Archive BacDiveID:10.13145/bacdive5852.20230509.8.1

Strain identifier

BacDive ID: 5852

Type strain:

Species: Halospina denitrificans

Strain history: <- D. Y. Sorokin, Winogradski Inst. Microbiol., RAS, Moscow, Russia; HGD 1-3

NCBI tax ID(s): 332522 (species)

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

General

@ref: 5965

BacDive-ID: 5852

DSM-Number: 15505

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Halospina denitrificans DSM 15505 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from hypersaline lake sediments.

NCBI tax id

NCBI tax id: 332522
Matching level: species

strain history

@ref: 5965
history: <- D. Y. Sorokin, Winogradski Inst. Microbiol., RAS, Moscow, Russia; HGD 1-3

doi: 10.13145/bacdive5852.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Oceanospirillales
family: Hahellaceae
genus: Halospina
species: Halospina denitrificans
full scientific name: Halospina denitrificans Sorokin et al. 2006

@ref: 5965

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Hahellaceae

genus: Halospina

species: Halospina denitrificans

full scientific name: Halospina denitrificans Sorokin et al. 2006

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31649	negative	03-07 µm	0.7-1 µm	rod-shaped	no
69480	negative					99.997

pigmentation

@ref: 31649
production: yes

Culture and growth conditions

culture medium

@ref: 5965
name: HALOVIBRIO MEDIUM (DSMZ Medium 1176)
growth: yes
link: https://mediadive.dsmz.de/medium/1176
composition: Name: HALOVIBRIO MEDIUM (DSMZ Medium 1176) Composition: NaCl 120.0 g/l K2HPO4 3.0 g/l HEPES 2.38 g/l Sodium acetate 1.6406 g/l NH4Cl 0.5 g/l MgSO4 x 7 H2O 0.492952 g/l Yeast extract 0.2 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.0022 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 H3BO3 3e-05 g/l NiCl2 x 6 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l CuCl2 x 2 H2O 3e-05 g/l Distilled water

culture temp

@ref: 5965
growth: positive
type: growth
temperature: 28
range: mesophilic

culture pH

@ref	ability	type	pH	PH range
31649	positive	growth	6.7-8.5	alkaliphile
31649	positive	optimum	6.7-8.5

Physiology and metabolism

oxygen tolerance

@ref: 31649
oxygen tolerance: facultative anaerobe

spore formation

@ref	spore formation	confidence
31649	no
69481	no	100
69480	no	99.998

halophily

@ref	salt	growth	tested relation	concentration
31649	NaCl	positive	growth	11.8-29 %
31649	NaCl	positive	optimum	14.5-17.4 %

observation

@ref: 31649
observation: aggregates in chains

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31649	15361	pyruvate	+	carbon source
31649	30031	succinate	+	carbon source
31649	17632	nitrate	+	reduction

Isolation, sampling and environmental information

isolation

@ref: 5965
sample type: hypersaline lake sediments
geographic location: south Siberia, Altai, Kulunda Steppe
country: Russia
origin.country: RUS
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment
#Condition	#Saline

Safety information

risk assessment

@ref: 5965
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 5965
description: Halospina denitrificans strain HGD 1-3 16S ribosomal RNA gene, partial sequence
accession: DQ072719
length: 1427
database: ena
NCBI tax ID: 332522

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Halospina denitrificans DSM 15505	GCA_004364635	scaffold	ncbi	332522
66792	Halospina denitrificans strain DSM 15505	332522.3	wgs	patric	332522
66792	Halospina denitrificans DSM 15505	2770939660	draft	img	332522

GC content

@ref: 31649
GC-content: 60

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	76.457	no
flagellated	no	77.531	no
gram-positive	no	98.688	yes
anaerobic	no	96.541	no
aerobic	yes	65.64	yes
halophile	yes	96.335	no
spore-forming	no	96.946	yes
glucose-util	yes	56.292	no
thermophile	no	99.462	yes
glucose-ferment	no	86.055	no

External links

@ref: 5965

culture collection no.: DSM 15505, UNIQEM U233, HGD 1-3

straininfo link

@ref: 75333
straininfo: 405370

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	16449444	Extremely halophilic denitrifying bacteria from hypersaline inland lakes, Halovibrio denitrificans sp. nov. and Halospina denitrificans gen. nov., sp. nov., and evidence that the genus name Halovibrio Fendrich 1989 with the type species Halovibrio variabilis should be associated with DSM 3050.	Sorokin DY, Tourova TP, Galinski EA, Belloch C, Tindall BJ	Int J Syst Evol Microbiol	10.1099/ijs.0.63964-0	2006	Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/microbiology, Gammaproteobacteria/classification/genetics/isolation & purification/physiology, Genes, rRNA, Geologic Sediments/microbiology, Halomonas/classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nitrates/metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Species Specificity	Enzymology
Phylogeny	22393767	Isolation and characterization of halophilic bacteria from Urmia Lake in Iran.	Vahed SZ, Forouhandeh H, Hassanzadeh S, Klenk HP, Hejazi MA, Hejazi MS	Mikrobiologiia		2011	Bacterial Typing Techniques, Catalase/metabolism, Culture Media, Gammaproteobacteria/classification/drug effects/enzymology/genetics/isolation & purification, Genes, rRNA, Genotype, Halomonadaceae/classification/drug effects/enzymology/genetics/isolation & purification, Hydrogen-Ion Concentration, Iran, Lakes/microbiology, Microbial Consortia/drug effects/genetics, Oxidoreductases/metabolism, Phenotype, Phylogeny, Pseudomonadaceae/classification/drug effects/enzymology/genetics/isolation & purification, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNA, Sodium Chloride/*pharmacology, Urease/metabolism	Enzymology

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
5965	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15505)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-15505
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
31649	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	27931	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
75333	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID405370.1	StrainInfo: A central database for resolving microbial strain identifiers