Archive BacDiveID:10.13145/bacdive13751.20230509.8.1

Strain identifier

BacDive ID: 13751

Type strain:

Species: Rhodovulum steppense

Strain Designation: A-20s

Strain history: <- E. I. Kompantseva, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; A-20s

NCBI tax ID(s): 540251 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 15566

BacDive-ID: 13751

DSM-Number: 21153

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile, rod-shaped

description: Rhodovulum steppense A-20s is an anaerobe, mesophilic, motile bacterium that was isolated from microbial mat from a soda lake.

NCBI tax id

NCBI tax id: 540251
Matching level: species

strain history

@ref: 15566
history: <- E. I. Kompantseva, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; A-20s

doi: 10.13145/bacdive13751.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodobacterales
family: Roseobacteraceae
genus: Rhodovulum
species: Rhodovulum steppense
full scientific name: Rhodovulum steppense Kompantseva et al. 2010

@ref: 15566

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rhodovulum

species: Rhodovulum steppense

full scientific name: Rhodovulum steppense Kompantseva et al. 2010

strain designation: A-20s

type strain: yes

Morphology

cell morphology

@ref	cell length	cell width	cell shape	motility	gram stain	confidence
29512	1.75 µm	0.55 µm	rod-shaped	yes
69480					negative	99.999

pigmentation

@ref: 29512
production: yes

Culture and growth conditions

culture medium

@ref: 15566
name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)
growth: yes
link: https://mediadive.dsmz.de/medium/27
composition: Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water

culture temp

@ref: 15566
growth: positive
type: growth
temperature: 30
range: mesophilic

culture pH

@ref	ability	type	pH	PH range
29512	positive	growth	7.5-10	alkaliphile
29512	positive	optimum	8.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
15566	anaerobe
29512	aerobe

spore formation

@ref: 69480
spore formation: no
confidence: 99.991

halophily

@ref	salt	growth	tested relation	concentration
29512	NaCl	positive	growth	0.3-10 %
29512	NaCl	positive	optimum	3 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29512	30089	acetate	+	carbon source
29512	22653	asparagine	+	carbon source
29512	16236	ethanol	+	carbon source
29512	15740	formate	+	carbon source
29512	29987	glutamate	+	carbon source
29512	17754	glycerol	+	carbon source
29512	24996	lactate	+	carbon source
29512	25115	malate	+	carbon source
29512	37684	mannose	+	carbon source
29512	17272	propionate	+	carbon source
29512	15361	pyruvate	+	carbon source
29512	30031	succinate	+	carbon source
29512	31011	valerate	+	carbon source

Isolation, sampling and environmental information

isolation

@ref: 15566
sample type: microbial mat from a soda lake
geographic location: South Siberia, lake Khilganta (50° 42' 53'' N 115° 06' 08'' E)
country: Russia
origin.country: RUS
continent: Asia
latitude: 50.7147
longitude: 115.102

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_38455.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_15318;97_22412;98_28205;99_38455&stattab=map
Last taxonomy: Rhodovulum
16S sequence: EU741680
Sequence Identity:
Total samples: 40
soil counts: 1
aquatic counts: 37
animal counts: 2

Safety information

risk assessment

@ref: 15566
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 15566
description: Rhodovulum steppense strain A-20s 16S ribosomal RNA gene, partial sequence
accession: EU741680
length: 1349
database: ena
NCBI tax ID: 540251

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Rhodovulum steppense DSM 21153	GCA_004339675	contig	ncbi	540251
66792	Rhodovulum steppense strain DSM 21153	540251.3	wgs	patric	540251
66792	Rhodovulum steppense DSM 21153	2802429724	draft	img	540251

GC content

@ref	GC-content	method
15566	66.1	thermal denaturation, midpoint method (Tm)
29512	66.1

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	71	no
gram-positive	no	98.794	no
anaerobic	no	62.699	no
halophile	yes	61.795	no
spore-forming	no	94.262	no
glucose-util	yes	65.769	no
aerobic	no	77.822	no
flagellated	no	81.095	no
thermophile	no	95.192	yes
motile	yes	75.483	yes
glucose-ferment	no	89.142	no

