Geomonas bemidjiensis (DSM 16622, ATCC BAA-1014, JCM 12645)

Name: Geomonas bemidjiensis (DSM 16622, ATCC BAA-1014, JCM 12645)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5803

Type strain

Strain Designation Bem

Culture col. no. DSM 16622 ATCC BAA-1014 JCM 12645 Bem

NCBI tax ID(s) 225194

Special Collections DSMZ JCM Literature strains

History DSMZ <- K. P. Nevin, University of Massachusetts, Department of Geosciences, Amherst, USA; Bem <- K. P. Nevin; {1998}

Links

Geomonas bemidjiensis Bem is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from subsurface sediment.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 265392

ATCC BAA-1014,DSM 16622,JCM 12645

@ref 20215

Last LPSN update 2026-05-29 08:26:15

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfuromonadia

Order Geobacterales

Family Geobacteraceae

Genus Geomonas

Species Geomonas bemidjiensis

Full scientific name Geomonas bemidjiensis (Nevin et al. 2005) Xu et al. 2020

Synonyms (2)

Geobacter bemidjiensis
Citrifermentans bemidjiense

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31372	negative	3.25 µm	0.5 µm	rod-shaped
125439	negative					93.865

Colony morphology

6529

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6529	GEOBACTER MEDIUM (DSMZ Medium 579)		Medium recipe at MediaDive	Name: GEOBACTER MEDIUM (DSMZ Medium 579) Composition: Fe(III) citrate 13.5509 g/l Na-acetate 2.4728 g/l NaHCO3 2.4728 g/l NH4Cl 1.48368 g/l NaH2PO4 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 CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l CaCl2 x 2 H2O 0.00098912 g/l NiCl2 x 6 H2O 0.000296736 g/l Na2WO4 x 2 H2O 0.00024728 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 (DL)-alpha-Lipoic 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 Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 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)
6529	positive	growth	30
31372	positive	growth	15-37
31372	positive	optimum	30

Culture pH

@ref	Ability	Type	PH
31372	positive	optimum	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6529	anaerobe
31372	anaerobe
125439	anaerobe	97.237

Spore formation

@ref	Spore formation	Confidence
31372
125439		99.514

Observation

31372

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31372	30089 ChEBI	acetate	+	carbon source
31372	28885 ChEBI	butanol	+	carbon source
31372	16236 ChEBI	ethanol	+	carbon source
31372	24996 ChEBI	lactate	+	carbon source
31372	25115 ChEBI	malate	+	carbon source
31372	17272 ChEBI	propionate	+	carbon source
31372	15361 ChEBI	pyruvate	+	carbon source
31372	30031 ChEBI	succinate	+	carbon source
31372	31011 ChEBI	valerate	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6529	subsurface sediment	Minnesota, Bemidji	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence AY187307 (>99% sequence identity) for Geobacter from Microbeatlas

Aquatic Samples	150
Soil Samples	200
Animal Samples	25
Plant Samples	48
Total Samples	423

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6529	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	ASM2072v1 assembly for Citrifermentans bemidjiense Bem	complete	GCA_000020725	404380.4	642555129	404380	97.48

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6529	Geobacter bemidjiensis 16S ribosomal RNA gene, partial sequence	AY187307	1354		404380

GC content

@ref	GC-content (mol%)	Method
6529	60.9	high performance liquid chromatography (HPLC)
31372	60.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2072v1 assembly for Citrifermentans bemidjiense Bem
NCBI: GCA_000020725

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	97.24	no
125439	gram_stain	BacteriaNetⓘ	negative	93.87	no
125439	motility	BacteriaNetⓘ	no	68.39	no
125439	spore_formation	BacteriaNetⓘ	no	99.51	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Unprecedented N₂O production by nitrate-ammonifying Geobacteraceae with distinctive N₂O isotopocule signatures.	Xu Z, Hattori S, Masuda Y, Toyoda S, Koba K, Yu P, Yoshida N, Du Z-J, Senoo K.	mBio	10.1128/mbio.02540-24	2024
Phylogeny	Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates.	Nevin KP, Holmes DE, Woodard TL, Hinlein ES, Ostendorf DW, Lovley DR	Int J Syst Evol Microbiol	10.1099/ijs.0.63417-0	2005

References

#6529	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16622
#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 )
#27685	IJSEM 1667 2005 ( DOI 10.1099/ijs.0.63417-0 , PubMed 16014499 )
#31372	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27685
#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 .
#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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Geomonas bemidjiensis (DSM 16622, ATCC BAA-1014, JCM 12645)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000020725

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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