Geobacter hydrogenophilus (DSM 13691, H-2)

Name: Geobacter hydrogenophilus (DSM 13691, H-2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5800

Type strain

Strain Designation H-2

Culture col. no. DSM 13691 H-2

NCBI tax ID(s) 40983

Special Collections DSMZ

Links

Geobacter hydrogenophilus H-2 is an anaerobe, mesophilic prokaryote that was isolated from Petroleum-contaminated water table aquifer.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 43065

ATCC 51590,DSM 13691

@ref 20215

Last LPSN update 2025-12-16 09:48:09

Domain Pseudomonadati

Phylum Thermodesulfobacteriota

Class Desulfuromonadia

Order Geobacterales

Family Geobacteraceae

Genus Geobacter

Species Geobacter hydrogenophilus

Full scientific name Geobacter hydrogenophilus Coates et al. 2001

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	96.5
125438	negative	94.354

Colony morphology

5116

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5116	GEOBACTER SULFURREDUCENS MEDIUM (DSMZ Medium 826)		Medium recipe at MediaDive	Name: GEOBACTER SULFURREDUCENS MEDIUM (DSMZ Medium 826) Composition: Na2-fumarate 7.91296 g/l NaHCO3 2.4728 g/l NH4Cl 1.48368 g/l Na-acetate 0.811078 g/l Na2HPO4 0.593472 g/l KCl 0.098912 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l CaCl2 x 2 H2O 0.00098912 g/l FeSO4 x 7 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5116	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
5116	anaerobe
125439	anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.2

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Contamination
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5116	Petroleum-contaminated water table aquifer	South Carolina, Hanahan, Defense Fuel Supply Center	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence U28173 (>99% sequence identity) for Geobacter hydrogenophilus subclade from Microbeatlas

Aquatic Samples	16
Soil Samples	1
Animal Samples	1
Plant Samples	1
Total Samples	19

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5116	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1850122v1 assembly for Geobacter hydrogenophilus DSM 13691	contig	GCA_018501225	40983.3	3001929196	40983	69.12

Genome browser: GCA_018501225

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5116	Geobacter hydrogenophilus 16S ribosomal RNA gene, partial sequence	U28173	1418		40983

GC content

@ref	GC-content (mol%)	Method
5116	58.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Geobacter hydrogenophilus DSM 13691
NCBI: GCA_018501225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	no	52.20	no
125439	gram_stain	BacteriaNetⓘ	negative	96.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Geobacter hydrogenophilus strain DSM 13691
PATRIC: 40983.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.35	no
125438	anaerobic	anaerobicⓘ	yes	73.61	yes
125438	spore-forming	spore-formingⓘ	no	78.61	no
125438	aerobic	aerobicⓘ	no	80.12	yes
125438	thermophilic	thermophileⓘ	no	88.68	no
125438	flagellated	motile2+ⓘ	yes	70.25	no

Literature

Title	Authors	Journal	DOI	Year
Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer.	Gonzalez V, Abarca-Hurtado J, Arancibia A, Claverias F, Guevara MR, Orellana R.	Microorganisms	10.3390/microorganisms12091796	2024
Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes.	Yee MO, Rotaru AE.	Sci Rep	10.1038/s41598-019-57206-z	2020

References

#5116	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13691
#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) .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Geobacter hydrogenophilus (DSM 13691, H-2)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_018501225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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