Roseinatronobacter bogoriensis subsp. barguzinensis (DSM 19920, VKM B-2406, alga-05)

Name: Roseinatronobacter bogoriensis subsp. barguzinensis (DSM 19920, VKM B-2406, alga-05)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13828

Type strain

Strain Designation alga-05

Culture col. no. DSM 19920 VKM B-2406 alga-05

NCBI tax ID(s) 441209

Special Collections DSMZ

History <- V. M. Gorlenko, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; alga-05 <- E. N. Boldareva

Links

Roseinatronobacter bogoriensis subsp. barguzinensis alga-05 is an anaerobe bacterium that was isolated from thin bacterial mat from a soda lake.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 408062

DSM 19920

@ref 20215

Last LPSN update 2026-02-09 11:21:15

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Roseinatronobacter

Species Roseinatronobacter bogoriensis subsp. barguzinensis

Full scientific name Roseinatronobacter bogoriensis subsp. barguzinensis (Boldareva et al. 2009) Hu et al. 2024

Synonyms (2)

"Rhodobaca bogoriensis subsp. barguzinensis"
Rhodobaca barguzinensis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.2
125438	negative	99.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8389	RHODOBACA BARGUZINENSIS MEDIUM (DSMZ Medium 1227)		Medium recipe at MediaDive	Name: RHODOBACA BARGUZINENSIS MEDIUM (DSMZ Medium 1227) Composition: NaCl 20.0 g/l Na2CO3 10.0 g/l NaHCO3 5.0 g/l Yeast extract 1.0 g/l Na2S2O3 x 5 H2O 1.0 g/l KH2PO4 0.5 g/l Na2SO4 0.5 g/l KCl 0.5 g/l NaNO3 0.4 g/l NH4Cl 0.4 g/l MgCl2 x 6 H2O 0.2 g/l CoCl2 x 6 H2O 0.0001998 g/l MnCl2 x 4 H2O 9.99001e-05 g/l ZnCl2 6.99301e-05 g/l H3BO3 5.99401e-05 g/l Na2MoO4 x 2 H2O 3.996e-05 g/l NiCl2 x 6 H2O 1.998e-05 g/l CuCl2 x 2 H2O 1.998e-05 g/l HCl Vitamin B12 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8389	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
8389	anaerobe
125439	obligate aerobe	96.2

Spore formation

@ref	Spore formation	Confidence
125439		98.4
125438		93.554

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	octane oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	quinate degradation	100	2 of 2
66794	resorcinol degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	methane metabolism	100	3 of 3
66794	denitrification	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	leucine metabolism	92.31	12 of 13
66794	vitamin B12 metabolism	91.18	31 of 34
66794	threonine metabolism	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	pyrimidine metabolism	86.67	39 of 45
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	glutathione metabolism	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	methionine metabolism	76.92	20 of 26
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	lipid metabolism	74.19	23 of 31
66794	pentose phosphate pathway	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	alanine metabolism	72.41	21 of 29
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	tyrosine metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	tryptophan metabolism	71.05	27 of 38
66794	propionate fermentation	70	7 of 10
66794	sulfate reduction	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	oxidative phosphorylation	67.03	61 of 91
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	cysteine metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	chlorophyll metabolism	66.67	12 of 18
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	lysine metabolism	64.29	27 of 42
66794	vitamin B6 metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	polyamine pathway	60.87	14 of 23
66794	non-pathway related	60.53	23 of 38
66794	3-phenylpropionate degradation	60	9 of 15
66794	glycogen metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	phenol degradation	55	11 of 20
66794	d-xylose degradation	54.55	6 of 11
66794	degradation of pentoses	53.57	15 of 28
66794	degradation of sugar acids	52	13 of 25
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	biotin biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	toluene degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	arachidonic acid metabolism	44.44	8 of 18
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	ascorbate metabolism	40.91	9 of 22
66794	vitamin K metabolism	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	degradation of hexoses	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	carotenoid biosynthesis	31.82	7 of 22
66794	starch degradation	30	3 of 10
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Microbial community	#Microbial mat
#Condition	#Alkaline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8389	thin bacterial mat from a soda lake	East Siberia, Buryatia, Bargusin Valley	Russia	RUS	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF554833 (>99% sequence identity) for Rhodobaca from Microbeatlas

