Archive BacDiveID:10.13145/bacdive3946.20230509.8.1

Strain identifier

BacDive ID: 3946

Type strain:

Species: Desulfatibacillum aliphaticivorans

Strain Designation: CV2803

Strain history: <- C. Cravo-Laureau, IMEP CNRS UMR 6116, Faculté des Sciences et Techniques de Saint-Jérôme, Marseille, France; CV2803 <- C. Cravo-Laureau {1999}

NCBI tax ID(s): 1121392 (strain), 218208 (species)

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

General

@ref: 6005

BacDive-ID: 3946

DSM-Number: 15576

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

description: Desulfatibacillum aliphaticivorans CV2803 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment.

NCBI tax id

NCBI tax id	Matching level
218208	species
1121392	strain

strain history

@ref: 6005
history: <- C. Cravo-Laureau, IMEP CNRS UMR 6116, Faculté des Sciences et Techniques de Saint-Jérôme, Marseille, France; CV2803 <- C. Cravo-Laureau {1999}

doi: 10.13145/bacdive3946.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobacteraceae
genus: Desulfatibacillum
species: Desulfatibacillum aliphaticivorans
full scientific name: Desulfatibacillum aliphaticivorans Cravo-Laureau et al. 2004

@ref: 6005

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfobacterales

family: Desulfobacteraceae

genus: Desulfatibacillum

species: Desulfatibacillum aliphaticivorans

full scientific name: Desulfatibacillum aliphaticivorans Cravo-Laureau et al. 2004

strain designation: CV2803

type strain: yes

Morphology

cell morphology

@ref: 29936
gram stain: negative
cell length: 2.0-5.5 µm
cell width: 0.6-2.2 µm
cell shape: rod-shaped
motility: no

multimedia

@ref	multimedia content	caption	intellectual property rights
66793	EM_DSM_15576_1.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_15576_2.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_15576_3.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_15576_4.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_15576_5.jpg	electron microscopic image	© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 6005
name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383)
growth: yes
link: https://mediadive.dsmz.de/medium/383
composition: Name: DESULFOBACTERIUM MEDIUM (DSMZ Medium 383; with strain-specific modifications) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l None 0.997009 g/l Na2CO3 0.997009 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
6005	positive	growth	30	mesophilic
29936	positive	growth	15-40
29936	positive	optimum	28-35	mesophilic

culture pH

@ref	ability	type	pH
29936	positive	growth	6.6-7.8
29936	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref: 6005
oxygen tolerance: anaerobe

spore formation

@ref: 29936
spore formation: no

halophily

@ref: 29936
salt: NaCl
growth: positive
tested relation: optimum
concentration: 2.4 %

observation

@ref: 29936
observation: aggregates in clumps

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29936	30089	acetate	+	carbon source
29936	15740	formate	+	carbon source
29936	17272	propionate	+	carbon source
29936	15361	pyruvate	+	carbon source

Isolation, sampling and environmental information

isolation

@ref: 6005
sample type: marine sediment
geographic location: Canal Vieilcove, Lavera, Gulf of Fos
country: France
origin.country: FRA
continent: Europe

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

taxonmaps

@ref: 69479
File name: preview.99_587.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_127;96_374;97_422;98_481;99_587&stattab=map
Last taxonomy: Desulfatibacillum
16S sequence: AY184360
Sequence Identity:
Total samples: 820
soil counts: 81
aquatic counts: 692
animal counts: 30
plant counts: 17

Safety information

risk assessment

@ref: 6005
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6005
description: Desulfatibacillum aliphaticivorans strain CV2803 16S ribosomal RNA gene, partial sequence
accession: AY184360
length: 1446
database: ena
NCBI tax ID: 218208

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Desulfatibacillum aliphaticivorans DSM 15576	GCA_000429905	scaffold	ncbi	1121392
66792	Desulfatibacillum aliphaticivorans DSM 15576	1121392.3	wgs	patric	1121392
66792	Desulfatibacillum aliphaticivorans DSM 15576	2522572160	draft	img	1121392

GC content

@ref: 6005
GC-content: 41.4

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	71.336	yes
flagellated	no	85.59	yes
gram-positive	no	99.128	yes
anaerobic	yes	99.054	yes
aerobic	no	97.332	yes
halophile	no	67.983	no
spore-forming	no	88.342	yes
thermophile	no	96.136	yes
glucose-util	no	50.594	no
glucose-ferment	no	82.692	no

External links

@ref: 6005

culture collection no.: DSM 15576, ATCC BAA 743

straininfo link

@ref: 73455
straininfo: 130837

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	14742462	Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium.	Cravo-Laureau C, Matheron R, Cayol JL, Joulian C, Hirschler-Rea A	Int J Syst Evol Microbiol	10.1099/ijs.0.02717-0	2004	Alkanes/pharmacokinetics, Alkenes/pharmacokinetics, Biodegradation, Environmental, Deltaproteobacteria/classification/genetics/isolation & purification/metabolism, Gram-Negative Bacteria/classification/isolation & purification/metabolism, Inactivation, Metabolic, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Seawater/microbiology, Sulfates/metabolism, Water Pollution, Chemical	Enzymology
Metabolism	15344818	Growth and cellular fatty-acid composition of a sulphate-reducing bacterium, Desulfatibacillum aliphaticivorans strain CV2803T, grown on n-alkenes.	Cravo-Laureau C, Hirschler-Rea A, Matheron R, Grossi V	C R Biol	10.1016/j.crvi.2004.05.005	2004	Alkenes, Bacteria, Anaerobic/growth & development/metabolism, Fatty Acids/metabolism, Oxidation-Reduction, Sulfates/metabolism
Metabolism	16000749	Anaerobic n-alkane metabolism by a sulfate-reducing bacterium, Desulfatibacillum aliphaticivorans strain CV2803T.	Cravo-Laureau C, Grossi V, Raphel D, Matheron R, Hirschler-Rea A	Appl Environ Microbiol	10.1128/AEM.71.7.3458-3467.2005	2005	Alkanes/metabolism, Anaerobiosis, Biodegradation, Environmental, Culture Media, Deltaproteobacteria/growth & development/isolation & purification/metabolism, Fatty Acids/metabolism, Geologic Sediments/microbiology, Seawater/microbiology, Sulfur-Reducing Bacteria/growth & development/isolation & purification/*metabolism	Cultivation
Metabolism	17965214	Anaerobic 1-alkene metabolism by the alkane- and alkene-degrading sulfate reducer Desulfatibacillum aliphaticivorans strain CV2803T.	Grossi V, Cravo-Laureau C, Meou A, Raphel D, Garzino F, Hirschler-Rea A	Appl Environ Microbiol	10.1128/AEM.01097-07	2007	Alcohols/metabolism, Alkanes/metabolism, Anaerobiosis, Bicarbonates/metabolism, Carbon Radioisotopes/metabolism, Deltaproteobacteria/growth & development/metabolism, Fatty Acids/analysis/chemistry, Gas Chromatography-Mass Spectrometry, Oxidation-Reduction, Sulfates/*metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
6005	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15576)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-15576
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
29936	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	26307	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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life		28604660	35: 676-683 2017
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
73455	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID130837.1	StrainInfo: A central database for resolving microbial strain identifiers