Name: Rhodoblastus sphagnicola RS
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1801

Type strain:

Species: Rhodoblastus sphagnicola

Strain Designation: RS

Culture col. no.: DSM 16996, VKM B-2361

Strain history: <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; RS <- I. S. Kulichevskaya

NCBI tax ID(s): 333368 (species)

SI-ID 286030

DSM 16996, VKM B-2361

Special Collections

Section

Rhodoblastus sphagnicola RS is an anaerobe, photoheterotroph, Gram-negative bacterium that was isolated from acidic Sphagnum peat sampled from Sosvyatskoe bog .

Gram-negative
motile
rod-shaped
anaerobe
photoheterotroph
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Roseiarcaceae*
	Genus	*Rhodoblastus*
	Species	**Rhodoblastus sphagnicola**
	Full Scientific Name (LPSN)	Rhodoblastus sphagnicola Kulichevskaya et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #23326]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.315

[Ref.: #23326]	Cell length	2.0-6.0 µm

[Ref.: #23326]	Cell width	0.8-1.0 µm

[Ref.: #23326]	Cell shape	rod-shaped

[Ref.: #23326]	Motility	yes

[Ref.: #23326]	Flagellum arrangement	monotrichous, polar

[Ref.: #23326]	Pigment production	yes
[Ref.: #23326]	Pigment name	Bacteriochlorophyll a
[Ref.: #23326]	Pigment production	yes
[Ref.: #23326]	Pigment name	carotenoids Rhodopin, Rhodopinal, Lycopene, Rhodopinol, Lycopenal, Rhodopinal glucoside, Lycopenal glucoside

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6680]

Culture medium

RHODOBLASTUS MEDIUM (DSMZ Medium 1142)

[Ref.: #6680]

Culture medium growth

[Ref.: #6680]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6680]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #6680]			growth	20 °C
[Ref.: #23326]			optimum	25-30 °C

	pH	Kind of pH		pH
[Ref.: #23326]			optimum	5.2-5.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6680]	Oxygen tolerance	anaerobe
[Ref.: #6680]	Oxygen tolerance	microaerophile
[Ref.: #23326]	Oxygen tolerance	anaerobe

[Ref.: #23326]	Nutrition type	photoheterotroph
[Ref.: #23326]	Nutrition type	photoautotroph

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23326]		NaCl	no	growth	>1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23326]	acetate ChEBI	+	growth
[Ref.: #23326]	ammonium ChEBI	+	nitrogen source
[Ref.: #23326]	benzoate ChEBI	-	growth
[Ref.: #23326]	butyrate ChEBI	+	growth
[Ref.: #23326]	citrate ChEBI	-	growth
[Ref.: #23326]	decanoate ChEBI	+	growth
[Ref.: #23326]	dinitrogen ChEBI	+	nitrogen source
[Ref.: #23326]	ethanol ChEBI	+	growth
[Ref.: #23326]	formate ChEBI	+	growth
[Ref.: #23326]	fructose ChEBI	-	growth
[Ref.: #23326]	glucose ChEBI	-	growth
[Ref.: #23326]	glutamate ChEBI	-	growth
[Ref.: #23326]	glycerol ChEBI	+	growth
[Ref.: #23326]	lactate ChEBI	+	growth
[Ref.: #23326]	malate ChEBI	+	growth
[Ref.: #23326]	malonate ChEBI	+	growth
[Ref.: #23326]	methanol ChEBI	+	growth
[Ref.: #23326]	propionate ChEBI	+	growth
[Ref.: #23326]	pyruvate ChEBI	+	growth
[Ref.: #23326]	succinate ChEBI	+	growth
[Ref.: #23326]	tartrate ChEBI	-	growth
[Ref.: #23326]	thiosulfate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	benzoyl-CoA degradation	100	7 of 7
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	chlorophyll metabolism	61.11	11 of 18
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	41.18	7 of 17
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
		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.: #6680]	Sample type/isolated from	acidic Sphagnum peat sampled from Sosvyatskoe bog (56° 10' N 32° 12' E)
[Ref.: #6680]	Host species	Sphagnum
[Ref.: #6680]	Geographic location (country and/or sea, region)	West Dvinskiy district, Tver Region
[Ref.: #6680]	Country	Russia
[Ref.: #6680]	Country ISO 3 Code	RUS
[Ref.: #6680]	Continent	Europe

[Ref.: #23326]	Sample type/isolated from	from an acidic Sphagnum peat bog (pH 3.5-4.2)
[Ref.: #23326]	Geographic location (country and/or sea, region)	Tver Region, field station of the Institute of Forestry, Russian academy of Sciences
[Ref.: #23326]	Country	Russia
[Ref.: #23326]	Country ISO 3 Code	RUS
[Ref.: #23326]	Continent	Europe
[Ref.: #23326]	Geographic location	56.1667°/32.2000°
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Peat moss
#Condition	#Acidic	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM040096 (>99% sequence identity) for Rhodoblastus sphagnicola subclade from Microbeatlas

Aquatic Samples	72
Soil Samples	64
Animal Samples	10
Plant Samples	2
Total Samples	148

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

[Ref.: #6680]

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.: #6680]	Rhodoblastus sphagnicola partial 16S rRNA gene, type strain RST	AM040096	1418	GenBank ENA	333368 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodoblastus sphagnicola DSM 16996	GCA_002937075	scaffold	GenBank ENA	333368 tax ID	*
[Ref.: #66792]	Rhodoblastus sphagnicola DSM 16996	GCA_014197735	scaffold	GenBank ENA	333368 tax ID	*
[Ref.: #66792]	Rhodoblastus sphagnicola strain DSM 16996	333368.4	wgs	PATRIC	333368 tax ID	*
[Ref.: #66792]	Rhodoblastus sphagnicola strain DSM 16996	333368.5	wgs	PATRIC	333368 tax ID	*
[Ref.: #66792]	Rhodoblastus sphagnicola DSM 16996	2831675700	draft	JGI IMG/M	333368 tax ID	*
[Ref.: #66792]	Rhodoblastus sphagnicola DSM 16996	2838086310	draft	JGI IMG/M	333368 tax ID	*

[Ref.: #6680]	GC-content	62.6 mol%
[Ref.: #23326]	GC-content	62.6 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodoblastus sphagnicola DSM 16996 NCBI: GCA_002937075.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.315	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	57.619	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	53.867	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.165	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	96.542	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	74.123	no

Availability in culture collections External links

[Ref.: #6680]

Culture collection no.

DSM 16996, VKM B-2361

[Ref.: #71448]

SI-ID 286030

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog.	Kulichevskaya IS, Guzev VS, Gorlenko VM, Liesack W, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.63962-0	2006	*

References

#6680

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16996

#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 )

#23326

Irina S. Kulichevskaya, Vladimir S. Guzev, Vladimir M. Gorlenko, Werner Liesack, Svetlana N. Dedysh: Rhodoblastus sphagnicola sp. nov., a novel acidophilic purple non-sulfur bacterium from Sphagnum peat bog. IJSEM 56: 1397 - 1402 2006 ( DOI 10.1099/ijs.0.63962-0 , PubMed 16738120 )

#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 .

#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) .

#71448

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-ID286030.1 )

* These data were automatically processed and therefore are not curated

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Rhodoblastus sphagnicola DSM 16996

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