBI: GCA_003072505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.90	no
125439	motility	BacteriaNetⓘ	no	58.30	no
125439	gram_stain	BacteriaNetⓘ	negative	91.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Polynucleobacter rarus MT-CBb6A5
NCBI: GCA_003072505.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.99	no
125438	anaerobic	anaerobicⓘ	no	92.98	no
125438	aerobic	aerobicⓘ	yes	82.89	no
125438	spore-forming	spore-formingⓘ	no	92.95	no
125438	thermophilic	thermophileⓘ	no	91.66	yes
125438	flagellated	motile2+ⓘ	no	77.30	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake.	Hahn MW, Lang E, Tarao M, Brandt U	Int J Syst Evol Microbiol	10.1099/ijs.0.017350-0	2010

References

#15865	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21648
#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 )
#23165	Martin W. Hahn, Elke Lang, Mitsunori Tarao, Ulrike Brandt: Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake. IJSEM 61: 781 - 787 2011 ( DOI 10.1099/ijs.0.017350-0 , PubMed 20435748 )
#37883	; 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) .
#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 .
#122139	Collection of Institut Pasteur ; Curators of the CIP; CIP 109928
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Polynucleobacter rarus (DSM 21648, CIP 109928, MT-CBb6A5)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003072505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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