Archive BacDiveID:10.13145/bacdive4039.20230509.8.1

Strain identifier

BacDive ID: 4039

Type strain:

Species: Desulfonauticus submarinus

Strain Designation: 6N

Strain history: <- B. Ollivier, IRD, Marseille; 6N <- C. Audiffrin {2001}

NCBI tax ID(s): 206665 (species)

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

General

@ref: 5786

BacDive-ID: 4039

DSM-Number: 15269

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, motile

description: Desulfonauticus submarinus 6N is an anaerobe, thermophilic, motile bacterium that was isolated from matrixes of Alvinella and Riftia, deep-sea hydrothermal vent samples, 2600 m depth.

NCBI tax id

NCBI tax id: 206665
Matching level: species

strain history

@ref: 5786
history: <- B. Ollivier, IRD, Marseille; 6N <- C. Audiffrin {2001}

doi: 10.13145/bacdive4039.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Desulfovibrionales
family: Desulfohalobiaceae
genus: Desulfonauticus
species: Desulfonauticus submarinus
full scientific name: Desulfonauticus submarinus Audiffrin et al. 2003

@ref: 5786

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfovibrionales

family: Desulfohalobiaceae

genus: Desulfonauticus

species: Desulfonauticus submarinus

full scientific name: Desulfonauticus submarinus Audiffrin et al. 2003

strain designation: 6N

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	98.264
69480		99.993	negative

Culture and growth conditions

culture medium

@ref: 5786
name: DESULFONAUTICUS MEDIUM (DSMZ Medium 383b)
growth: yes
link: https://mediadive.dsmz.de/medium/383b
composition: Name: DESULFONAUTICUS MEDIUM (DSMZ Medium 383b; with strain-specific modifications) Composition: NaCl 20.8747 g/l Na2SO4 2.9821 g/l MgCl2 x 6 H2O 2.9821 g/l Trypticase peptone 1.98807 g/l Yeast extract 1.98807 g/l Na2CO3 0.994036 g/l Na-acetate 0.994036 g/l KCl 0.497018 g/l Na2S x 9 H2O 0.397614 g/l NH4Cl 0.29821 g/l KH2PO4 0.198807 g/l CaCl2 x 2 H2O 0.149105 g/l HCl 0.00248509 g/l FeCl2 x 4 H2O 0.00149105 g/l Sodium resazurin 0.000497018 g/l NaOH 0.000497018 g/l CoCl2 x 6 H2O 0.000188867 g/l MnCl2 x 4 H2O 9.94036e-05 g/l Pyridoxine hydrochloride 9.94036e-05 g/l ZnCl2 6.95825e-05 g/l (DL)-alpha-Lipoic acid 4.97018e-05 g/l Calcium D-(+)-pantothenate 4.97018e-05 g/l Nicotinic acid 4.97018e-05 g/l Riboflavin 4.97018e-05 g/l Thiamine HCl 4.97018e-05 g/l p-Aminobenzoic acid 4.97018e-05 g/l Na2MoO4 x 2 H2O 3.57853e-05 g/l NiCl2 x 6 H2O 2.38569e-05 g/l Folic acid 1.98807e-05 g/l Biotin 1.98807e-05 g/l H3BO3 5.96421e-06 g/l Na2WO4 x 2 H2O 3.97614e-06 g/l Na2SeO3 x 5 H2O 2.98211e-06 g/l CuCl2 x 2 H2O 1.98807e-06 g/l Vitamin B12 9.94036e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
5786	positive	growth	45	thermophilic
69480				thermophilic	99.999

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
5786	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.84

Isolation, sampling and environmental information

isolation

@ref: 5786
sample type: matrixes of Alvinella and Riftia, deep-sea hydrothermal vent samples, 2600 m depth
host species: Alvinella;Riftia
geographic location: East-Pacific Rise, Grandbonum vent site
country: International waters
latitude: 13
longitude: -103.933

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Host	#Invertebrates (Other)	#Annelida
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_17615.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2080;96_9019;97_10844;98_13313;99_17615&stattab=map
Last taxonomy: Desulfonauticus submarinus subclade
16S sequence: AF524933
Sequence Identity:
Total samples: 55
soil counts: 6
aquatic counts: 41
animal counts: 8

Safety information

risk assessment

@ref: 5786
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 5786
description: Desulfonauticus submarinus 16S ribosomal RNA gene, partial sequence
accession: AF524933
length: 1566
database: ena
NCBI tax ID: 206665

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Desulfonauticus submarinus DSM 15269	GCA_900104045	contig	ncbi	206665
66792	Desulfonauticus submarinus strain DSM 15269	206665.4	wgs	patric	206665
66792	Desulfonauticus submarinus DSM 15269	2619619038	draft	img	206665

GC content

@ref: 5786
GC-content: 34.4
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	89.149	no
gram-positive	no	99.722	no
anaerobic	yes	99.999	yes
aerobic	no	99.531	yes
halophile	no	80.221	no
spore-forming	no	95.898	no
glucose-util	no	61.157	no
flagellated	no	70.402	no
thermophile	yes	99.999	yes
glucose-ferment	no	76.321	no

External links

@ref: 5786

culture collection no.: DSM 15269, CIP 107713

straininfo link

@ref: 73544
straininfo: 127990

literature

topic: Phylogeny
Pubmed-ID: 13130052
title: Desulfonauticus submarinus gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a deep-sea hydrothermal vent.
authors: Audiffrin C, Cayol JL, Joulian C, Casalot L, Thomas P, Garcia JL, Ollivier B
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.02551-0
year: 2003
mesh: Bacterial Outer Membrane Proteins/genetics, Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Deltaproteobacteria/classification/genetics/*isolation & purification/*metabolism, Genes, Bacterial, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sulfates/metabolism
topic2: Metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
5786	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15269)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-15269
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
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	Nucleic Acids Res. 49: D498-D508 2020	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.		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)
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
73544	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID127990.1	StrainInfo: A central database for resolving microbial strain identifiers