Archive BacDiveID:10.13145/bacdive16789.20230509.8.1

Strain identifier

BacDive ID: 16789

Type strain:

Species: Ammonifex degensii

Strain Designation: KC4

Strain history: <- R. Huber and K. O. Stetter; KC4

NCBI tax ID(s): 42838 (species)

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

General

@ref: 3946

BacDive-ID: 16789

DSM-Number: 10501

keywords: genome sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile

description: Ammonifex degensii KC4 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from volcanic hot spring.

NCBI tax id

NCBI tax id: 42838
Matching level: species

strain history

@ref: 3946
history: <- R. Huber and K. O. Stetter; KC4

doi: 10.13145/bacdive16789.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Thermoanaerobacterales
family: Thermoanaerobacteraceae
genus: Ammonifex
species: Ammonifex degensii
full scientific name: Ammonifex degensii Huber and Stetter 1996

@ref: 3946

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Thermoanaerobacterales

family: Thermoanaerobacteraceae

genus: Ammonifex

species: Ammonifex degensii

full scientific name: Ammonifex degensii Huber and Stetter 1996

strain designation: KC4

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	95.104
69480		98.846	positive

Culture and growth conditions

culture medium

@ref: 3946
name: AMMONIFEX DEGENSII MEDIUM (DSMZ Medium 716)
growth: yes
link: https://mediadive.dsmz.de/medium/716
composition: Name: AMMONIFEX DEGENSII MEDIUM (DSMZ Medium 716) Composition: Na2CO3 1.49551 g/l KNO3 0.997009 g/l K2HPO4 x 3 H2O 0.299103 g/l Na2S x 9 H2O 0.299103 g/l KH2PO4 0.219342 g/l (NH4)2SO4 0.219342 g/l MgSO4 x 7 H2O 0.00299103 g/l Nitrilotriacetic acid 0.00149551 g/l NaCl 0.000997009 g/l Sodium resazurin 0.000498504 g/l MnSO4 x H2O 0.000498504 g/l CoSO4 x 7 H2O 0.000179462 g/l ZnSO4 x 7 H2O 0.000179462 g/l FeSO4 x 7 H2O 9.97009e-05 g/l CaCl2 x 2 H2O 9.97009e-05 g/l NiCl2 x 6 H2O 2.99103e-05 g/l AlK(SO4)2 x 12 H2O 1.99402e-05 g/l CuSO4 x 5 H2O 9.97009e-06 g/l Na2MoO4 x 2 H2O 9.97009e-06 g/l H3BO3 9.97009e-06 g/l Na2WO4 x 2 H2O 3.98804e-07 g/l Na2SeO3 x 5 H2O 2.99103e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
3946	positive	growth	70	thermophilic
69480				thermophilic	99.999

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
3946	anaerobe
69480	anaerobe	100

spore formation

@ref: 69480
spore formation: yes
confidence: 99.693

Isolation, sampling and environmental information

isolation

@ref: 3946
sample type: volcanic hot spring
geographic location: Java, Dieng Plateau, Kawah Candradimuka crater
country: Indonesia
origin.country: IDN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Environmental	#Terrestrial	#Volcanic
#Condition	#Thermophilic (>45°C)

Safety information

risk assessment

@ref: 3946
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Ammonifex degensii KC4	GCA_000024605	complete	ncbi	429009
66792	Ammonifex degensii KC4	429009.3	complete	patric	429009
66792	Ammonifex degensii KC4	429009.21	plasmid	patric	429009
66792	Ammonifex degensii KC4	646311904	complete	img	429009

GC content

@ref: 3946
GC-content: 54
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	89	no
motile	yes	84.803	no
flagellated	no	95.587	no
gram-positive	no	87.224	no
anaerobic	yes	99.998	yes
aerobic	no	98.674	no
halophile	no	96.723	no
spore-forming	yes	72.323	no
thermophile	yes	100	no
glucose-util	yes	71.466	no
glucose-ferment	no	72.253	no

External links

@ref: 3946

culture collection no.: DSM 10501

straininfo link

@ref: 85805
straininfo: 48832

literature

topic: Phylogeny
Pubmed-ID: 11539844
title: Formation of ammonium from nitrate during chemolithoautotrophic growth of the extremely thermophilic bacterium ammonifex degensii gen. nov. sp. nov.
authors: Huber R, Rossnagel P, Woese CR, Rachel R, Langworthy TA, Stetter KO
journal: Syst Appl Microbiol
DOI: 10.1016/S0723-2020(96)80007-5
year: 1996
mesh: Fresh Water, Gram-Positive Bacteria/chemistry/*classification/metabolism/ultrastructure, *Hot Temperature, Indonesia, Lipids/analysis, Microscopy, Electron, Nitrates/*metabolism, Oxidation-Reduction, Phylogeny, Quaternary Ammonium Compounds/*metabolism, Sulfur-Reducing Bacteria/chemistry/classification/*metabolism/ultrastructure, Water Microbiology
topic2: Metabolism

Reference

@id	authors	catalogue	doi/url	title
3946	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10501)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-10501
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)
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)
85805	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID48832.1	StrainInfo: A central database for resolving microbial strain identifiers