External links

@ref: 15566

culture collection no.: DSM 21153, VKM B-2489

straininfo link

@ref: 82933
straininfo: 398137

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19667383	Rhodovulum steppense sp. nov., an obligately haloalkaliphilic purple nonsulfur bacterium widespread in saline soda lakes of Central Asia.	Kompantseva EI, Komova AV, Kostrikina NA	Int J Syst Evol Microbiol	10.1099/ijs.0.014639-0	2009	Asia, Central, Bacterial Typing Techniques, Chemoautotrophic Growth, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/microbiology, Genes, rRNA, Genotype, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phototrophic Processes, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/classification/genetics/growth & development/isolation & purification, Rhodovulum/classification/genetics/growth & development/isolation & purification, Sequence Analysis, DNA, Sodium Chloride, Species Specificity	Genetics
	21549386	Zeta potential of anoxygenic phototrophic bacteria and Ca adsorption at the cell surface: possible implications for cell protection from CaCO3 precipitation in alkaline solutions.	Bundeleva IA, Shirokova LS, Benezeth P, Pokrovsky OS, Kompantseva EI, Balor S	J Colloid Interface Sci	10.1016/j.jcis.2011.04.033	2011	Adsorption, Calcium/chemistry, Calcium Carbonate/chemistry, Rhodovulum/*chemistry/cytology, Solutions, Surface Properties
Phylogeny	24425825	Rhodovulum salis sp. nov. and Rhodovulum viride sp. nov., phototrophic Alphaproteobacteria isolated from marine habitats.	Srinivas A, Kumar BV, Sree BD, Tushar L, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.058974-0	2013	Bacteriochlorophyll A/chemistry, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, Pigmentation, Ponds/microbiology, RNA, Ribosomal, 16S/genetics, Rhodovulum/classification/genetics/isolation & purification, Seawater, Sequence Analysis, DNA, Sodium Chloride, Ubiquinone/chemistry, Water Microbiology	Genetics
Enzymology	25739304	[Physicochemical, catalytic, and regulatory properties of malate dehydrogenase from Rhodovulum steppense bacteria, strain A-20s].	Eprintsev AT, Falaleeva MI, Parfenova IV, Liashchenko MS, Kompantseva EI, Tret'iakova AIu	Izv Akad Nauk Ser Biol		2014	Adaptation, Physiological, Catalytic Domain, Chromatography, Ion Exchange, Electrophoresis, Polyacrylamide Gel, Enzyme Inhibitors/pharmacology, Enzyme Stability, Malate Dehydrogenase/chemistry/isolation & purification/metabolism, Molecular Weight, Protein Conformation, Rhodovulum/enzymology/physiology, Substrate Specificity, Temperature	Phylogeny
Enzymology	27266245	[Isoformes of Malate Dehydrogenase from Rhodovulum Steppense A-20s Grown Chemotrophically under Aerobic Condtions].	Eprintsev AT, Falaleeva MI, Lyashchenko MS, Gataullinaa MO, Kompantseva EI	Prikl Biokhim Mikrobiol		2016	Aerobiosis, Malate Dehydrogenase/chemistry/isolation & purification/metabolism, Protein Isoforms/chemistry/metabolism, Protein Subunits/*chemistry, Rhodovulum/enzymology	Metabolism
Enzymology	29297253	Oligomeric forms of bacterial malate dehydrogenase: a study of the enzyme from the phototrophic non-sulfur bacterium Rhodovulum steppense A-20s.	Eprintsev AT, Falaleeva MI, Lyashchenko MS, Toropygin IY, Igamberdiev AU	Biosci Biotechnol Biochem	10.1080/09168451.2017.1411776	2018	Cations, Citrates/chemistry, Dimerization, Hydrogen-Ion Concentration, Malate Dehydrogenase/chemistry/classification/genetics, Oxidative Stress, Oxygen/physiology, Phototrophic Processes, Polymerization, *Rhodovulum, Temperature	Phylogeny
	36014033	Nitrogen Fixation Activity and Genome Analysis of a Moderately Haloalkaliphilic Anoxygenic Phototrophic Bacterium Rhodovulum tesquicola.	Komova AV, Bakhmutova ED, Izotova AO, Kochetova ES, Toshchakov SV, Namsaraev ZB, Golichenkov MV, Korzhenkov AA	Microorganisms	10.3390/microorganisms10081615	2022

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
15566	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21153)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-21153
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29512	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	25910	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates		33211880	Nucleic Acids Res. 49: D498-D508 2020
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
82933	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID398137.1	StrainInfo: A central database for resolving microbial strain identifiers