Archive BacDiveID:10.13145/bacdive3844.20240510.9

Strain identifier

BacDive ID: 3844

Type strain:

Species: Deferribacter abyssi

Strain Designation: JR

Strain history: M. Miroshnichenko strain JR.

NCBI tax ID(s): 213806 (species)

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

General

@ref: 5590

BacDive-ID: 3844

DSM-Number: 14873

keywords: 16S sequence, Bacteria, anaerobe

description: Deferribacter abyssi JR is an anaerobe bacterium that was isolated from deep-sea hot vent, 2400 m depth.

NCBI tax id

NCBI tax id: 213806
Matching level: species

strain history

@ref	history
5590	<- M. L. Miroshnichenko, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; JR <- M. L. Miroshnichenko {2001}
67770	M. Miroshnichenko strain JR.

doi: 10.13145/bacdive3844.20240510.9

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/deferribacterota
domain: Bacteria
phylum: Deferribacterota
class: Deferribacteres
order: Deferribacterales
family: Deferribacteraceae
genus: Deferribacter
species: Deferribacter abyssi
full scientific name: Deferribacter abyssi Miroshnichenko et al. 2003

@ref: 5590

domain: Bacteria

phylum: Deferribacteres

class: Deferribacteres

order: Deferribacterales

family: Deferribacteraceae

genus: Deferribacter

species: Deferribacter abyssi

full scientific name: Deferribacter abyssi Miroshnichenko et al. 2003

strain designation: JR

type strain: yes

Culture and growth conditions

culture medium

@ref: 5590
name: DEFERRIBACTER MEDIUM (DSMZ Medium 935)
growth: yes
link: https://mediadive.dsmz.de/medium/935
composition: Name: DEFERRIBACTER MEDIUM (DSMZ Medium 935) Composition: NaCl 29.9103 g/l MgCl2 x 6 H2O 4.48654 g/l Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l NH4Cl 0.997009 g/l Na-pyruvate 0.498504 g/l KNO3 0.498504 g/l CaCl2 x 2 H2O 0.378863 g/l K2HPO4 0.0797607 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 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
5590	positive	growth	60
67770	positive	growth	60

Physiology and metabolism

oxygen tolerance

@ref: 5590
oxygen tolerance: anaerobe

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	latitude	longitude
5590	deep-sea hot vent, 2400 m depth	Mid-Atlantic Ridge, Rainbow vent field	International waters	36.2667	-33.9
67770	Rainbow hydrothermal vent field of the Mid-Atlantic Ridge

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_114607.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16611;96_45561;97_58437;98_77558;99_114607&stattab=map
Last taxonomy: Deferribacter abyssi subclade
16S sequence: AJ515882
Sequence Identity:
Total samples: 1
aquatic counts: 1

Safety information

risk assessment

@ref: 5590
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 5590
description: Deferribacter sp. JR 16S rRNA gene, strain JR
accession: AJ515882
length: 1519
database: nuccore
NCBI tax ID: 213806

GC content

@ref: 5590
GC-content: 30.8

External links

@ref: 5590

culture collection no.: DSM 14873, JCM 11955

straininfo link

@ref: 73354
straininfo: 127987

literature

topic: Phylogeny
Pubmed-ID: 13130062
title: Deferribacter abyssi sp. nov., an anaerobic thermophile from deep-sea hydrothermal vents of the Mid-Atlantic Ridge.
authors: Miroshnichenko ML, Slobodkin AI, Kostrikina NA, L'Haridon S, Nercessian O, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.02673-0
year: 2003
mesh: Atlantic Ocean, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*classification/genetics/*isolation & purification/metabolism, Hot Temperature, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology
topic2: Stress

Reference

@id	authors	catalogue	doi/url	title
5590	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14873)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-14873
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
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
73354	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID127987.1	StrainInfo: A central database for resolving microbial strain identifiers