Archive BacDiveID:10.13145/bacdive13853.20230509.8.1

Strain identifier

BacDive ID: 13853

Type strain:

Species: Roseibaca ekhonensis

Strain Designation: EL-50

Strain history: <- P. Hirsch and M. Labrenz, Univ. Kiel, Germany

NCBI tax ID(s): 254356 (species)

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

General

@ref: 4379

BacDive-ID: 13853

DSM-Number: 11469

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped

description: Roseibaca ekhonensis EL-50 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from water at a depth of 6m.

NCBI tax id

NCBI tax id: 254356
Matching level: species

strain history

@ref: 4379
history: <- P. Hirsch and M. Labrenz, Univ. Kiel, Germany

doi: 10.13145/bacdive13853.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodobacterales
family: Paracoccaceae
genus: Roseibaca
species: Roseibaca ekhonensis
full scientific name: Roseibaca ekhonensis Labrenz et al. 2009

@ref: 4379

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Roseibaca

species: Roseibaca ekhonensis

full scientific name: Roseibaca ekhonensis Labrenz et al. 2009

strain designation: EL-50

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29597	negative	2.5 µm	1 µm	rod-shaped	no
69480	negative					99.946

pigmentation

@ref: 29597
production: yes

Culture and growth conditions

culture medium

@ref: 4379
name: EKHO LAKE STRAINS MEDIUM (DSMZ Medium 621a)
growth: yes
link: https://mediadive.dsmz.de/medium/621a
composition: Name: EKHO LAKE STRAINS MEDIUM (DSMZ Medium 621a) Composition: NaCl 22.6553 g/l Agar 15.0 g/l MgCl2 x 6 H2O 4.80666 g/l Na2SO4 3.77991 g/l CaCl2 1.06343 g/l KCl 0.64076 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 NaHCO3 0.18528 g/l CaCl2 x 2 H2O 0.0703158 g/l H3BO3 0.02509 g/l SrCl2 0.02316 g/l KBr 0.00579 g/l NaF 0.002895 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 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 p-Aminobenzoic acid 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	range
4379	positive	growth	20	psychrophilic
29597	positive	growth	10-30
29597	positive	optimum	16	psychrophilic

culture pH

@ref: 29597
ability: positive
type: optimum
pH: 8.25

Physiology and metabolism

oxygen tolerance

@ref: 29597
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
29597	no
69481	no	100
69480	no	99.978

halophily

@ref	salt	growth	tested relation	concentration
29597	NaCl	positive	growth	0.0-4.0 %
29597	NaCl	positive	optimum	2.5 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29597	30089	acetate	+	carbon source
29597	21217	L-alaninamide	+	carbon source
29597	16449	alanine	+	carbon source
29597	28644	2-oxopentanoate	+	carbon source
29597	18403	L-arabitol	+	carbon source
29597	22653	asparagine	+	carbon source
29597	35391	aspartate	+	carbon source
29597	17057	cellobiose	+	carbon source
29597	16947	citrate	+	carbon source
29597	28757	fructose	+	carbon source
29597	28260	galactose	+	carbon source
29597	24175	galacturonate	+	carbon source
29597	17234	glucose	+	carbon source
29597	32323	glucuronamide	+	carbon source
29597	29987	glutamate	+	carbon source
29597	17754	glycerol	+	carbon source
29597	27570	histidine	+	carbon source
29597	17596	inosine	+	carbon source
29597	17240	itaconate	+	carbon source
29597	17716	lactose	+	carbon source
29597	25115	malate	+	carbon source
29597	15792	malonate	+	carbon source
29597	17306	maltose	+	carbon source
29597	29864	mannitol	+	carbon source
29597	37684	mannose	+	carbon source
29597	17272	propionate	+	carbon source
29597	15361	pyruvate	+	carbon source
29597	26490	quinate	+	carbon source
29597	26546	rhamnose	+	carbon source
29597	17814	salicin	+	carbon source
29597	17822	serine	+	carbon source
29597	30911	sorbitol	+	carbon source
29597	30031	succinate	+	carbon source
29597	17992	sucrose	+	carbon source
29597	26986	threonine	+	carbon source
29597	17748	thymidine	+	carbon source
29597	27082	trehalose	+	carbon source
29597	53423	tween 40	+	carbon source
29597	16704	uridine	+	carbon source

enzymes

@ref	value	activity	ec
29597	catalase	+	1.11.1.6
29597	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref: 4379
sample type: water at a depth of 6m
geographic location: Vestfold Hills, Ekho Lake
continent: Australia and Oceania

isolation source categories

Cat1: #Environmental
Cat2: #Aquatic

Safety information

risk assessment

@ref: 4379
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 4379
description: Roseibaca ekhonensis 16S rRNA gene, strain EL-50
accession: AJ605746
length: 1425
database: ena
NCBI tax ID: 254356

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Roseibaca ekhonensis CECT 7235	GCA_900499075	contig	ncbi	254356
66792	Roseibaca ekhonensis strain CECT 7235	254356.4	wgs	patric	254356
66792	Roseibaca ekhonensis CECT 7235	2831655652	draft	img	254356

GC content

@ref	GC-content	method
4379	61	high performance liquid chromatography (HPLC)
29597	61

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	63.42	yes
gram-positive	no	98.521	yes
anaerobic	no	95.607	yes
aerobic	yes	66.019	no
halophile	no	50	no
spore-forming	no	96.52	yes
glucose-util	yes	77.034	no
flagellated	no	90.744	yes
thermophile	no	93.621	yes
glucose-ferment	no	90.452	no

External links

@ref: 4379

culture collection no.: DSM 11469, CECT 7235

straininfo link

@ref: 83029
straininfo: 364186

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19567566	Roseibaca ekhonensis gen. nov., sp. nov., an alkalitolerant and aerobic bacteriochlorophyll a-producing alphaproteobacterium from hypersaline Ekho Lake.	Labrenz M, Lawson PA, Tindall BJ, Hirsch P	Int J Syst Evol Microbiol	10.1099/ijs.0.016717-0	2009	Aerobiosis, Alcohols/metabolism, Alphaproteobacteria/chemistry/classification/isolation & purification/physiology, Bacteriochlorophyll A/analysis, Base Composition, Carbohydrate Metabolism, Carboxylic Acids/metabolism, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysis, Water Microbiology	Metabolism
Phylogeny	30942687	Alkalilacustris brevis gen. nov., sp. nov., isolated from a soda lake.	Zhang R, Ju Z, Han S, Hou X, Yu Y, Zhang X, Ye Y, Sun C, Zhang G, Wu M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003373	2019	Alkalies, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Lakes/chemistry/microbiology, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
4379	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11469)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-11469
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
29597	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	25988	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
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)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
83029	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID364186.1	StrainInfo: A central database for resolving microbial strain identifiers