Aquatic Samples	120
Soil Samples	20
Animal Samples	24
Plant Samples	3
Total Samples	167

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8389	1	Risk group (German 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	ASM436588v1 assembly for Roseinatronobacter bogoriensis subsp. barguzinensis DSM 19920	scaffold	GCA_004365885	441209.10	2593339286	441209	73.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8389	Rhodobaca barguzinensis strain VKM B-2406 16S ribosomal RNA gene, partial sequence	EF554833	1367		441209
124043	Rhodobaca barguzinensis strain DSM 19920 16S ribosomal RNA gene, partial sequence.	MK598755	1387		441209

GC content

8389

GC-content (mol%)59.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodobaca barguzinensis DSM 19920
NCBI: GCA_004365885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.40	no
125439	motility	BacteriaNetⓘ	yes	67.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodobaca barguzinensis DSM 19920
NCBI: GCA_004365885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	82.41	yes
125438	aerobic	aerobicⓘ	yes	75.17	yes
125438	spore-forming	spore-formingⓘ	no	93.55	no
125438	thermophilic	thermophileⓘ	no	98.11	yes
125438	flagellated	motile2+ⓘ	yes	62.98	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Clustered Core- and Pan-Genome Content on Rhodobacteraceae Chromosomes.	Kopejtka K, Lin Y, Jakubovicova M, Koblizek M, Tomasch J.	Genome Biol Evol	10.1093/gbe/evz138	2019
Genetics	Osmotic Adaptation and Compatible Solute Biosynthesis of Phototrophic Bacteria as Revealed from Genome Analyses.	Imhoff JF, Rahn T, Kunzel S, Keller A, Neulinger SC.	Microorganisms	10.3390/microorganisms9010046	2020
	Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales.	Kopejtka K, Tomasch J, Zeng Y, Tichy M, Sorokin DY, Koblizek M.	Genome Biol Evol	10.1093/gbe/evx141	2017
Enzymology	Distribution and origin of oxygen-dependent and oxygen-independent forms of Mg-protoporphyrin monomethylester cyclase among phototrophic proteobacteria.	Boldareva-Nuianzina EN, Blahova Z, Sobotka R, Koblizek M.	Appl Environ Microbiol	10.1128/aem.00104-13	2013
Genetics	Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov.	Liang KYH, Orata FD, Boucher YF, Case RJ.	Front Microbiol	10.3389/fmicb.2021.683109	2021
Genetics	The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes.	Kopejtka K, Tomasch J, Bunk B, Sproer C, Wagner-Dobler I, Koblizek M	Extremophiles	10.1007/s00792-018-1041-8	2018
	Genome-based analysis of the family Paracoccaceae and description of Ostreiculturibacter nitratireducens gen. nov., sp. nov., isolated from an oyster farm on a tidal flat.	Huang Z, Li M, Oren A, Lai Q.	Front Microbiol	10.3389/fmicb.2024.1376777	2024
Phylogeny	[Rhodobaculum claviforme gen. nov., sp. nov., a New Alkaliphilic Nonsulfur Purple Bacterium].	Bryantseva IA, Gaisin VA, Gorlenko VM	Mikrobiologiia		2015
Phylogeny	[Rhodobaca barguzinensis sp. nov., a new alkaliphilic purple nonsulfur bacterium isolated from a soda lake of the Barguzin Valley (Buryat Republic, eastern Siberia)].	Boldareva EN, Akimov VN, Boichenko VA, Stadnichuk IN, Moskalenko AA, Makhneva ZK, Gorlenko VM	Mikrobiologiia		2008

References

#8389	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19920
#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 )
#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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Roseinatronobacter bogoriensis subsp. barguzinensis (DSM 19920, VKM B-2406, alga-05)

Name and taxonomic classification

Morphology

Cell 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_004365885

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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