Name: Deinobacterium chartae K-bf-PMWA-4.1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3901

Type strain:

Species: Deinobacterium chartae

Strain Designation: K-bf-PMWA-4.1, K4.1

Culture col. no.: DSM 21458, HAMBI 2721

Strain history: <- M. Salkinoja-Salonen, Univ. Helsinki; K4.1 <- Univ. Helsinki; HAMBI 2721 <- J.V. Ekman; K-bf-PMWA-4.1

NCBI tax ID(s): 521158 (species)

SI-ID 401948

DSM 21458

Section

Deinobacterium chartae K-bf-PMWA-4.1 is an aerobe, chemoorganotroph, mesophilic bacterium that was isolated from paper mill, biofim in the wire section.

Gram-negative
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	*Deinococcota*
	Class	*Deinococci*
	Order	*Deinococcales*
	Family	*Deinococcaceae*
	Genus	*Deinobacterium*
	Species	**Deinobacterium chartae**
	Full Scientific Name (LPSN)	Deinobacterium chartae Ekman et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #23351]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %94.733

[Ref.: #23351]	Cell length	1.4-2.5 µm

[Ref.: #23351]	Cell width	0.8-1.3 µm

[Ref.: #23351]	Cell shape	rod-shaped

[Ref.: #23351]	Motility	no

[Ref.: #23351]	Colony color	pale-pink
[Ref.: #23351]	Cultivation medium used	R2A

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15718]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15718]

Culture medium growth

[Ref.: #15718]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15718]

Culture medium composition

expand / minimize

[Ref.: #23351]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #23351]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #15718]			growth	37 °C
[Ref.: #23351]			optimum	37-45 °C

[Ref.: #15718]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #23351]			growth	6.0-10.3

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23351]

Oxygen tolerance

aerobe

[Ref.: #23351]

