Archive BacDiveID:10.13145/bacdive3838.20230509.8.1

Strain identifier

BacDive ID: 3838

Type strain:

Species: Denitrovibrio acetiphilus

Strain Designation: N2460

Strain history: <- S. Myhr, University of Bergen, Department of Microbiology, Bergen, Norway; N2460 <- S. Myhr {1995}

NCBI tax ID(s): 522772 (strain), 118000 (species)

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

General

@ref: 4832

BacDive-ID: 3838

DSM-Number: 12809

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

description: Denitrovibrio acetiphilus N2460 is an anaerobe, mesophilic, motile bacterium that was isolated from oil reservoir model column.

NCBI tax id

NCBI tax id	Matching level
118000	species
522772	strain

strain history

@ref: 4832
history: <- S. Myhr, University of Bergen, Department of Microbiology, Bergen, Norway; N2460 <- S. Myhr {1995}

doi: 10.13145/bacdive3838.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/deferribacterota
domain: Bacteria
phylum: Deferribacterota
class: Deferribacteres
order: Deferribacterales
family: Deferribacteraceae
genus: Denitrovibrio
species: Denitrovibrio acetiphilus
full scientific name: Denitrovibrio acetiphilus Myhr and Torsvik 2000

@ref: 4832

domain: Bacteria

phylum: Deferribacteres

class: Deferribacteres

order: Deferribacterales

family: Deferribacteraceae

genus: Denitrovibrio

species: Denitrovibrio acetiphilus

full scientific name: Denitrovibrio acetiphilus Myhr and Torsvik 2000

strain designation: N2460

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	95.012
69480		99.999	negative

multimedia

@ref: 66793
multimedia content: EM_DSM_12809_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 4832
name: DENITROVIBRIO MEDIUM (DSMZ Medium 881)
growth: yes
link: https://mediadive.dsmz.de/medium/881
composition: Name: DENITROVIBRIO MEDIUM (DSMZ Medium 881) Composition: NaCl 19.9402 g/l Na2-fumarate 6.38086 g/l MgCl2 x 6 H2O 2.99103 g/l Na-acetate 1.63509 g/l Na2CO3 0.997009 g/l KH2PO4 0.997009 g/l Na2S x 9 H2O 0.498504 g/l KCl 0.498504 g/l NH4Cl 0.249252 g/l CaCl2 x 2 H2O 0.149551 g/l Na2SO4 0.0199402 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l Nicotinic acid 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Vitamin B12 9.97009e-05 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-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 Distilled water

culture temp

@ref: 4832
growth: positive
type: growth
temperature: 35
range: mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
4832	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.938

Isolation, sampling and environmental information

isolation

@ref: 4832
sample type: oil reservoir model column
country: Norway
origin.country: NOR
continent: Europe

isolation source categories

Cat1: #Engineered
Cat2: #Industrial
Cat3: #Oil reservoir

taxonmaps

@ref: 69479
File name: preview.99_7481.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_645;96_3492;97_4280;98_5480;99_7481&stattab=map
Last taxonomy: Denitrovibrio acetiphilus subclade
16S sequence: AF146526
Sequence Identity:
Total samples: 762
soil counts: 36
aquatic counts: 557
animal counts: 128
plant counts: 41

Safety information

risk assessment

@ref: 4832
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 4832
description: Denitrovibrio acetophilus 16S ribosomal RNA gene, partial sequence
accession: AF146526
length: 1516
database: ena
NCBI tax ID: 522772

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Denitrovibrio acetiphilus DSM 12809	GCA_000025725	complete	ncbi	522772
66792	Denitrovibrio acetiphilus DSM 12809	522772.6	complete	patric	522772
66792	Denitrovibrio acetiphilus N2460, DSM 12809	646564527	complete	img	522772

GC content

@ref: 4832
GC-content: 42.6
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	91.232	no
flagellated	no	63.291	no
gram-positive	no	99.61	no
anaerobic	yes	99.266	yes
aerobic	no	98.104	yes
halophile	no	85.123	no
spore-forming	no	95.739	no
thermophile	no	89.116	yes
glucose-util	no	59.684	no
glucose-ferment	no	85.352	no

External links

@ref: 4832

culture collection no.: DSM 12809, NBRC 114555

straininfo link

@ref: 73348
straininfo: 49366

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	10939668	Denitrovibrio acetiphilus, a novel genus and species of dissimilatory nitrate-reducing bacterium isolated from an oil reservoir model column.	Myhr S, Torsvik T	Int J Syst Evol Microbiol	10.1099/00207713-50-4-1611	2000	Acetates/metabolism, Ammonia/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fermentation, Fuel Oils, Fumarates/metabolism, Gram-Negative Anaerobic Bacteria/classification/genetics/metabolism, *Industrial Microbiology, Molecular Sequence Data, Nitrates/metabolism, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Sequence Homology, Nucleic Acid	Metabolism
Genetics	21304711	Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460).	Kiss H, Lang E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Chen F, Lucas S, Tice H, Cheng JF, Han C, Goodwin L, Pitluck S, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Spring S, Rohde M, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.892105	2010
Metabolism	23735175	Precipitation of alacranite (As8S9) by a novel As(V)-respiring anaerobe strain MPA-C3.	Mumford AC, Yee N, Young LY	Environ Microbiol	10.1111/1462-2920.12136	2013	Arsenate Reductases/genetics/metabolism, Arsenic/metabolism, Arsenicals/chemistry/metabolism, Bacteria, Anaerobic/classification/enzymology/genetics/metabolism, Base Sequence, Genome, Bacterial/genetics, Molecular Sequence Data, Nitrate Reductase/genetics, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics/metabolism, Sequence Alignment, Sulfides/chemistry/metabolism, X-Ray Diffraction	Enzymology
Enzymology	23955655	Identification of a possible respiratory arsenate reductase in Denitrovibrio acetiphilus, a member of the phylum Deferribacteres.	Denton K, Atkinson MM, Borenstein SP, Carlson A, Carroll T, Cullity K, Demarsico C, Ellowitz D, Gialtouridis A, Gore R, Herleikson A, Ling AY, Martin R, McMahan K, Naksukpaiboon P, Seiz A, Yearwood K, O'Neill J, Wiatrowski H	Arch Microbiol	10.1007/s00203-013-0915-5	2013	Amino Acid Sequence, Arsenate Reductases/genetics/isolation & purification/metabolism, Bacteria/classification/enzymology/genetics, Operon, Phylogeny, Sequence Alignment, Shewanella/enzymology	Phylogeny
	25505896	Genomic analyses of bacterial porin-cytochrome gene clusters.	Shi L, Fredrickson JK, Zachara JM	Front Microbiol	10.3389/fmicb.2014.00657	2014

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
4832	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12809)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-12809
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)
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	35: 676-683 2017	28604660
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
73348	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID49366.1	StrainInfo: A central database for resolving microbial strain identifiers