Name: Geoalkalibacter ferrihydriticus Z-0531
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5808

Type strain:

Species: Geoalkalibacter ferrihydriticus

Strain Designation: Z-0531

Culture col. no.: DSM 17813, VKM B-2401

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

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

SI-ID 297651

DSM 17813, VKM B-2401

Special Collections

DSMZ

Section

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

Gram-negative
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfuromonadales*
	Family	*Desulfuromonadaceae*
	Genus	*Geoalkalibacter*
	Species	**Geoalkalibacter ferrihydriticus**
	Full Scientific Name (LPSN)	Geoalkalibacter ferrihydriticus Zavarzina et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %97.163

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7202]

Culture medium

GEOALKALIBACTER MEDIUM (DSMZ Medium 1059)

[Ref.: #7202]

Culture medium growth

[Ref.: #7202]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7202]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7202]			growth	35 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7202]

Oxygen tolerance

anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolysis	82.35	14 of 17
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	polyamine pathway	69.57	16 of 23
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	chlorophyll metabolism	38.89	7 of 18
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7202]	Sample type/isolated from	deposits of soda lake
[Ref.: #7202]	Geographic location (country and/or sea, region)	Tuva
[Ref.: #7202]	Country	Russia
[Ref.: #7202]	Country ISO 3 Code	RUS
[Ref.: #7202]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Waste	#Solid waste
#Environmental	#Aquatic	#Lake (large)
#Condition	#Alkaline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ309326 (>99% sequence identity) for Geoalkalibacter ferrihydriticus subclade from Microbeatlas

Aquatic Samples	139
Soil Samples	90
Animal Samples	37
Plant Samples	4
Total Samples	270

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7202]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7202]	Geoalkalibacter ferrihydriticus strain Z-0531 16S ribosomal RNA gene, partial sequence	DQ309326	1504	GenBank ENA	392333 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Geoalkalibacter ferrihydriticus DSM 17813	GCA_900103065	scaffold	GenBank ENA	392333 tax ID	*
[Ref.: #66792]	Geoalkalibacter ferrihydriticus DSM 17813	GCA_000820505	scaffold	GenBank ENA	1121915 tax ID	*
[Ref.: #66792]	Geoalkalibacter ferrihydriticus DSM 17813	1121915.3	wgs	PATRIC	1121915 tax ID	*
[Ref.: #66792]	Geoalkalibacter ferrihydriticus strain DSM 17813	392333.6	wgs	PATRIC	392333 tax ID	*
[Ref.: #66792]	Geoalkalibacter ferrihydriticus DSM 17813	2593339172	draft	JGI IMG/M	1121915 tax ID	*
[Ref.: #66792]	Geoalkalibacter ferrihydriticus DSM 17813	2599185148	draft	JGI IMG/M	1121915 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Geoalkalibacter ferrihydriticus DSM 17813 DSM 17813 NCBI: GCA_000820505.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Geoalkalibacter ferrihydriticus DSM 17813 DSM 17813 NCBI: GCA_000820505.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.163	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	71.359	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	76.193	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.215	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	84.33	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	78.286	no

Availability in culture collections External links

[Ref.: #7202]

Culture collection no.

DSM 17813, VKM B-2401

[Ref.: #75287]

SI-ID 297651

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	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	10.1099/ijs.0.001537-0	2009	*
Phylogeny	[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	*
Metabolism	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	10.1111/1462-2920.16200	2022	*
	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	10.1128/genomeA.00039-15	2015	*

References

#7202

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17813

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75287

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID297651.1 )

* These data were automatically processed and therefore are not curated

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Geoalkalibacter ferrihydriticus DSM 17813 DSM 17813

Geoalkalibacter ferrihydriticus DSM 17813 DSM 17813

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