Nutrition type

chemoorganotroph

[Ref.: #23351]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %91.961

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23351]		NaCl	no	growth	>3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23351]	(-)-quinic acid ChEBI	-	assimilation
[Ref.: #23351]	1,2-propandiol ChEBI	-	assimilation
[Ref.: #23351]	2,3-butanone	-	assimilation
[Ref.: #23351]	2-deoxy-d-ribose ChEBI	-	assimilation
[Ref.: #23351]	2-oxoglutarate ChEBI	-	assimilation
[Ref.: #23351]	2-oxopentanoate ChEBI	+	assimilation
[Ref.: #23351]	3-hydroxy 2-butanone	+	assimilation
[Ref.: #23351]	4-hydroxy-L-proline ChEBI	-	assimilation
[Ref.: #23351]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #23351]	4-hydroxyphenylacetic acid ChEBI	+	assimilation
[Ref.: #23351]	5-aminovaleric acid ChEBI	-	assimilation
[Ref.: #23351]	5-dehydro-D-gluconate ChEBI	+	assimilation
[Ref.: #23351]	acetate ChEBI	-	assimilation
[Ref.: #23351]	acetoacetate ChEBI	+	assimilation
[Ref.: #23351]	alpha-D-glucose ChEBI	-	assimilation
[Ref.: #23351]	amygdalin ChEBI	-	assimilation
[Ref.: #23351]	arbutin ChEBI	+	assimilation
[Ref.: #23351]	beta-D-allose ChEBI	-	assimilation
[Ref.: #23351]	bromosuccinate ChEBI	+	assimilation
[Ref.: #23351]	butyrate ChEBI	+	assimilation
[Ref.: #23351]	cellobiose ChEBI	-	assimilation
[Ref.: #23351]	chondroitin sulfate ChEBI	+	assimilation
[Ref.: #23351]	citraconate ChEBI	-	assimilation
[Ref.: #23351]	citramalic acid	-	assimilation
[Ref.: #23351]	citrate ChEBI	+	assimilation
[Ref.: #23351]	D-arabinose ChEBI	+	assimilation
[Ref.: #23351]	D-arabitol ChEBI	-	assimilation
[Ref.: #23351]	D-aspartate ChEBI	+	assimilation
[Ref.: #23351]	D-fructose ChEBI	-	assimilation
[Ref.: #23351]	D-galactonic acid lactone ChEBI	+	assimilation
[Ref.: #23351]	D-galactose ChEBI	-	assimilation
[Ref.: #23351]	D-galacturonic acid ChEBI	+	assimilation
[Ref.: #23351]	D-gluconate ChEBI	+	assimilation
[Ref.: #23351]	D-glucosamine ChEBI	+	assimilation
[Ref.: #23351]	D-glucosaminic acid ChEBI	+	assimilation
[Ref.: #23351]	D-glucose 6-phosphate ChEBI	+	assimilation
[Ref.: #23351]	D-glucuronate ChEBI	-	assimilation
[Ref.: #23351]	D-malate ChEBI	-	assimilation
[Ref.: #23351]	D-mannose ChEBI	-	assimilation
[Ref.: #23351]	D-ribono-1,4-lactone	-	assimilation
[Ref.: #23351]	D-serine ChEBI	-	assimilation
[Ref.: #23351]	D-sorbitol ChEBI	-	assimilation
[Ref.: #23351]	D-tagatose ChEBI	+	assimilation
[Ref.: #23351]	D-threonine ChEBI	+	assimilation
[Ref.: #23351]	D-trehalose ChEBI	-	assimilation
[Ref.: #23351]	D-xylose ChEBI	+	assimilation
[Ref.: #23351]	decanoate ChEBI	-	assimilation
[Ref.: #23351]	dextrin ChEBI	+	assimilation
[Ref.: #23351]	dihydroxyacetone ChEBI	+	assimilation
[Ref.: #23351]	DL-carnitine	-	assimilation
[Ref.: #23351]	dl-octopamine	-	assimilation
[Ref.: #23351]	erythritol ChEBI	-	assimilation
[Ref.: #23351]	fructose ChEBI	+	builds acid from
[Ref.: #23351]	fumarate ChEBI	+	assimilation
[Ref.: #23351]	galactarate ChEBI	-	assimilation
[Ref.: #23351]	galactitol ChEBI	-	assimilation
[Ref.: #23351]	gamma-aminobutyric acid ChEBI	-	assimilation
[Ref.: #23351]	gamma-cyclodextrin ChEBI	+	assimilation
[Ref.: #23351]	gelatin ChEBI	+	assimilation
[Ref.: #23351]	gentiobiose ChEBI	+	assimilation
[Ref.: #23351]	glucose ChEBI	+	builds acid from
[Ref.: #23351]	glucose 1-phosphate ChEBI	+	assimilation
[Ref.: #23351]	glucuronamide ChEBI	+	assimilation
[Ref.: #23351]	glycerol ChEBI	+	assimilation
[Ref.: #23351]	glycerol 1-phosphate ChEBI	-	assimilation
[Ref.: #23351]	glycine ChEBI	-	assimilation
[Ref.: #23351]	glycogen ChEBI	+	assimilation
[Ref.: #23351]	glycolate ChEBI	+	assimilation
[Ref.: #23351]	glycyl L-aspartic acid ChEBI	+	assimilation
[Ref.: #23351]	hexanoate ChEBI	+	assimilation
[Ref.: #23351]	inulin ChEBI	-	assimilation
[Ref.: #23351]	L-alanine ChEBI	+	assimilation
[Ref.: #23351]	L-arabinose ChEBI	-	assimilation
[Ref.: #23351]	L-arabitol ChEBI	-	assimilation
[Ref.: #23351]	L-asparagine ChEBI	+	assimilation
[Ref.: #23351]	L-aspartate ChEBI	+	assimilation
[Ref.: #23351]	L-fucose ChEBI	+	assimilation
[Ref.: #23351]	L-glutamate ChEBI	-	assimilation
[Ref.: #23351]	L-histidine ChEBI	+	assimilation
[Ref.: #23351]	L-homoserine ChEBI	-	assimilation
[Ref.: #23351]	L-lysine ChEBI	+	assimilation
[Ref.: #23351]	L-ornithine ChEBI	-	assimilation
[Ref.: #23351]	L-phenylalanine ChEBI	-	assimilation
[Ref.: #23351]	L-proline ChEBI	+	nitrogen source
[Ref.: #23351]	L-threonine ChEBI	-	assimilation
[Ref.: #23351]	L-valine ChEBI	-	assimilation
[Ref.: #23351]	lactate ChEBI	-	assimilation
[Ref.: #23351]	lactitol ChEBI	+	assimilation
[Ref.: #23351]	malate ChEBI	-	assimilation
[Ref.: #23351]	malonate ChEBI	+	assimilation
[Ref.: #23351]	maltose ChEBI	-	oxidation
[Ref.: #23351]	maltose ChEBI	+	builds acid from
[Ref.: #23351]	mannitol ChEBI	-	builds acid from
[Ref.: #23351]	melibionic acid	+	assimilation
[Ref.: #23351]	methyl alpha-D-mannoside ChEBI	-	assimilation
[Ref.: #23351]	methyl beta-D-galactoside ChEBI	+	assimilation
[Ref.: #23351]	methyl beta-D-glucuronic acid	-	assimilation
[Ref.: #23351]	methyl beta-D-xylopyranoside ChEBI	-	assimilation
[Ref.: #23351]	methyl pyruvate ChEBI	+	assimilation
[Ref.: #23351]	myo-inositol ChEBI	+	assimilation
[Ref.: #23351]	n-acetyl-neuraminic acid	-	assimilation
[Ref.: #23351]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #23351]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #23351]	oxalomalic acid	+	assimilation
[Ref.: #23351]	palatinose ChEBI	+	assimilation
[Ref.: #23351]	phenylethylamine ChEBI	+	assimilation
[Ref.: #23351]	propionate ChEBI	+	assimilation
[Ref.: #23351]	putrescine ChEBI	-	assimilation
[Ref.: #23351]	pyruvate ChEBI	-	assimilation
[Ref.: #23351]	ribitol ChEBI	-	assimilation
[Ref.: #23351]	ribose ChEBI	-	builds acid from
[Ref.: #23351]	salicin ChEBI	+	assimilation
[Ref.: #23351]	salicylate ChEBI	-	assimilation
[Ref.: #23351]	sebacic acid ChEBI	-	assimilation
[Ref.: #23351]	sec-butylamine	-	assimilation
[Ref.: #23351]	sedoheptulosan ChEBI	-	assimilation
[Ref.: #23351]	sorbic acid ChEBI	-	assimilation
[Ref.: #23351]	succinamate ChEBI	-	assimilation
[Ref.: #23351]	succinate ChEBI	+	assimilation
[Ref.: #23351]	sucrose ChEBI	-	assimilation
[Ref.: #23351]	tartrate ChEBI	+	assimilation
[Ref.: #23351]	thymidine ChEBI	+	nitrogen source
[Ref.: #23351]	tricarballylate ChEBI	-	assimilation
[Ref.: #23351]	turanose ChEBI	+	assimilation
[Ref.: #23351]	tween 20 ChEBI	-	assimilation
[Ref.: #23351]	uridine ChEBI	-	assimilation
[Ref.: #23351]	xylitol ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #23351]		catalase	+	1.11.1.6

