Archive BacDiveID:10.13145/bacdive5808.20230509.8.1

Strain identifier

BacDive ID: 5808

Type strain:

Species: Geoalkalibacter ferrihydriticus

Strain Designation: Z-0531

Strain history: <- D. G. Zavarzina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Z-0531

NCBI tax ID(s): 1121915 (strain), 392333 (species)

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

General

@ref: 7202

BacDive-ID: 5808

DSM-Number: 17813

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

description: Geoalkalibacter ferrihydriticus Z-0531 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from deposits of soda lake.

NCBI tax id

NCBI tax id	Matching level
1121915	strain
392333	species

strain history

@ref: 7202
history: <- D. G. Zavarzina, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; Z-0531

doi: 10.13145/bacdive5808.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Desulfuromonadales
family: Desulfuromonadaceae
genus: Geoalkalibacter
species: Geoalkalibacter ferrihydriticus
full scientific name: Geoalkalibacter ferrihydriticus Zavarzina et al. 2007

@ref: 7202

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfuromonadales

family: Desulfuromonadaceae

genus: Geoalkalibacter

species: Geoalkalibacter ferrihydriticus

full scientific name: Geoalkalibacter ferrihydriticus Zavarzina et al. 2007

strain designation: Z-0531

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.996

Culture and growth conditions

culture medium

@ref: 7202
name: GEOALKALIBACTER MEDIUM (DSMZ Medium 1059)
growth: yes
link: https://mediadive.dsmz.de/medium/1059
composition: Name: GEOALKALIBACTER MEDIUM (DSMZ Medium 1059) Composition: Sulfur 9.98004 g/l NaHCO3 9.98004 g/l Na2CO3 2.99401 g/l Na-acetate 2.49501 g/l NaCl 0.998004 g/l NH4Cl 0.499002 g/l KH2PO4 0.199601 g/l KCl 0.199601 g/l MgCl2 x 6 H2O 0.0998004 g/l Yeast extract 0.0998004 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l NaOH 0.000499002 g/l CoCl2 x 6 H2O 0.000189621 g/l MnCl2 x 4 H2O 9.98004e-05 g/l ZnCl2 6.98603e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l H3BO3 5.98802e-06 g/l Na2WO4 x 2 H2O 3.99202e-06 g/l Na2SeO3 x 5 H2O 2.99401e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Distilled water

culture temp

@ref: 7202
growth: positive
type: growth
temperature: 35
range: mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
7202	anaerobe
69480	anaerobe	98.895

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.978

Isolation, sampling and environmental information

isolation

@ref: 7202
sample type: deposits of soda lake
geographic location: Tuva
country: Russia
origin.country: RUS
continent: Europe

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Solid waste
#Environmental	#Aquatic	#Lake (large)
#Condition	#Alkaline

taxonmaps

@ref: 69479
File name: preview.99_5655.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_50;96_1625;97_3344;98_4215;99_5655&stattab=map
Last taxonomy: Geoalkalibacter ferrihydriticus subclade
16S sequence: DQ309326
Sequence Identity:
Total samples: 270
soil counts: 90
aquatic counts: 139
animal counts: 37
plant counts: 4

Safety information

risk assessment

@ref: 7202
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7202
description: Geoalkalibacter ferrihydriticus strain Z-0531 16S ribosomal RNA gene, partial sequence
accession: DQ309326
length: 1504
database: ena
NCBI tax ID: 392333

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Geoalkalibacter ferrihydriticus DSM 17813	GCA_900103065	scaffold	ncbi	392333
66792	Geoalkalibacter ferrihydriticus DSM 17813	GCA_000820505	scaffold	ncbi	1121915
66792	Geoalkalibacter ferrihydriticus DSM 17813	1121915.3	wgs	patric	1121915
66792	Geoalkalibacter ferrihydriticus strain DSM 17813	392333.6	wgs	patric	392333
66792	Geoalkalibacter ferrihydriticus DSM 17813	2593339172	draft	img	1121915
66792	Geoalkalibacter ferrihydriticus DSM 17813	2599185148	draft	img	1121915

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	87.363	no
flagellated	no	52.51	no
gram-positive	no	98.669	no
anaerobic	yes	97.465	yes
aerobic	no	96.764	no
halophile	no	69.222	no
spore-forming	no	91.566	no
glucose-util	yes	53.588	no
thermophile	no	95.581	no
glucose-ferment	no	84.633	no

External links

@ref: 7202

culture collection no.: DSM 17813, VKM B-2401

straininfo link

@ref: 75287
straininfo: 297651

literature

topic	Pubmed-ID	title	authors	journal	year	mesh	topic2	DOI
Phylogeny	17205802	[Geoalkalibacter ferrihydriticus gen. nov., sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake].	Zavarzina DG, Kolganova TV, Bulygina ES, Kostrikina NA, Turova TP, Zavarzin GA	Mikrobiologiia	2006	Acetates/metabolism, Alkalies, Base Composition, Culture Media, DNA, Bacterial/genetics, Fresh Water/chemistry/microbiology, Geobacter/classification/isolation & purification/physiology, Hydrogen-Ion Concentration, Iron/metabolism, Nitrogen Fixation, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Siberia, Species Specificity, *Water Microbiology	Metabolism
Phylogeny	19329606	Geoalkalibacter subterraneus sp. nov., an anaerobic Fe(III)- and Mn(IV)-reducing bacterium from a petroleum reservoir, and emended descriptions of the family Desulfuromonadaceae and the genus Geoalkalibacter.	Greene AC, Patel BK, Yacob S	Int J Syst Evol Microbiol	2009	Anaerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deltaproteobacteria/classification/genetics/isolation & purification/physiology, Environmental Microbiology, Molecular Sequence Data, Petroleum, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, United States	Genetics	10.1099/ijs.0.001537-0
	25767222	Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria.	Badalamenti JP, Krajmalnik-Brown R, Torres CI, Bond DR	Genome Announc	2015			10.1128/genomeA.00039-15
Metabolism	36066180	Geoalkalibacter halelectricus SAP-1 sp. nov. possessing extracellular electron transfer and mineral-reducing capabilities from a haloalkaline environment.	Yadav S, Singh R, Sundharam SS, Chaudhary S, Krishnamurthi S, Patil SA	Environ Microbiol	2022	Electrons, Geobacter/genetics, Electron Transport, Shewanella/metabolism, Minerals/metabolism	Phylogeny	10.1111/1462-2920.16200

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
7202	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17813)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17813
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)
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
75287	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID297651.1	StrainInfo: A central database for resolving microbial strain identifiers