Archive BacDiveID:10.13145/bacdive16890.20230509.8.1

Strain identifier

BacDive ID: 16890

Type strain:

Species: Thermodesulfatator atlanticus

Strain Designation: AT1325, T1

Strain history: A. Postec AT1325.

NCBI tax ID(s): 1123371 (strain), 501497 (species)

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

General

@ref: 15568

BacDive-ID: 16890

DSM-Number: 21156

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative, motile, rod-shaped

description: Thermodesulfatator atlanticus AT1325 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from black smoker chimney sample, 2275 m depth.

NCBI tax id

NCBI tax id	Matching level
501497	species
1123371	strain

strain history

@ref	history
15568	<- A. Postec, IUEM, Univ. Brest, Plouzané, France; AT1325 <- A. Godfroy {2004}
67770	A. Postec AT1325.

doi: 10.13145/bacdive16890.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/thermodesulfobacteriota
domain: Bacteria
phylum: Thermodesulfobacteriota
class: Thermodesulfobacteria
order: Thermodesulfobacteriales
family: Thermodesulfobacteriaceae
genus: Thermodesulfatator
species: Thermodesulfatator atlanticus
full scientific name: Thermodesulfatator atlanticus Alain et al. 2010

@ref: 15568

domain: Bacteria

phylum: Thermodesulfobacteria

class: Thermodesulfobacteria

order: Thermodesulfobacteriales

family: Thermodesulfobacteriaceae

genus: Thermodesulfatator

species: Thermodesulfatator atlanticus

full scientific name: Thermodesulfatator atlanticus Alain et al. 2010

strain designation: AT1325, T1

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29248	negative	3.54 µm	0.52 µm	rod-shaped	yes
69480					yes	94.498
69480	negative					99.994

Culture and growth conditions

culture medium

@ref: 15568
name: DESULFONAUTICUS MEDIUM (DSMZ Medium 383b)
growth: yes
link: https://mediadive.dsmz.de/medium/383b
composition: Name: DESULFONAUTICUS MEDIUM (DSMZ Medium 383b) Composition: NaCl 20.8747 g/l Na2SO4 2.9821 g/l MgCl2 x 6 H2O 2.9821 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 NaOH 0.000497018 g/l Sodium resazurin 0.000497018 g/l CoCl2 x 6 H2O 0.000188867 g/l Pyridoxine hydrochloride 9.94036e-05 g/l MnCl2 x 4 H2O 9.94036e-05 g/l ZnCl2 6.95825e-05 g/l p-Aminobenzoic acid 4.97018e-05 g/l (DL)-alpha-Lipoic acid 4.97018e-05 g/l Thiamine HCl 4.97018e-05 g/l Calcium D-(+)-pantothenate 4.97018e-05 g/l Riboflavin 4.97018e-05 g/l Nicotinic acid 4.97018e-05 g/l Na2MoO4 x 2 H2O 3.57853e-05 g/l NiCl2 x 6 H2O 2.38569e-05 g/l Biotin 1.98807e-05 g/l Folic acid 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
15568	positive	growth	70	thermophilic
29248	positive	growth	55-75	thermophilic
29248	positive	optimum	67.5	thermophilic
67770	positive	growth	70	thermophilic
69480				thermophilic	99.999

culture pH

@ref	ability	type	pH
29248	positive	growth	5.5-8
29248	positive	optimum	7

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
15568	anaerobe
29248	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.725

halophily

@ref	salt	growth	tested relation	concentration
29248	NaCl	positive	growth	1.5-4.5 %
29248	NaCl	positive	optimum	2.5 %

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	latitude	longitude
15568	black smoker chimney sample, 2275 m depth	Mid-Atlantic Ridge, Rainbow hydrothermal vent field	International waters	36.23	-33.902
67770	Deep-sea hydrothermal vent at the Rainbow site on the Mid-Atlantic Ridge

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_1717.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16725;96_977;97_1137;98_1356;99_1717&stattab=map
Last taxonomy: Thermodesulfatator atlanticus subclade
16S sequence: EU435435
Sequence Identity:
Total samples: 19
soil counts: 4
aquatic counts: 15

Safety information

risk assessment

@ref: 15568
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 15568
description: Thermodesulfatator atlanticus strain AT1325 16S ribosomal RNA gene, partial sequence
accession: EU435435
length: 1491
database: ena
NCBI tax ID: 1123371

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermodesulfatator atlanticus DSM 21156	1123371.3	wgs	patric	1123371
66792	Thermodesulfatator atlanticus DSM 21156	2523533580	draft	img	1123371
67770	Thermodesulfatator atlanticus DSM 21156	GCA_000421585	contig	ncbi	1123371

GC content

@ref	GC-content	method
15568	45.6	thermal denaturation, midpoint method (Tm)
29248	45.6

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	90.696	no
flagellated	no	90.002	no
gram-positive	no	99.309	yes
anaerobic	yes	99.998	yes
halophile	no	76.17	no
spore-forming	no	92.91	no
thermophile	yes	99.731	no
glucose-util	no	59.335	no
aerobic	no	99.303	yes
glucose-ferment	no	83.395	no

External links

@ref: 15568

culture collection no.: DSM 21156, JCM 15391

straininfo link

@ref: 85896
straininfo: 398625

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19648352	Thermodesulfatator atlanticus sp. nov., a thermophilic, chemolithoautotrophic, sulfate-reducing bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent.	Alain K, Postec A, Grinsard E, Lesongeur F, Prieur D, Godfroy A	Int J Syst Evol Microbiol	10.1099/ijs.0.009449-0	2009	Atlantic Ocean, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Desulfovibrio/classification/genetics/isolation & purification/metabolism, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sulfates/metabolism	Metabolism
Phylogeny	27405298	Thermodesulfatator autotrophicus sp. nov., a thermophilic sulfate-reducing bacterium from the Indian Ocean.	Lai Q, Cao J, Dupont S, Shao Z, Jebbar M, Alain K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001297	2016	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrothermal Vents/microbiology, Indian Ocean, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Sulfates/metabolism, Sulfur-Reducing Bacteria/classification/genetics/isolation & purification	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
15568	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21156)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-21156
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
29248	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	25668	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)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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
85896	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID398625.1	StrainInfo: A central database for resolving microbial strain identifiers