Paenibacillus darwinianus (DSM 27245, ICMP 19912, Br)

Name: Paenibacillus darwinianus (DSM 27245, ICMP 19912, Br)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24289

Type strain

Strain Designation Br

Culture col. no. DSM 27245 ICMP 19912 Br

NCBI tax ID(s) 1380763

Special Collections DSMZ

History <- M. Dsouza, University of Auckland, New Zealand; strain Br

Links

Paenibacillus darwinianus Br is a psychrophilic prokaryote that was isolated from gamma-irradiated soil.

psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 403781

ICMP 19912,DSM 27245

@ref 20215

Last LPSN update 2026-02-09 11:23:56

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus darwinianus

Full scientific name Paenibacillus darwinianus Dsouza et al. 2014

Morphology

Cell morphology

@ref	Motility	Confidence
125439		90.9

Colony morphology

20713

Incubation period>14 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20713	PYGV AGAR (DSMZ Medium 621)		Medium recipe at MediaDive	Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20713	positive	growth	20	psychrophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	96.4

Spore formation

@ref	Spore formation	Confidence
125439		93.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	glycogen metabolism	100	5 of 5
66794	aspartate and asparagine metabolism	100	9 of 9
66794	adipate degradation	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	denitrification	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	degradation of sugar alcohols	93.75	15 of 16
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	pyrimidine metabolism	73.33	33 of 45
66794	proline metabolism	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	71.28	67 of 94
66794	phenylalanine metabolism	69.23	9 of 13
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	degradation of hexoses	66.67	12 of 18
66794	non-pathway related	65.79	25 of 38
66794	glycolysis	64.71	11 of 17
66794	vitamin B12 metabolism	64.71	22 of 34
66794	citric acid cycle	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	oxidative phosphorylation	62.64	57 of 91
66794	isoleucine metabolism	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	NAD metabolism	61.11	11 of 18
66794	myo-inositol biosynthesis	60	6 of 10
66794	coenzyme M biosynthesis	60	6 of 10
66794	arginine metabolism	58.33	14 of 24
66794	propanol degradation	57.14	4 of 7
66794	d-mannose degradation	55.56	5 of 9
66794	leucine metabolism	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	histidine metabolism	51.72	15 of 29
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	CMP-KDO biosynthesis	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	cysteine metabolism	50	9 of 18
66794	glutathione metabolism	50	7 of 14
66794	kanosamine biosynthesis II	50	1 of 2
66794	tryptophan metabolism	50	19 of 38
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	lipid metabolism	48.39	15 of 31
66794	sulfate reduction	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	vitamin B6 metabolism	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	nitrate assimilation	44.44	4 of 9
66794	lipoate biosynthesis	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	metabolism of disaccharids	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	tyrosine metabolism	35.71	5 of 14
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Continent	Latitude	Longitude
20713	gamma-irradiated soil	Britannia drift, Lake Wellman Region in the the south-eastern Darwin Mountains (79° 55' 16.2'' S 156° 55' 30.7'' E)	Australia and Oceania	-54.665	-69.664 -54.665/-69.664

Taxonmaps

69479

Global distribution of 16S sequence KF264455 (>99% sequence identity) for Paenibacillus darwinianus subclade from Microbeatlas

Aquatic Samples	79
Soil Samples	168
Animal Samples	357
Plant Samples	31
Total Samples	635

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20713	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Brdraft1 assembly for Paenibacillus darwinianus Br	scaffold	GCA_000598065	1380763.3	2609460045	1380763	8.55

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20713	Paenibacillus darwinianus strain Br 16S ribosomal RNA gene, partial sequence	KF264455	1412	1380763
124043	Paenibacillus darwinianus strain MB 16S ribosomal RNA gene, partial sequence.	KF264456	1412	1380763
124043	Paenibacillus darwinianus strain MB 16S ribosomal RNA gene, partial sequence.	KF264457	1409	1380763

GC content

@ref	GC-content (mol%)	Method
20713	55.6	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: Paenibacillus darwinianus Br
NCBI: GCA_000598065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	93.50	no
125439	motility	BacteriaNetⓘ	yes	90.90	no
125439	gram_stain	BacteriaNetⓘ	variable	81.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus darwinianus Br
NCBI: GCA_000598065.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	71.57	no
125438	anaerobic	anaerobicⓘ	no	92.25	no
125438	aerobic	aerobicⓘ	yes	73.30	no
125438	spore-forming	spore-formingⓘ	yes	84.43	no
125438	thermophilic	thermophileⓘ	no	76.02	no
125438	flagellated	motile2+ⓘ	yes	79.74	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus.	Dsouza M, Taylor MW, Turner SJ, Aislabie J.	PLoS One	10.1371/journal.pone.0108009	2014
Phylogeny	Paenibacillus darwinianus sp. nov., isolated from gamma-irradiated Antarctic soil.	Dsouza M, Taylor MW, Ryan J, MacKenzie A, Lagutin K, Anderson RF, Turner SJ, Aislabie J	Int J Syst Evol Microbiol	10.1099/ijs.0.056697-0	2014

References

#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 )
#20713	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27245
#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) .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Paenibacillus darwinianus (DSM 27245, ICMP 19912, Br)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000598065

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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