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

[Ref.: #15718]	Sample type/isolated from	paper mill, biofim in the wire section
[Ref.: #15718]	Country	Finland
[Ref.: #15718]	Country ISO 3 Code	FIN
[Ref.: #15718]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Plant (Factory)
#Environmental	#Biofilm	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM988777 (>99% sequence identity) for Deinobacterium chartae subclade from Microbeatlas

Aquatic Samples	276
Soil Samples	65
Animal Samples	60
Plant Samples	22
Total Samples	423

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

[Ref.: #15718]

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.: #15718]	Deinobacterium chartae partial 16S rRNA gene, type strain K4.1T	AM988777	1461	ENA	521158 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Deinobacterium chartae DSM 21458	GCA_014202645	scaffold	GenBank	521158 tax ID	*
[Ref.: #66792]	Deinobacterium chartae strain DSM 21458	521158.3	wgs	PATRIC	521158 tax ID	*
[Ref.: #66792]	Deinobacterium chartae DSM 21458	2861587418	draft	JGI IMG/M	521158 tax ID	*

[Ref.: #15718]

GC-content

66.8 mol%

high performance liquid chromatography (HPLC)

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: Deinobacterium chartae DSM 21458 NCBI: GCA_014202645.1
[Ref.: #69481]	spore-forming	no	60	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Deinobacterium chartae DSM 21458 NCBI: GCA_014202645.1
[Ref.: #69480]	flagellated	no	94.008	yes
[Ref.: #69480]	gram-positive	yes	69.667	no
[Ref.: #69480]	anaerobic	no	97.188	no
[Ref.: #69480]	aerobic	yes	85.442	yes
[Ref.: #69480]	halophile	no	89.989	no
[Ref.: #69480]	spore-forming	no	88.359	no
[Ref.: #69480]	glucose-util	yes	81.108	yes
[Ref.: #69480]	thermophile	no	67.964	no
[Ref.: #69480]	motile	no	87.46	yes
[Ref.: #69480]	glucose-ferment	no	90.765	no

Availability in culture collections External links

[Ref.: #15718]

Culture collection no.

DSM 21458, HAMBI 2721

[Ref.: #73411]

SI-ID 401948

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper mill.	Ekman JV, Raulio M, Busse HJ, Fewer DP, Salkinoja-Salonen M	Int J Syst Evol Microbiol	10.1099/ijs.0.017970-0	2010	*

References

#15718

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21458

#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 )

#23351

Jaakko V. Ekman, Mari Raulio, Hans-Jürgen Busse, David P. Fewer, Mirja Salkinoja-Salonen: Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper mill. IJSEM 61: 540 - 548 2011 ( DOI 10.1099/ijs.0.017970-0 , PubMed 20382794 )

#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 .

#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 )

#73411

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-ID401948.1 )

* These data were automatically processed and therefore are not curated

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Deinobacterium chartae DSM 21458

Deinobacterium chartae DSM 21458

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