Strain identifier

BacDive ID: 5803

Type strain: Yes

Species: Geomonas bemidjiensis

Strain Designation: Bem

Strain history: <- K. P. Nevin, University of Massachusetts, Department of Geosciences, Amherst, USA; Bem <- K. P. Nevin {1998}

NCBI tax ID(s): 225194 (species)

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General

@ref: 6529

BacDive-ID: 5803

DSM-Number: 16622

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

description: Geomonas bemidjiensis Bem is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from subsurface sediment.

NCBI tax id

  • NCBI tax id: 225194
  • Matching level: species

strain history

  • @ref: 6529
  • history: <- K. P. Nevin, University of Massachusetts, Department of Geosciences, Amherst, USA; Bem <- K. P. Nevin {1998}

doi: 10.13145/bacdive5803.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfuromonadales
  • family: Geobacteraceae
  • genus: Geomonas
  • species: Geomonas bemidjiensis
  • full scientific name: Geomonas bemidjiensis (Nevin et al. 2005) Xu et al. 2020

  • synonyms

    @refsynonym
    20215Citrifermentans bemidjiense
    20215Geobacter bemidjiensis

@ref: 6529

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfuromonadales

family: Geobacteraceae

genus: Geomonas

species: Geomonas bemidjiensis

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

strain designation: Bem

type strain: yes

Morphology

cell morphology

  • @ref: 31372
  • gram stain: negative
  • cell length: 3.25 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 6529
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 6529
  • name: GEOBACTER MEDIUM (DSMZ Medium 579)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/579
  • composition: 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

@refgrowthtypetemperaturerange
6529positivegrowth30mesophilic
31372positivegrowth15-37
31372positiveoptimum30mesophilic

culture pH

  • @ref: 31372
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6529anaerobe
31372anaerobe

spore formation

  • @ref: 31372
  • spore formation: no

observation

  • @ref: 31372
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3137230089acetate+carbon source
3137228885butanol+carbon source
3137216236ethanol+carbon source
3137224996lactate+carbon source
3137225115malate+carbon source
3137217272propionate+carbon source
3137215361pyruvate+carbon source
3137230031succinate+carbon source
3137231011valerate+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 6529
  • sample type: subsurface sediment
  • geographic location: Minnesota, Bemidji
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4757.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15357;96_1511;97_1803;98_2745;99_4757&stattab=map
  • Last taxonomy: Geobacter
  • 16S sequence: AY187307
  • Sequence Identity:
  • Total samples: 423
  • soil counts: 200
  • aquatic counts: 150
  • animal counts: 25
  • plant counts: 48

Safety information

risk assessment

  • @ref: 6529
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6529
  • description: Geobacter bemidjiensis 16S ribosomal RNA gene, partial sequence
  • accession: AY187307
  • length: 1354
  • database: ena
  • NCBI tax ID: 404380

Genome sequences

  • @ref: 66792
  • description: Geobacter bemidjiensis Bem, DSM 16622
  • accession: 642555129
  • assembly level: complete
  • database: img
  • NCBI tax ID: 404380

GC content

@refGC-contentmethod
652960.9high performance liquid chromatography (HPLC)
3137260.9

External links

@ref: 6529

culture collection no.: DSM 16622, ATCC BAA 1014, JCM 12645

straininfo link

  • @ref: 75282
  • straininfo: 265392

literature

  • topic: Phylogeny
  • Pubmed-ID: 16014499
  • title: Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates.
  • authors: Nevin KP, Holmes DE, Woodard TL, Hinlein ES, Ostendorf DW, Lovley DR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63417-0
  • year: 2005
  • mesh: Bacterial Proteins/genetics, Bacterial Typing Techniques, Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Ferric Compounds/*metabolism, Fresh Water/*microbiology, Genes, rRNA, Geobacter/*classification/genetics/isolation & purification/metabolism, Geologic Sediments/*microbiology, Massachusetts, Minnesota, Molecular Sequence Data, Oxidation-Reduction, RNA, Ribosomal, 16S/genetics, Species Specificity, *Water Supply
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6529Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16622)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16622
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31372Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2768528776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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
75282Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265392.1StrainInfo: A central database for resolving microbial strain identifiers