Strain identifier

BacDive ID: 5798

Type strain: Yes

Species: Geobacter grbiciae

Strain Designation: TACP-2

Strain history: <- J. D. Coates, Southern Illinois University Carbondale, USA; TACP-2 <- J. D. Coates {1994}

NCBI tax ID(s): 155042 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 4954

BacDive-ID: 5798

DSM-Number: 13689

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile

description: Geobacter grbiciae TACP-2 is an anaerobe, mesophilic, motile bacterium that was isolated from freshwater aquatic sediment.

NCBI tax id

  • NCBI tax id: 155042
  • Matching level: species

strain history

  • @ref: 4954
  • history: <- J. D. Coates, Southern Illinois University Carbondale, USA; TACP-2 <- J. D. Coates {1994}

doi: 10.13145/bacdive5798.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Deltaproteobacteria
  • order: Desulfuromonadales
  • family: Geobacteraceae
  • genus: Geobacter
  • species: Geobacter grbiciae
  • full scientific name: Geobacter grbiciae Coates et al. 2001

@ref: 4954

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfuromonadales

family: Geobacteraceae

genus: Geobacter

species: Geobacter grbiciae

full scientific name: Geobacter grbiciae Coates et al. 2001

strain designation: TACP-2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes91.612
6948099.999negative

colony morphology

  • @ref: 4954
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 4954
  • 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

  • @ref: 4954
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4954anaerobe
69480anaerobe97.395

spore formation

@refspore formationconfidence
69481no92
69480no99.943

Isolation, sampling and environmental information

isolation

  • @ref: 4954
  • sample type: freshwater aquatic sediment
  • geographic location: Virginia, Potomac River Estuary
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4529.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15357;96_2263;97_2742;98_3405;99_4529&stattab=map
  • Last taxonomy: Geobacter
  • 16S sequence: AF335183
  • Sequence Identity:
  • Total samples: 695
  • soil counts: 237
  • aquatic counts: 409
  • animal counts: 37
  • plant counts: 12

Safety information

risk assessment

  • @ref: 4954
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Geobacter grbicium strain TACP-2 16S ribosomal RNA gene, complete sequenceAF3351821527ena155042
20218Geobacter sp. 16S ribosomal RNA gene, partial sequenceU46862277ena46610
4954Geobacter grbicium strain TACP-5 16S ribosomal RNA gene, complete sequenceAF3351831542ena155042

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geobacter grbiciae DSM 13689GCA_018531165contigncbi155042
66792Geobacter grbiciae strain DSM 13689155042.3wgspatric155042

GC content

  • @ref: 4954
  • GC-content: 57.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileyes84.376no
gram-positiveno98.527no
anaerobicyes96.986yes
aerobicno95.058no
halophileno93.006no
spore-formingno90.841no
thermophileno94.484yes
glucose-utilno60.245no
flagellatedno76.895no
glucose-fermentno87.206no

External links

@ref: 4954

culture collection no.: DSM 13689

straininfo link

  • @ref: 75277
  • straininfo: 126174

literature

  • topic: Phylogeny
  • Pubmed-ID: 11321104
  • title: Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers.
  • authors: Coates JD, Bhupathiraju VK, Achenbach LA, Mclnerney MJ, Lovley DR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-2-581
  • year: 2001
  • mesh: Base Composition, Deltaproteobacteria/classification/isolation & purification/*metabolism, Ferric Compounds/*metabolism, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification/isolation & purification/*metabolism, Hydrocarbons/metabolism, Iron/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, RNA, Ribosomal, 16S/genetics
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4954Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13689)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13689
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75277Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID126174.1StrainInfo: A central database for resolving microbial strain identifiers