Archive BacDiveID:10.13145/bacdive3947.20230509.8.1

Strain identifier

BacDive ID: 3947

Type strain:

Species: Desulfatibacillum alkenivorans

Strain Designation: PF2803

Strain history: <- C. Cravo-Laureau, IMEP CNRS UMR 6116, Faculté des Sciences et Techniques de Saint-Jérôme, Marseille, France; PF2803 <- C. Cravo-Laureau {2000}

NCBI tax ID(s): 1121393 (strain), 259354 (species)

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

General

@ref: 6334

BacDive-ID: 3947

DSM-Number: 16219

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

description: Desulfatibacillum alkenivorans PF2803 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from oil polluted sediment of operation station of ballast water and tank water cleanning.

NCBI tax id

NCBI tax id	Matching level
1121393	strain
259354	species

strain history

@ref: 6334
history: <- C. Cravo-Laureau, IMEP CNRS UMR 6116, Faculté des Sciences et Techniques de Saint-Jérôme, Marseille, France; PF2803 <- C. Cravo-Laureau {2000}

doi: 10.13145/bacdive3947.20230509.8.1

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

@ref: 6334

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfobacterales

family: Desulfobacteraceae

genus: Desulfatibacillum

species: Desulfatibacillum alkenivorans

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

strain designation: PF2803

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
31235	negative	1.2-4.5 µm	0.68 µm	rod-shaped	no
69480					yes	91.278
69480	negative					100

colony morphology

@ref: 6334
incubation period: 3-7 days

Culture and growth conditions

culture medium

@ref: 6334
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
6334	positive	growth	30	mesophilic
31235	positive	growth	22-38
31235	positive	optimum	29	mesophilic

culture pH

@ref	ability	type	pH
31235	positive	growth	6.2-8.0
31235	positive	optimum	6.8

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
6334	anaerobe
69480	anaerobe	99.033

spore formation

@ref	spore formation	confidence
31235	no
69481	no	100
69480	no	99.474

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31235	28885	butanol	+	carbon source
31235	17754	glycerol	+	carbon source
31235	25115	malate	+	carbon source
31235	15361	pyruvate	+	carbon source
31235	31011	valerate	+	carbon source

Isolation, sampling and environmental information

isolation

@ref: 6334
sample type: oil polluted sediment of operation station of ballast water and tank water cleanning
geographic location: Fos Harbor
country: France
origin.country: FRA
continent: Europe

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	#Oil (Fuel)
#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: AY493562
Sequence Identity:
Total samples: 820
soil counts: 81
aquatic counts: 692
animal counts: 30
plant counts: 17

Safety information

risk assessment

@ref: 6334
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6334
description: Desulfatibacillum alkenivorans 16S ribosomal RNA gene, partial sequence
accession: AY493562
length: 1524
database: ena
NCBI tax ID: 259354

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Desulfatibacillum alkenivorans DSM 16219	GCA_900142135	scaffold	ncbi	1121393
66792	Desulfatibacillum alkenivorans DSM 16219	1121393.3	wgs	patric	1121393
66792	Desulfatibacillum alkenivorans DSM 16219	2585428156	draft	img	1121393

GC content

@ref	GC-content	method
6334	57.8	high performance liquid chromatography (HPLC)
31235	57.8

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	70.029	no
flagellated	no	84.136	no
gram-positive	no	98.969	yes
anaerobic	yes	98.968	no
aerobic	no	97.296	no
halophile	no	65.891	no
spore-forming	no	90.44	yes
thermophile	no	95.539	no
glucose-util	no	51.094	no
glucose-ferment	no	85.629	no

External links

@ref: 6334

culture collection no.: DSM 16219, ATCC BAA 924

straininfo link

@ref: 73456
straininfo: 134284

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	15388722	Desulfatibacillum alkenivorans sp. nov., a novel n-alkene-degrading, sulfate-reducing bacterium, and emended description of the genus Desulfatibacillum.	Cravo-Laureau C, Matheron R, Joulian C, Cayol JL, Hirschler-Rea A	Int J Syst Evol Microbiol	10.1099/ijs.0.63104-0	2004	Alkenes/metabolism, Anti-Bacterial Agents/pharmacology, Bacterial Outer Membrane Proteins/genetics, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Deltaproteobacteria/classification/cytology/isolation & purification/metabolism/physiology, Environmental Microbiology, France, Genes, rRNA, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Sodium Chloride/pharmacology, Spores, Bacterial, Sulfates/*metabolism	Metabolism
Metabolism	25724965	Mono- and dialkyl glycerol ether lipids in anaerobic bacteria: biosynthetic insights from the mesophilic sulfate reducer Desulfatibacillum alkenivorans PF2803T.	Grossi V, Mollex D, Vincon-Laugier A, Hakil F, Pacton M, Cravo-Laureau C	Appl Environ Microbiol	10.1128/AEM.03794-14	2015	Aerobiosis, Alkenes/metabolism, Bacteria, Anaerobic/growth & development/metabolism, Carbon/metabolism, Deltaproteobacteria/growth & development/metabolism, Energy Metabolism, Glyceryl Ethers/metabolism, Lipid Metabolism, Metabolic Networks and Pathways, Oxidation-Reduction, Sulfates/*metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
6334	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16219)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16219
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
31235	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	27559	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)
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
73456	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID134284.1	StrainInfo: A central database for resolving microbial strain identifiers