Geopsychrobacter electrodiphilus (DSM 16401, ATCC BAA-880, JCM 12469)

Name: Geopsychrobacter electrodiphilus (DSM 16401, ATCC BAA-880, JCM 12469)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5789

Type strain

Strain Designation A1

Culture col. no. DSM 16401 ATCC BAA-880 JCM 12469 A1

NCBI tax ID(s) 1121918 225196

Special Collections DSMZ JCM

Links

Geopsychrobacter electrodiphilus A1 is an anaerobe, psychrophilic prokaryote that was isolated from electrode and Fe oxide.

anaerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 138005

ATCC BAA-880,DSM 16401,JCM 12469

@ref 20215

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

Domain Pseudomonadati

Phylum Thermodesulfobacteriota

Class Desulfuromonadia

Order Desulfuromonadales

Family Geopsychrobacteraceae

Genus Geopsychrobacter

Species Geopsychrobacter electrodiphilus

Full scientific name Geopsychrobacter electrodiphilus Holmes et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.158
125439	negative	99.9

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6430	GEOANAEROBACTER MEDIUM (DSMZ Medium 838)		Medium recipe at MediaDive	Name: GEOANAEROBACTER MEDIUM (DSMZ Medium 838) Composition: Ferric citrate monohydrate 9.98004 g/l Na2CO3 1.49701 g/l Na-acetate 0.798403 g/l Na-ascorbate 0.798403 g/l KH2PO4 0.598802 g/l MgSO4 x 7 H2O 0.499002 g/l NH4Cl 0.299401 g/l CaCl2 x 2 H2O 0.0998004 g/l Na2-EDTA x 2 H2O 0.00518962 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	Growth	Type	Temperature (°C)	Range
6430	positive	growth	22	psychrophilic
67770	positive	growth	22	psychrophilic

Physiology and metabolism

Oxygen tolerance

6430

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Industrial production

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6430	electrode and Fe oxide	Boston Harbor	USA	USA	North America
67770	Marine sediment fuel cell constructed with sediments	Boston Harbor, MA	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AY187303 (>99% sequence identity) for Geopsychrobacter electrodiphilus subclade from Microbeatlas

Aquatic Samples	725
Soil Samples	111
Animal Samples	30
Plant Samples	7
Total Samples	873

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6430	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
67770	ASM38439v1 assembly for Geopsychrobacter electrodiphilus DSM 16401	contig	GCA_000384395	1121918.7	2522572047	1121918	78.47

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6430	Geopsychrobacter electrodiphilus strain A1 16S ribosomal RNA gene, partial sequence	AY187303	1493		225196

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Geopsychrobacter electrodiphilus DSM 16401
NCBI: GCA_000384395

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	yes	83.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	59.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Geopsychrobacter electrodiphilus DSM 16401
PATRIC: 1121918.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.16	no
125438	anaerobic	anaerobicⓘ	yes	66.87	yes
125438	spore-forming	spore-formingⓘ	no	85.14	no
125438	aerobic	aerobicⓘ	no	77.77	yes
125438	thermophilic	thermophileⓘ	no	86.78	yes
125438	flagellated	motile2+ⓘ	yes	53.52	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains.	Guo Y, Aoyagi T, Hori T.	BMC Genomics	10.1186/s12864-021-07809-6	2021
Metabolism	Cloning, characterization and analysis of cat and ben genes from the phenol degrading halophilic bacterium Halomonas organivorans.	de Lourdes Moreno M, Sanchez-Porro C, Piubeli F, Frias L, Garcia MT, Mellado E.	PLoS One	10.1371/journal.pone.0021049	2011
	Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.	Babbitt GA, Alawad MA, Schulze KV, Hudson AO.	Nucleic Acids Res	10.1093/nar/gku811	2014
Genetics	Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica.	Lee H, Hwang K, Cho A, Kim S, Kim M, Morgan-Kiss R, Priscu JC, Kim KM, Kim OS.	Environ Microbiome	10.1186/s40793-024-00605-1	2024
Pathogenicity	Nonproteinogenic D-amino acids at millimolar concentrations are a toxin for anaerobic microorganisms relevant to early Earth and other anoxic planets.	Nixon SL, Cockell CS.	Astrobiology	10.1089/ast.2014.1252	2015
	Contrasting Marine Microbial Communities of the Fram Strait with the First Confirmed Record of Cyanobacteria Prochlorococcus marinus in the Arctic Region.	Mioduchowska M, Pawlowska J, Mazanowski K, Weydmann-Zwolicka A.	Biology (Basel)	10.3390/biology12091246	2023
Metabolism	Timing the evolution of antioxidant enzymes in cyanobacteria.	Boden JS, Konhauser KO, Robbins LJ, Sanchez-Baracaldo P.	Nat Commun	10.1038/s41467-021-24396-y	2021
Enzymology	Genomic Analyses of the Quinol Oxidases and/or Quinone Reductases Involved in Bacterial Extracellular Electron Transfer.	Zhong Y, Shi L.	Front Microbiol	10.3389/fmicb.2018.03029	2018
Phylogeny	Diversity and Evolution of Myxobacterial Type IV Pilus Systems.	Sharma G, Burrows LL, Singer M.	Front Microbiol	10.3389/fmicb.2018.01630	2018
Metabolism	Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs.	Gionfriddo CM, Stott MB, Power JF, Ogorek JM, Krabbenhoft DP, Wick R, Holt K, Chen LX, Thomas BC, Banfield JF, Moreau JW.	Appl Environ Microbiol	10.1128/aem.00176-20	2020
	Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus.	Sharma G, Narwani T, Subramanian S.	PLoS One	10.1371/journal.pone.0148593	2016
	Comparative Analysis of Type IV Pilin in Desulfuromonadales.	Shu C, Xiao K, Yan Q, Sun X.	Front Microbiol	10.3389/fmicb.2016.02080	2016
Phylogeny	Electrochemical Characterization of a Novel Exoelectrogenic Bacterium Strain SCS5, Isolated from a Mediator-Less Microbial Fuel Cell and Phylogenetically Related to Aeromonas jandaei.	Sharma SC, Feng C, Li J, Hu A, Wang H, Qin D, Yu CP.	Microbes Environ	10.1264/jsme2.me15185	2016
Phylogeny	Bacterial diversity associated with Blood Falls, a subglacial outflow from the Taylor Glacier, Antarctica.	Mikucki JA, Priscu JC.	Appl Environ Microbiol	10.1128/aem.01396-06	2007
Phylogeny	Generation of electricity and analysis of microbial communities in wheat straw biomass-powered microbial fuel cells.	Zhang Y, Min B, Huang L, Angelidaki I.	Appl Environ Microbiol	10.1128/aem.02240-08	2009
Phylogeny	Potential role of a novel psychrotolerant member of the family Geobacteraceae, Geopsychrobacter electrodiphilus gen. nov., sp. nov., in electricity production by a marine sediment fuel cell.	Holmes DE, Nicoll JS, Bond DR, Lovley DR	Appl Environ Microbiol	10.1128/AEM.70.10.6023-6030.2004	2004

References

#6430	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16401
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Geopsychrobacter electrodiphilus (DSM 16401, ATCC BAA-880, JCM 12469)

Name and taxonomic classification

Morphology

Cell 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_000384395

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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